Starting phenix.real_space_refine on Wed Feb 12 06:58:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ofy_16863/02_2025/8ofy_16863.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ofy_16863/02_2025/8ofy_16863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ofy_16863/02_2025/8ofy_16863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ofy_16863/02_2025/8ofy_16863.map" model { file = "/net/cci-nas-00/data/ceres_data/8ofy_16863/02_2025/8ofy_16863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ofy_16863/02_2025/8ofy_16863.cif" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= -0.023 sd= 0.424 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5004 2.51 5 N 1140 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7420 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1830 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 230} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'PNT': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 3.37, per 1000 atoms: 0.45 Number of scatterers: 7420 At special positions: 0 Unit cell: (82.318, 82.318, 66.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1244 8.00 N 1140 7.00 C 5004 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=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 971.5 milliseconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 71 through 98 Processing helix chain 'A' and resid 102 through 126 removed outlier: 5.685A pdb=" N GLY A 123 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 178 removed outlier: 5.612A pdb=" N ASP A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.084A pdb=" N PHE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 227 Processing helix chain 'A' and resid 236 through 252 Processing helix chain 'A' and resid 261 through 277 removed outlier: 3.602A pdb=" N ASP A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 288 through 310 Proline residue: A 295 - end of helix Processing helix chain 'B' and resid 71 through 98 Processing helix chain 'B' and resid 102 through 126 removed outlier: 5.685A pdb=" N GLY B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 147 through 178 removed outlier: 5.612A pdb=" N ASP B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.084A pdb=" N PHE B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 227 Processing helix chain 'B' and resid 236 through 252 Processing helix chain 'B' and resid 261 through 277 removed outlier: 3.602A pdb=" N ASP B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 288 through 310 Proline residue: B 295 - end of helix Processing helix chain 'C' and resid 71 through 98 Processing helix chain 'C' and resid 102 through 126 removed outlier: 5.685A pdb=" N GLY C 123 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 140 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 178 removed outlier: 5.612A pdb=" N ASP C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU C 173 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.084A pdb=" N PHE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 227 Processing helix chain 'C' and resid 236 through 252 Processing helix chain 'C' and resid 261 through 277 removed outlier: 3.602A pdb=" N ASP C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 288 through 310 Proline residue: C 295 - end of helix Processing helix chain 'D' and resid 71 through 98 Processing helix chain 'D' and resid 102 through 126 removed outlier: 5.685A pdb=" N GLY D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 140 Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 147 through 178 removed outlier: 5.612A pdb=" N ASP D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU D 173 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 removed outlier: 4.084A pdb=" N PHE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 227 Processing helix chain 'D' and resid 236 through 252 Processing helix chain 'D' and resid 261 through 277 removed outlier: 3.602A pdb=" N ASP D 265 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 288 through 310 Proline residue: D 295 - end of helix 544 hydrogen bonds defined for protein. 1632 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: 2.17 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1420 1.34 - 1.46: 2312 1.46 - 1.58: 3868 1.58 - 1.70: 0 1.70 - 1.81: 52 Bond restraints: 7652 Sorted by residual: bond pdb=" C9 PNT C 401 " pdb=" N2 PNT C 401 " ideal model delta sigma weight residual 1.368 1.284 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C9 PNT D 401 " pdb=" N2 PNT D 401 " ideal model delta sigma weight residual 1.368 1.284 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C9 PNT A 401 " pdb=" N2 PNT A 401 " ideal model delta sigma weight residual 1.368 1.284 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C9 PNT B 401 " pdb=" N2 PNT B 401 " ideal model delta sigma weight residual 1.368 1.284 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C9 PNT A 401 " pdb=" N1 PNT A 401 " ideal model delta sigma weight residual 1.279 1.343 -0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 7647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 9080 2.11 - 4.22: 1168 4.22 - 6.33: 156 6.33 - 8.44: 24 8.44 - 10.55: 12 Bond angle restraints: 10440 Sorted by residual: angle pdb=" CA ASN C 202 " pdb=" CB ASN C 202 " pdb=" CG ASN C 202 " ideal model delta sigma weight residual 112.60 117.71 -5.11 1.00e+00 1.00e+00 2.61e+01 angle pdb=" CA ASN D 202 " pdb=" CB ASN D 202 " pdb=" CG ASN D 202 " ideal model delta sigma weight residual 112.60 117.71 -5.11 1.00e+00 1.00e+00 2.61e+01 angle pdb=" CA ASN A 202 " pdb=" CB ASN A 202 " pdb=" CG ASN A 202 " ideal model delta sigma weight residual 112.60 117.71 -5.11 1.00e+00 1.00e+00 2.61e+01 angle pdb=" CA ASN B 202 " pdb=" CB ASN B 202 " pdb=" CG ASN B 202 " ideal model delta sigma weight residual 112.60 117.71 -5.11 1.00e+00 1.00e+00 2.61e+01 angle pdb=" C ASN C 230 " pdb=" CA ASN C 230 " pdb=" CB ASN C 230 " ideal model delta sigma weight residual 110.42 119.89 -9.47 1.99e+00 2.53e-01 2.26e+01 ... (remaining 10435 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 19.05: 3932 19.05 - 38.06: 220 38.06 - 57.07: 48 57.07 - 76.08: 16 76.08 - 95.10: 16 Dihedral angle restraints: 4232 sinusoidal: 1512 harmonic: 2720 Sorted by residual: dihedral pdb=" CA SER A 282 " pdb=" C SER A 282 " pdb=" N HIS A 283 " pdb=" CA HIS A 283 " ideal model delta harmonic sigma weight residual 180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA SER B 282 " pdb=" C SER B 282 " pdb=" N HIS B 283 " pdb=" CA HIS B 283 " ideal model delta harmonic sigma weight residual 180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA SER D 282 " pdb=" C SER D 282 " pdb=" N HIS D 283 " pdb=" CA HIS D 283 " ideal model delta harmonic sigma weight residual -180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 4229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 756 0.061 - 0.121: 304 0.121 - 0.181: 84 0.181 - 0.241: 8 0.241 - 0.302: 4 Chirality restraints: 1156 Sorted by residual: chirality pdb=" CA ASN B 202 " pdb=" N ASN B 202 " pdb=" C ASN B 202 " pdb=" CB ASN B 202 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ASN A 202 " pdb=" N ASN A 202 " pdb=" C ASN A 202 " pdb=" CB ASN A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ASN C 202 " pdb=" N ASN C 202 " pdb=" C ASN C 202 " pdb=" CB ASN C 202 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1153 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 246 " 0.033 2.00e-02 2.50e+03 2.62e-02 1.20e+01 pdb=" CG PHE A 246 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 246 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 246 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 246 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 246 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 246 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 246 " 0.033 2.00e-02 2.50e+03 2.62e-02 1.20e+01 pdb=" CG PHE D 246 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE D 246 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 246 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 246 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 246 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE D 246 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 246 " -0.033 2.00e-02 2.50e+03 2.62e-02 1.20e+01 pdb=" CG PHE B 246 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE B 246 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 246 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 246 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 246 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE B 246 " 0.000 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 56 2.71 - 3.26: 7664 3.26 - 3.80: 13252 3.80 - 4.35: 17652 4.35 - 4.90: 28350 Nonbonded interactions: 66974 Sorted by model distance: nonbonded pdb=" OG1 THR A 94 " pdb=" O ASN B 251 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR B 94 " pdb=" O ASN C 251 " model vdw 2.159 3.040 nonbonded pdb=" O ASN A 251 " pdb=" OG1 THR D 94 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR C 94 " pdb=" O ASN D 251 " model vdw 2.159 3.040 nonbonded pdb=" O GLY A 235 " pdb=" OH TYR B 236 " model vdw 2.491 3.040 ... (remaining 66969 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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 group one per residue 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: 0.140 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.380 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 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 : 0.009 0.084 7652 Z= 0.576 Angle : 1.507 10.552 10440 Z= 1.002 Chirality : 0.069 0.302 1156 Planarity : 0.009 0.069 1316 Dihedral : 15.132 95.097 2536 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.72 % Favored : 95.87 % Rotamer: Outliers : 2.21 % Allowed : 4.97 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 968 helix: 0.17 (0.17), residues: 632 sheet: None (None), residues: 0 loop : -1.19 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.005 TRP D 289 HIS 0.012 0.004 HIS D 177 PHE 0.057 0.008 PHE D 246 TYR 0.040 0.007 TYR A 151 ARG 0.018 0.006 ARG D 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.762 Fit side-chains REVERT: A 248 MET cc_start: 0.6966 (mmt) cc_final: 0.6383 (mmt) REVERT: B 248 MET cc_start: 0.6967 (mmt) cc_final: 0.6382 (mmt) REVERT: C 248 MET cc_start: 0.6968 (mmt) cc_final: 0.6384 (mmt) REVERT: D 248 MET cc_start: 0.6967 (mmt) cc_final: 0.6382 (mmt) outliers start: 16 outliers final: 4 residues processed: 144 average time/residue: 0.2043 time to fit residues: 39.0225 Evaluate side-chains 120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 174 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 137 ASN B 81 ASN B 137 ASN C 81 ASN C 137 ASN D 81 ASN D 137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.146086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.130445 restraints weight = 8532.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.133620 restraints weight = 5293.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.135816 restraints weight = 3688.248| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7652 Z= 0.232 Angle : 0.635 6.156 10440 Z= 0.325 Chirality : 0.042 0.154 1156 Planarity : 0.005 0.040 1316 Dihedral : 11.775 87.584 1096 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.66 % Allowed : 7.73 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.26), residues: 968 helix: 1.56 (0.18), residues: 656 sheet: None (None), residues: 0 loop : -1.06 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 289 HIS 0.001 0.000 HIS D 283 PHE 0.009 0.001 PHE D 304 TYR 0.024 0.002 TYR B 206 ARG 0.000 0.000 ARG D 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.616 Fit side-chains REVERT: A 140 PHE cc_start: 0.7747 (m-10) cc_final: 0.7478 (m-80) REVERT: A 196 MET cc_start: 0.6785 (mmt) cc_final: 0.6540 (mmt) REVERT: A 219 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7165 (mp) REVERT: B 140 PHE cc_start: 0.7750 (m-10) cc_final: 0.7479 (m-80) REVERT: B 196 MET cc_start: 0.6788 (mmt) cc_final: 0.6544 (mmt) REVERT: B 219 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7173 (mp) REVERT: C 140 PHE cc_start: 0.7749 (m-10) cc_final: 0.7480 (m-80) REVERT: C 196 MET cc_start: 0.6784 (mmt) cc_final: 0.6538 (mmt) REVERT: C 219 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7172 (mp) REVERT: D 140 PHE cc_start: 0.7745 (m-10) cc_final: 0.7478 (m-80) REVERT: D 196 MET cc_start: 0.6776 (mmt) cc_final: 0.6532 (mmt) REVERT: D 219 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7161 (mp) outliers start: 12 outliers final: 4 residues processed: 152 average time/residue: 0.2041 time to fit residues: 41.2183 Evaluate side-chains 140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.146655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.130521 restraints weight = 8672.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.133642 restraints weight = 5383.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.136013 restraints weight = 3772.388| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7652 Z= 0.182 Angle : 0.580 6.571 10440 Z= 0.293 Chirality : 0.040 0.131 1156 Planarity : 0.005 0.045 1316 Dihedral : 11.164 87.678 1088 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.21 % Allowed : 8.29 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.27), residues: 968 helix: 1.98 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 289 HIS 0.001 0.000 HIS B 128 PHE 0.024 0.002 PHE C 288 TYR 0.018 0.001 TYR B 206 ARG 0.005 0.001 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.720 Fit side-chains REVERT: A 219 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7194 (mp) REVERT: A 258 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8153 (pp) REVERT: B 219 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7194 (mp) REVERT: B 258 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8155 (pp) REVERT: C 219 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7198 (mp) REVERT: C 258 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8155 (pp) REVERT: D 219 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7197 (mp) REVERT: D 258 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8154 (pp) outliers start: 16 outliers final: 8 residues processed: 144 average time/residue: 0.2348 time to fit residues: 43.8128 Evaluate side-chains 140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.148628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.131993 restraints weight = 8625.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.135252 restraints weight = 5473.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.137528 restraints weight = 3840.582| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7652 Z= 0.184 Angle : 0.581 6.770 10440 Z= 0.285 Chirality : 0.039 0.129 1156 Planarity : 0.005 0.053 1316 Dihedral : 10.572 84.627 1088 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.66 % Allowed : 12.15 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.27), residues: 968 helix: 2.17 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -1.14 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 289 HIS 0.001 0.000 HIS C 128 PHE 0.008 0.001 PHE C 185 TYR 0.008 0.001 TYR C 86 ARG 0.006 0.001 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.716 Fit side-chains REVERT: A 219 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7305 (mp) REVERT: A 258 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8165 (pp) REVERT: B 219 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7308 (mp) REVERT: C 219 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7311 (mp) REVERT: D 219 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7312 (mp) outliers start: 12 outliers final: 4 residues processed: 128 average time/residue: 0.2085 time to fit residues: 35.5316 Evaluate side-chains 121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.147329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.128889 restraints weight = 8584.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.132668 restraints weight = 5263.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.135226 restraints weight = 3611.678| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7652 Z= 0.185 Angle : 0.573 6.459 10440 Z= 0.277 Chirality : 0.039 0.117 1156 Planarity : 0.005 0.044 1316 Dihedral : 10.146 83.950 1088 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.80 % Allowed : 14.23 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.27), residues: 968 helix: 2.30 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -1.15 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 289 HIS 0.003 0.001 HIS A 283 PHE 0.010 0.001 PHE D 185 TYR 0.019 0.001 TYR A 206 ARG 0.004 0.001 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.703 Fit side-chains REVERT: A 219 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7210 (mp) REVERT: B 219 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7217 (mp) REVERT: C 219 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7220 (mp) REVERT: D 219 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7225 (mp) outliers start: 13 outliers final: 4 residues processed: 137 average time/residue: 0.2079 time to fit residues: 38.0929 Evaluate side-chains 128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 307 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.149180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.130743 restraints weight = 8561.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.134473 restraints weight = 5257.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.137005 restraints weight = 3607.493| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7652 Z= 0.177 Angle : 0.580 6.965 10440 Z= 0.279 Chirality : 0.039 0.125 1156 Planarity : 0.005 0.043 1316 Dihedral : 10.015 85.309 1088 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.38 % Allowed : 16.30 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 968 helix: 2.40 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -1.17 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 289 HIS 0.004 0.001 HIS D 283 PHE 0.016 0.001 PHE A 185 TYR 0.007 0.001 TYR B 306 ARG 0.003 0.001 ARG D 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.677 Fit side-chains REVERT: A 219 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6799 (mp) REVERT: B 219 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6800 (mp) REVERT: C 219 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.6803 (mp) REVERT: D 219 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6801 (mp) outliers start: 10 outliers final: 4 residues processed: 131 average time/residue: 0.2451 time to fit residues: 41.7158 Evaluate side-chains 131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 307 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.148322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.130616 restraints weight = 8584.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.134147 restraints weight = 5274.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.136591 restraints weight = 3637.881| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7652 Z= 0.186 Angle : 0.578 6.360 10440 Z= 0.278 Chirality : 0.039 0.123 1156 Planarity : 0.005 0.044 1316 Dihedral : 10.109 85.091 1088 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.07 % Allowed : 14.64 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 968 helix: 2.55 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -1.26 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 289 HIS 0.003 0.001 HIS D 283 PHE 0.014 0.001 PHE C 185 TYR 0.015 0.001 TYR A 206 ARG 0.002 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.720 Fit side-chains REVERT: A 175 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7340 (mttt) REVERT: B 175 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7348 (mttt) REVERT: C 175 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7346 (mttt) REVERT: D 175 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7355 (mttt) outliers start: 15 outliers final: 4 residues processed: 138 average time/residue: 0.2244 time to fit residues: 40.5490 Evaluate side-chains 124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 307 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 283 HIS C 283 HIS D 283 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.149516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.131253 restraints weight = 8659.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.134993 restraints weight = 5260.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.137524 restraints weight = 3595.400| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7652 Z= 0.179 Angle : 0.581 6.504 10440 Z= 0.279 Chirality : 0.039 0.134 1156 Planarity : 0.005 0.044 1316 Dihedral : 9.923 83.667 1088 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.76 % Allowed : 13.40 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.28), residues: 968 helix: 2.37 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -1.26 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 289 HIS 0.004 0.001 HIS A 283 PHE 0.017 0.001 PHE C 185 TYR 0.007 0.001 TYR D 306 ARG 0.003 0.001 ARG D 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.783 Fit side-chains REVERT: A 175 LYS cc_start: 0.7792 (mtpp) cc_final: 0.7340 (mttt) REVERT: A 219 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6905 (mp) REVERT: A 229 ASN cc_start: 0.5533 (m110) cc_final: 0.5158 (t0) REVERT: B 175 LYS cc_start: 0.7795 (mtpp) cc_final: 0.7345 (mttt) REVERT: B 219 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6942 (mp) REVERT: B 229 ASN cc_start: 0.5544 (m110) cc_final: 0.5169 (t0) REVERT: C 175 LYS cc_start: 0.7799 (mtpp) cc_final: 0.7347 (mttt) REVERT: C 219 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6936 (mp) REVERT: C 229 ASN cc_start: 0.5527 (m110) cc_final: 0.5159 (t0) REVERT: D 175 LYS cc_start: 0.7798 (mtpp) cc_final: 0.7348 (mttt) REVERT: D 219 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6936 (mp) REVERT: D 229 ASN cc_start: 0.5536 (m110) cc_final: 0.5167 (t0) outliers start: 20 outliers final: 8 residues processed: 136 average time/residue: 0.2174 time to fit residues: 38.8235 Evaluate side-chains 124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 307 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.0050 chunk 95 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 chunk 43 optimal weight: 0.0270 chunk 64 optimal weight: 0.4980 overall best weight: 0.2452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.156586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.137983 restraints weight = 8783.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.142177 restraints weight = 4946.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.145086 restraints weight = 3229.879| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7652 Z= 0.181 Angle : 0.605 6.232 10440 Z= 0.300 Chirality : 0.039 0.131 1156 Planarity : 0.005 0.042 1316 Dihedral : 9.927 82.914 1088 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.66 % Allowed : 16.16 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.28), residues: 968 helix: 2.60 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.56 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.001 0.000 HIS C 177 PHE 0.031 0.002 PHE D 209 TYR 0.031 0.001 TYR A 206 ARG 0.002 0.001 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.791 Fit side-chains REVERT: A 219 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6620 (mp) REVERT: A 229 ASN cc_start: 0.5571 (m110) cc_final: 0.5312 (t0) REVERT: B 219 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6622 (mp) REVERT: B 229 ASN cc_start: 0.5570 (m110) cc_final: 0.5312 (t0) REVERT: C 219 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6628 (mp) REVERT: C 229 ASN cc_start: 0.5572 (m110) cc_final: 0.5310 (t0) REVERT: D 219 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6627 (mp) REVERT: D 229 ASN cc_start: 0.5576 (m110) cc_final: 0.5318 (t0) outliers start: 12 outliers final: 4 residues processed: 124 average time/residue: 0.2149 time to fit residues: 35.2903 Evaluate side-chains 109 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.161259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.143745 restraints weight = 8633.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.147643 restraints weight = 4999.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.150291 restraints weight = 3322.053| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7652 Z= 0.197 Angle : 0.648 9.910 10440 Z= 0.303 Chirality : 0.041 0.155 1156 Planarity : 0.005 0.044 1316 Dihedral : 9.776 81.908 1088 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.07 % Allowed : 16.85 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 968 helix: 2.55 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -1.51 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 289 HIS 0.001 0.000 HIS C 177 PHE 0.032 0.002 PHE C 209 TYR 0.010 0.001 TYR B 206 ARG 0.002 0.001 ARG D 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.760 Fit side-chains REVERT: A 219 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6786 (mp) REVERT: B 219 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6783 (mp) REVERT: D 219 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6790 (mp) outliers start: 15 outliers final: 8 residues processed: 147 average time/residue: 0.1996 time to fit residues: 39.1202 Evaluate side-chains 131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 43 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 285 ASN B 229 ASN B 285 ASN C 229 ASN C 285 ASN D 229 ASN D 285 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.157225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.138853 restraints weight = 8633.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.142890 restraints weight = 4841.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.145601 restraints weight = 3160.804| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7652 Z= 0.187 Angle : 0.629 7.635 10440 Z= 0.309 Chirality : 0.040 0.135 1156 Planarity : 0.005 0.045 1316 Dihedral : 9.701 81.305 1088 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.35 % Allowed : 18.23 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 968 helix: 2.27 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -1.85 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 289 HIS 0.002 0.001 HIS D 283 PHE 0.024 0.002 PHE D 271 TYR 0.008 0.001 TYR C 206 ARG 0.002 0.001 ARG A 269 =============================================================================== Job complete usr+sys time: 1997.29 seconds wall clock time: 37 minutes 2.95 seconds (2222.95 seconds total)