Starting phenix.real_space_refine on Thu Nov 14 21:28:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofy_16863/11_2024/8ofy_16863.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofy_16863/11_2024/8ofy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofy_16863/11_2024/8ofy_16863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofy_16863/11_2024/8ofy_16863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofy_16863/11_2024/8ofy_16863.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofy_16863/11_2024/8ofy_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 3.65, per 1000 atoms: 0.49 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: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.63 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: 2.05 Time building geometry restraints manager: 2.22 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.200 Find NCS groups from input model: 0.240 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.480 ------------------------------------------------------------------------------- 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 : 0.753 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: 0.2132 time to fit residues: 40.4434 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 : 0.801 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 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 : 0.816 Fit side-chains REVERT: A 196 MET cc_start: 0.6603 (mmt) cc_final: 0.6118 (mmt) REVERT: B 196 MET cc_start: 0.6603 (mmt) cc_final: 0.6119 (mmt) REVERT: C 196 MET cc_start: 0.6603 (mmt) cc_final: 0.6121 (mmt) REVERT: D 196 MET cc_start: 0.6604 (mmt) cc_final: 0.6120 (mmt) outliers start: 12 outliers final: 4 residues processed: 152 average time/residue: 0.2204 time to fit residues: 44.3291 Evaluate side-chains 136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 247 VAL 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 48 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7652 Z= 0.233 Angle : 0.594 6.692 10440 Z= 0.303 Chirality : 0.041 0.132 1156 Planarity : 0.005 0.040 1316 Dihedral : 11.117 87.176 1088 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.66 % Allowed : 8.84 % 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: 1.33 (0.26), residues: 968 helix: 1.83 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -1.22 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 289 HIS 0.002 0.001 HIS B 128 PHE 0.020 0.002 PHE B 288 TYR 0.019 0.002 TYR B 206 ARG 0.006 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: 12 poor density : 136 time to evaluate : 0.776 Fit side-chains REVERT: A 258 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7375 (pp) REVERT: B 258 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7374 (pp) REVERT: C 258 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7376 (pp) REVERT: D 258 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7375 (pp) outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 0.2195 time to fit residues: 41.4616 Evaluate side-chains 140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 258 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 161 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 258 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 161 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 86 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7652 Z= 0.289 Angle : 0.627 6.908 10440 Z= 0.313 Chirality : 0.042 0.149 1156 Planarity : 0.005 0.040 1316 Dihedral : 10.463 84.834 1088 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.21 % Allowed : 12.15 % Favored : 85.64 % 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: 1.21 (0.26), residues: 968 helix: 1.78 (0.18), residues: 656 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 289 HIS 0.003 0.001 HIS B 128 PHE 0.013 0.002 PHE D 226 TYR 0.011 0.002 TYR C 306 ARG 0.006 0.001 ARG D 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 156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.690 Fit side-chains REVERT: A 269 ARG cc_start: 0.7356 (ttm170) cc_final: 0.7154 (ttm170) REVERT: A 271 PHE cc_start: 0.7532 (t80) cc_final: 0.7142 (t80) REVERT: B 269 ARG cc_start: 0.7354 (ttm170) cc_final: 0.7151 (ttm170) REVERT: B 271 PHE cc_start: 0.7532 (t80) cc_final: 0.7144 (t80) REVERT: C 269 ARG cc_start: 0.7353 (ttm170) cc_final: 0.7151 (ttm170) REVERT: C 271 PHE cc_start: 0.7533 (t80) cc_final: 0.7145 (t80) REVERT: D 271 PHE cc_start: 0.7531 (t80) cc_final: 0.7142 (t80) outliers start: 16 outliers final: 12 residues processed: 156 average time/residue: 0.2208 time to fit residues: 46.0365 Evaluate side-chains 144 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 247 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7652 Z= 0.223 Angle : 0.611 6.722 10440 Z= 0.297 Chirality : 0.040 0.124 1156 Planarity : 0.005 0.046 1316 Dihedral : 10.577 86.475 1088 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.76 % Allowed : 14.36 % Favored : 82.87 % 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: 1.53 (0.27), residues: 968 helix: 1.99 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -1.16 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 289 HIS 0.003 0.001 HIS C 283 PHE 0.032 0.002 PHE D 209 TYR 0.009 0.001 TYR D 306 ARG 0.004 0.001 ARG C 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 156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.750 Fit side-chains REVERT: A 219 LEU cc_start: 0.5280 (OUTLIER) cc_final: 0.4879 (mp) REVERT: B 219 LEU cc_start: 0.5279 (OUTLIER) cc_final: 0.4878 (mp) REVERT: C 219 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4880 (mp) REVERT: D 219 LEU cc_start: 0.5279 (OUTLIER) cc_final: 0.4878 (mp) outliers start: 20 outliers final: 8 residues processed: 156 average time/residue: 0.1873 time to fit residues: 40.0400 Evaluate side-chains 140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 283 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7652 Z= 0.271 Angle : 0.624 6.807 10440 Z= 0.308 Chirality : 0.041 0.127 1156 Planarity : 0.005 0.046 1316 Dihedral : 10.381 84.967 1088 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.73 % Allowed : 14.92 % Favored : 81.35 % 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: 1.45 (0.26), residues: 968 helix: 1.93 (0.18), residues: 656 sheet: None (None), residues: 0 loop : -1.19 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 289 HIS 0.003 0.001 HIS D 283 PHE 0.021 0.002 PHE D 271 TYR 0.010 0.001 TYR C 306 ARG 0.004 0.001 ARG C 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 172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.794 Fit side-chains REVERT: A 219 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4958 (mp) REVERT: A 269 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7179 (ttm170) REVERT: B 219 LEU cc_start: 0.5202 (OUTLIER) cc_final: 0.4957 (mp) REVERT: B 269 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7177 (ttm170) REVERT: C 219 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4959 (mp) REVERT: C 269 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7176 (ttm170) REVERT: D 219 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.4960 (mp) REVERT: D 271 PHE cc_start: 0.7488 (t80) cc_final: 0.7058 (t80) outliers start: 27 outliers final: 12 residues processed: 161 average time/residue: 0.2297 time to fit residues: 47.8741 Evaluate side-chains 160 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 247 VAL Chi-restraints excluded: chain A residue 269 ARG 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 247 VAL Chi-restraints excluded: chain B residue 269 ARG 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 247 VAL Chi-restraints excluded: chain C residue 269 ARG 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 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7652 Z= 0.241 Angle : 0.608 6.648 10440 Z= 0.299 Chirality : 0.040 0.123 1156 Planarity : 0.005 0.047 1316 Dihedral : 10.267 85.017 1088 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.62 % Allowed : 15.88 % Favored : 81.49 % 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: 1.45 (0.27), residues: 968 helix: 1.85 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -1.23 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 289 HIS 0.001 0.001 HIS C 128 PHE 0.034 0.002 PHE D 209 TYR 0.009 0.001 TYR D 306 ARG 0.003 0.001 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 160 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.775 Fit side-chains REVERT: A 219 LEU cc_start: 0.5202 (OUTLIER) cc_final: 0.4964 (mp) REVERT: B 219 LEU cc_start: 0.5201 (OUTLIER) cc_final: 0.4962 (mp) REVERT: C 219 LEU cc_start: 0.5205 (OUTLIER) cc_final: 0.4966 (mp) REVERT: D 219 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.4965 (mp) REVERT: D 271 PHE cc_start: 0.7523 (t80) cc_final: 0.7285 (t80) outliers start: 19 outliers final: 4 residues processed: 160 average time/residue: 0.2169 time to fit residues: 45.5828 Evaluate side-chains 145 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.4089 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= 0.194 Angle : 0.589 6.484 10440 Z= 0.291 Chirality : 0.040 0.121 1156 Planarity : 0.005 0.044 1316 Dihedral : 10.148 84.624 1088 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.10 % Allowed : 17.27 % Favored : 81.63 % 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: 1.54 (0.27), residues: 968 helix: 1.64 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -0.85 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 289 HIS 0.002 0.000 HIS D 283 PHE 0.019 0.002 PHE C 185 TYR 0.007 0.001 TYR D 306 ARG 0.002 0.000 ARG A 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 144 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.783 Fit side-chains REVERT: A 185 PHE cc_start: 0.7366 (m-80) cc_final: 0.6951 (m-10) REVERT: A 219 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.4833 (mp) REVERT: B 185 PHE cc_start: 0.7365 (m-80) cc_final: 0.6951 (m-10) REVERT: B 219 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.4830 (mp) REVERT: C 185 PHE cc_start: 0.7364 (m-80) cc_final: 0.6949 (m-10) REVERT: C 219 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.4831 (mp) REVERT: D 185 PHE cc_start: 0.7380 (m-80) cc_final: 0.6936 (m-10) REVERT: D 219 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.4833 (mp) REVERT: D 271 PHE cc_start: 0.7480 (t80) cc_final: 0.7229 (t80) outliers start: 8 outliers final: 4 residues processed: 144 average time/residue: 0.1987 time to fit residues: 38.5065 Evaluate side-chains 139 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 56 optimal weight: 0.0970 chunk 91 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.4151 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= 0.188 Angle : 0.615 7.935 10440 Z= 0.290 Chirality : 0.040 0.136 1156 Planarity : 0.005 0.042 1316 Dihedral : 10.012 84.030 1088 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.21 % Allowed : 17.54 % Favored : 80.25 % 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: 1.54 (0.27), residues: 968 helix: 1.64 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -0.85 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 289 HIS 0.002 0.001 HIS D 283 PHE 0.033 0.002 PHE C 209 TYR 0.012 0.001 TYR A 206 ARG 0.002 0.000 ARG C 72 *********************** 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 147 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.783 Fit side-chains REVERT: A 185 PHE cc_start: 0.7376 (m-80) cc_final: 0.6970 (m-10) REVERT: A 219 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4846 (mp) REVERT: B 185 PHE cc_start: 0.7374 (m-80) cc_final: 0.6968 (m-10) REVERT: B 219 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.4844 (mp) REVERT: C 185 PHE cc_start: 0.7374 (m-80) cc_final: 0.6969 (m-10) REVERT: C 219 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.4847 (mp) REVERT: D 185 PHE cc_start: 0.7339 (m-80) cc_final: 0.6930 (m-10) REVERT: D 219 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.4847 (mp) REVERT: D 271 PHE cc_start: 0.7509 (t80) cc_final: 0.7250 (t80) outliers start: 16 outliers final: 4 residues processed: 147 average time/residue: 0.1997 time to fit residues: 39.4329 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 : 0.802 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7652 Z= 0.224 Angle : 0.666 10.906 10440 Z= 0.307 Chirality : 0.042 0.198 1156 Planarity : 0.005 0.043 1316 Dihedral : 9.940 83.855 1088 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.24 % Allowed : 19.34 % 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: 1.60 (0.27), residues: 968 helix: 1.81 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -0.97 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 289 HIS 0.001 0.001 HIS D 283 PHE 0.033 0.002 PHE A 209 TYR 0.010 0.001 TYR B 306 ARG 0.002 0.000 ARG D 72 ********************** 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 133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.809 Fit side-chains REVERT: A 185 PHE cc_start: 0.7434 (m-80) cc_final: 0.7011 (m-10) REVERT: A 219 LEU cc_start: 0.5267 (OUTLIER) cc_final: 0.5026 (mp) REVERT: B 185 PHE cc_start: 0.7434 (m-80) cc_final: 0.7012 (m-10) REVERT: B 219 LEU cc_start: 0.5267 (OUTLIER) cc_final: 0.5026 (mp) REVERT: C 185 PHE cc_start: 0.7434 (m-80) cc_final: 0.7012 (m-10) REVERT: C 219 LEU cc_start: 0.5267 (OUTLIER) cc_final: 0.5026 (mp) REVERT: D 185 PHE cc_start: 0.7368 (m-80) cc_final: 0.6942 (m-10) REVERT: D 219 LEU cc_start: 0.5277 (OUTLIER) cc_final: 0.4946 (mp) outliers start: 9 outliers final: 5 residues processed: 133 average time/residue: 0.2278 time to fit residues: 40.3105 Evaluate side-chains 136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 161 LEU 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 23 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.148861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.130292 restraints weight = 8737.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.134364 restraints weight = 4971.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.137019 restraints weight = 3285.109| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4352 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= 0.209 Angle : 0.643 8.547 10440 Z= 0.299 Chirality : 0.041 0.138 1156 Planarity : 0.005 0.044 1316 Dihedral : 9.903 84.401 1088 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.38 % Allowed : 19.61 % Favored : 79.01 % 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: 1.49 (0.27), residues: 968 helix: 1.64 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -0.94 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 289 HIS 0.002 0.001 HIS D 283 PHE 0.034 0.002 PHE A 209 TYR 0.008 0.001 TYR D 306 ARG 0.002 0.000 ARG D 72 =============================================================================== Job complete usr+sys time: 1571.06 seconds wall clock time: 29 minutes 27.08 seconds (1767.08 seconds total)