Starting phenix.real_space_refine on Thu Jun 12 02:41:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9f_25756/06_2025/7t9f_25756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9f_25756/06_2025/7t9f_25756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t9f_25756/06_2025/7t9f_25756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9f_25756/06_2025/7t9f_25756.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9f_25756/06_2025/7t9f_25756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9f_25756/06_2025/7t9f_25756.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4456 2.51 5 N 1046 2.21 5 O 1128 1.98 5 H 6958 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6820 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6820 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.17, per 1000 atoms: 0.53 Number of scatterers: 13640 At special positions: 0 Unit cell: (88.81, 100.43, 76.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1128 8.00 N 1046 7.00 C 4456 6.00 H 6958 1.00 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: 3.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 19 through 38 Processing helix chain 'A' and resid 42 through 62 Processing helix chain 'A' and resid 65 through 80 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 114 removed outlier: 3.718A pdb=" N PHE A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 130 through 147 removed outlier: 3.652A pdb=" N ALA A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.795A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 175 through 193 removed outlier: 4.400A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.770A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 240 Proline residue: A 223 - end of helix Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 260 through 277 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.633A pdb=" N LEU A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 removed outlier: 5.025A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N MET A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 375 removed outlier: 4.334A pdb=" N PHE A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 397 Proline residue: A 387 - end of helix removed outlier: 3.765A pdb=" N THR A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.066A pdb=" N LEU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 434 through 460 Processing helix chain 'B' and resid 19 through 38 Processing helix chain 'B' and resid 42 through 62 Processing helix chain 'B' and resid 65 through 80 Proline residue: B 74 - end of helix Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 114 removed outlier: 3.719A pdb=" N PHE B 98 " --> pdb=" O ASN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 130 through 147 removed outlier: 3.652A pdb=" N ALA B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 135 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 166 removed outlier: 3.795A pdb=" N MET B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 175 through 193 removed outlier: 4.400A pdb=" N VAL B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.771A pdb=" N ALA B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 240 Proline residue: B 223 - end of helix Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 260 through 277 Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 319 through 339 removed outlier: 3.632A pdb=" N LEU B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 356 removed outlier: 5.026A pdb=" N ASP B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N MET B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 375 removed outlier: 4.334A pdb=" N PHE B 375 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 397 Proline residue: B 387 - end of helix removed outlier: 3.765A pdb=" N THR B 391 " --> pdb=" O PRO B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 413 removed outlier: 4.066A pdb=" N LEU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 429 Processing helix chain 'B' and resid 434 through 460 512 hydrogen bonds defined for protein. 1536 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: 4.72 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6952 1.03 - 1.23: 6 1.23 - 1.42: 2758 1.42 - 1.62: 3984 1.62 - 1.82: 98 Bond restraints: 13798 Sorted by residual: bond pdb=" CA ASP A 251 " pdb=" HA ASP A 251 " ideal model delta sigma weight residual 0.970 0.930 0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" CB PHE B 428 " pdb=" CG PHE B 428 " ideal model delta sigma weight residual 1.502 1.544 -0.042 2.30e-02 1.89e+03 3.27e+00 bond pdb=" CB PHE A 428 " pdb=" CG PHE A 428 " ideal model delta sigma weight residual 1.502 1.542 -0.040 2.30e-02 1.89e+03 2.97e+00 bond pdb=" CB ASP B 251 " pdb=" CG ASP B 251 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.87e+00 bond pdb=" CB ASP A 251 " pdb=" CG ASP A 251 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.80e+00 ... (remaining 13793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.16: 25043 8.16 - 16.31: 6 16.31 - 24.47: 12 24.47 - 32.63: 18 32.63 - 40.78: 5 Bond angle restraints: 25084 Sorted by residual: angle pdb=" N ASP A 251 " pdb=" CA ASP A 251 " pdb=" HA ASP A 251 " ideal model delta sigma weight residual 110.00 69.22 40.78 3.00e+00 1.11e-01 1.85e+02 angle pdb=" C ASP A 251 " pdb=" CA ASP A 251 " pdb=" HA ASP A 251 " ideal model delta sigma weight residual 109.00 69.94 39.06 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C SER A 213 " pdb=" CA SER A 213 " pdb=" HA SER A 213 " ideal model delta sigma weight residual 109.00 70.70 38.30 3.00e+00 1.11e-01 1.63e+02 angle pdb=" N SER A 213 " pdb=" CA SER A 213 " pdb=" HA SER A 213 " ideal model delta sigma weight residual 110.00 74.82 35.18 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB SER A 213 " pdb=" CA SER A 213 " pdb=" HA SER A 213 " ideal model delta sigma weight residual 109.00 74.29 34.71 3.00e+00 1.11e-01 1.34e+02 ... (remaining 25079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5715 17.97 - 35.94: 515 35.94 - 53.91: 174 53.91 - 71.87: 50 71.87 - 89.84: 16 Dihedral angle restraints: 6470 sinusoidal: 3394 harmonic: 3076 Sorted by residual: dihedral pdb=" CA MET B 398 " pdb=" C MET B 398 " pdb=" N SER B 399 " pdb=" CA SER B 399 " ideal model delta harmonic sigma weight residual -180.00 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA MET A 398 " pdb=" C MET A 398 " pdb=" N SER A 399 " pdb=" CA SER A 399 " ideal model delta harmonic sigma weight residual -180.00 -152.04 -27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLY B 397 " pdb=" C GLY B 397 " pdb=" N MET B 398 " pdb=" CA MET B 398 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 6467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.398: 1156 0.398 - 0.795: 0 0.795 - 1.193: 0 1.193 - 1.590: 0 1.590 - 1.988: 2 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CG LEU A 250 " pdb=" CB LEU A 250 " pdb=" CD1 LEU A 250 " pdb=" CD2 LEU A 250 " both_signs ideal model delta sigma weight residual False -2.59 -0.60 -1.99 2.00e-01 2.50e+01 9.88e+01 chirality pdb=" CG LEU B 250 " pdb=" CB LEU B 250 " pdb=" CD1 LEU B 250 " pdb=" CD2 LEU B 250 " both_signs ideal model delta sigma weight residual False -2.59 -0.60 -1.99 2.00e-01 2.50e+01 9.86e+01 chirality pdb=" CA ASP B 251 " pdb=" N ASP B 251 " pdb=" C ASP B 251 " pdb=" CB ASP B 251 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1155 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 28 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" CG ASP B 28 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP B 28 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP B 28 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 28 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" CG ASP A 28 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP A 28 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP A 28 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 428 " 0.004 2.00e-02 2.50e+03 1.02e-02 3.11e+00 pdb=" CG PHE A 428 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 428 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 428 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 428 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 428 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 428 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 428 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 428 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 428 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 428 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 428 " -0.006 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 456 2.16 - 2.77: 26456 2.77 - 3.38: 40023 3.38 - 3.99: 48857 3.99 - 4.60: 77944 Nonbonded interactions: 193736 Sorted by model distance: nonbonded pdb=" H ASP A 251 " pdb=" HA ASP A 251 " model vdw 1.556 1.816 nonbonded pdb=" H SER A 213 " pdb=" HA SER A 213 " model vdw 1.612 1.816 nonbonded pdb=" OE1 GLU B 313 " pdb=" H GLU B 313 " model vdw 1.639 2.450 nonbonded pdb=" OE1 GLU A 313 " pdb=" H GLU A 313 " model vdw 1.639 2.450 nonbonded pdb=" HB3 ARG A 252 " pdb=" HG2 ARG A 252 " model vdw 1.692 1.952 ... (remaining 193731 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.240 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.930 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6840 Z= 0.194 Angle : 0.841 13.513 9326 Z= 0.428 Chirality : 0.092 1.988 1158 Planarity : 0.004 0.043 1128 Dihedral : 13.184 88.850 2300 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.28 % Allowed : 1.42 % Favored : 98.30 % 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: 0.16 (0.29), residues: 886 helix: 0.92 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -3.50 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 217 HIS 0.004 0.001 HIS A 19 PHE 0.026 0.002 PHE B 428 TYR 0.011 0.002 TYR B 187 ARG 0.004 0.001 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.11774 ( 512) hydrogen bonds : angle 5.24326 ( 1536) covalent geometry : bond 0.00427 ( 6840) covalent geometry : angle 0.84077 ( 9326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6506 (mpp) cc_final: 0.6298 (mpp) REVERT: A 313 GLU cc_start: 0.7787 (mp0) cc_final: 0.7512 (mp0) outliers start: 2 outliers final: 2 residues processed: 125 average time/residue: 0.3202 time to fit residues: 56.7888 Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.0050 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.135666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105615 restraints weight = 37964.352| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.62 r_work: 0.3339 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6840 Z= 0.138 Angle : 0.621 11.259 9326 Z= 0.317 Chirality : 0.084 1.800 1158 Planarity : 0.004 0.037 1128 Dihedral : 5.507 55.585 914 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.71 % Allowed : 6.39 % Favored : 92.90 % 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: 0.44 (0.29), residues: 886 helix: 1.11 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -3.41 (0.40), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.002 0.001 HIS A 310 PHE 0.012 0.001 PHE A 371 TYR 0.010 0.001 TYR B 178 ARG 0.002 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.04991 ( 512) hydrogen bonds : angle 4.37450 ( 1536) covalent geometry : bond 0.00283 ( 6840) covalent geometry : angle 0.62071 ( 9326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7107 (mpp) cc_final: 0.6763 (mpp) REVERT: A 313 GLU cc_start: 0.8472 (mp0) cc_final: 0.8237 (mp0) REVERT: A 367 THR cc_start: 0.9175 (m) cc_final: 0.8964 (p) REVERT: B 131 MET cc_start: 0.7269 (mpp) cc_final: 0.6918 (mpp) REVERT: B 247 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7163 (mmm) REVERT: B 367 THR cc_start: 0.9143 (m) cc_final: 0.8920 (p) outliers start: 5 outliers final: 4 residues processed: 119 average time/residue: 0.2914 time to fit residues: 50.6766 Evaluate side-chains 110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.132587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100036 restraints weight = 39320.674| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.76 r_work: 0.3291 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6840 Z= 0.152 Angle : 0.608 11.189 9326 Z= 0.307 Chirality : 0.083 1.804 1158 Planarity : 0.004 0.038 1128 Dihedral : 5.141 46.982 914 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.57 % Allowed : 8.66 % Favored : 90.77 % 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: 0.69 (0.29), residues: 886 helix: 1.28 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -3.45 (0.37), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 311 HIS 0.003 0.001 HIS A 310 PHE 0.012 0.001 PHE B 371 TYR 0.010 0.001 TYR A 178 ARG 0.002 0.000 ARG B 20 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 512) hydrogen bonds : angle 4.16540 ( 1536) covalent geometry : bond 0.00332 ( 6840) covalent geometry : angle 0.60778 ( 9326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7189 (mpp) cc_final: 0.6879 (mpp) REVERT: B 131 MET cc_start: 0.7533 (mpp) cc_final: 0.7199 (mpp) REVERT: B 367 THR cc_start: 0.9183 (m) cc_final: 0.8968 (p) outliers start: 4 outliers final: 3 residues processed: 110 average time/residue: 0.3225 time to fit residues: 51.3848 Evaluate side-chains 108 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 0.0670 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.132840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.100814 restraints weight = 39176.006| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.70 r_work: 0.3298 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6840 Z= 0.128 Angle : 0.570 11.220 9326 Z= 0.289 Chirality : 0.082 1.772 1158 Planarity : 0.004 0.038 1128 Dihedral : 4.790 50.344 911 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.85 % Allowed : 9.38 % Favored : 89.77 % 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: 0.83 (0.29), residues: 886 helix: 1.37 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -3.38 (0.38), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.002 0.001 HIS A 310 PHE 0.008 0.001 PHE A 396 TYR 0.011 0.001 TYR B 178 ARG 0.003 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 512) hydrogen bonds : angle 4.04761 ( 1536) covalent geometry : bond 0.00276 ( 6840) covalent geometry : angle 0.57049 ( 9326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7251 (mpp) cc_final: 0.6962 (mpp) REVERT: B 131 MET cc_start: 0.7535 (mpp) cc_final: 0.7242 (mpp) outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 0.3048 time to fit residues: 47.7226 Evaluate side-chains 107 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 144 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 84 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.133531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.101701 restraints weight = 39929.280| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.66 r_work: 0.3373 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6840 Z= 0.207 Angle : 0.611 11.340 9326 Z= 0.318 Chirality : 0.083 1.783 1158 Planarity : 0.004 0.037 1128 Dihedral : 4.353 24.169 908 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.85 % Allowed : 9.80 % Favored : 89.35 % 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: 0.73 (0.29), residues: 886 helix: 1.31 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -3.37 (0.38), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 311 HIS 0.005 0.001 HIS A 310 PHE 0.016 0.002 PHE B 98 TYR 0.006 0.001 TYR B 178 ARG 0.003 0.001 ARG B 20 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 512) hydrogen bonds : angle 4.18147 ( 1536) covalent geometry : bond 0.00458 ( 6840) covalent geometry : angle 0.61140 ( 9326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7428 (mpp) cc_final: 0.7138 (mpp) REVERT: B 131 MET cc_start: 0.7539 (mpp) cc_final: 0.7296 (mpp) outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 0.3097 time to fit residues: 48.4182 Evaluate side-chains 105 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 432 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.135159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103686 restraints weight = 40259.016| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.71 r_work: 0.3395 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6840 Z= 0.138 Angle : 0.565 10.942 9326 Z= 0.288 Chirality : 0.081 1.736 1158 Planarity : 0.004 0.036 1128 Dihedral : 4.335 25.331 908 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.99 % Allowed : 10.23 % Favored : 88.78 % 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: 0.95 (0.29), residues: 886 helix: 1.46 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -3.33 (0.39), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 311 HIS 0.003 0.001 HIS B 65 PHE 0.009 0.001 PHE A 268 TYR 0.011 0.001 TYR A 178 ARG 0.003 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 512) hydrogen bonds : angle 4.00373 ( 1536) covalent geometry : bond 0.00304 ( 6840) covalent geometry : angle 0.56471 ( 9326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7416 (mpp) cc_final: 0.7107 (mpp) REVERT: B 131 MET cc_start: 0.7508 (mpp) cc_final: 0.7245 (mpp) REVERT: B 157 MET cc_start: 0.8119 (pmm) cc_final: 0.7726 (pmm) outliers start: 7 outliers final: 6 residues processed: 107 average time/residue: 0.4139 time to fit residues: 65.8180 Evaluate side-chains 107 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.128988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095888 restraints weight = 39865.453| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.74 r_work: 0.3223 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6840 Z= 0.145 Angle : 0.567 10.967 9326 Z= 0.289 Chirality : 0.081 1.726 1158 Planarity : 0.004 0.037 1128 Dihedral : 4.297 24.283 908 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.28 % Allowed : 10.94 % Favored : 87.78 % 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: 1.04 (0.29), residues: 886 helix: 1.52 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -3.42 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 311 HIS 0.003 0.001 HIS B 65 PHE 0.010 0.001 PHE A 100 TYR 0.011 0.001 TYR A 187 ARG 0.001 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 512) hydrogen bonds : angle 3.93793 ( 1536) covalent geometry : bond 0.00318 ( 6840) covalent geometry : angle 0.56736 ( 9326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7474 (mpp) cc_final: 0.7152 (mpp) REVERT: B 131 MET cc_start: 0.7524 (mpp) cc_final: 0.7211 (mpp) REVERT: B 427 VAL cc_start: 0.6603 (OUTLIER) cc_final: 0.6279 (p) outliers start: 9 outliers final: 6 residues processed: 112 average time/residue: 0.4248 time to fit residues: 71.3875 Evaluate side-chains 112 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 427 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.130629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098579 restraints weight = 39867.624| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.61 r_work: 0.3255 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6840 Z= 0.109 Angle : 0.555 11.062 9326 Z= 0.278 Chirality : 0.080 1.714 1158 Planarity : 0.004 0.037 1128 Dihedral : 4.279 25.299 908 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.99 % Allowed : 11.08 % Favored : 87.93 % 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: 1.22 (0.29), residues: 886 helix: 1.65 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -3.38 (0.38), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 311 HIS 0.003 0.001 HIS A 65 PHE 0.008 0.001 PHE A 396 TYR 0.007 0.001 TYR B 187 ARG 0.006 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 512) hydrogen bonds : angle 3.81666 ( 1536) covalent geometry : bond 0.00236 ( 6840) covalent geometry : angle 0.55506 ( 9326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7467 (mpp) cc_final: 0.7147 (mpp) REVERT: B 131 MET cc_start: 0.7504 (mpp) cc_final: 0.7242 (mpp) REVERT: B 427 VAL cc_start: 0.6600 (OUTLIER) cc_final: 0.6276 (p) outliers start: 7 outliers final: 6 residues processed: 112 average time/residue: 0.5374 time to fit residues: 88.3227 Evaluate side-chains 113 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 427 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.130103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.096948 restraints weight = 39673.701| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.72 r_work: 0.3240 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6840 Z= 0.129 Angle : 0.561 11.074 9326 Z= 0.284 Chirality : 0.081 1.722 1158 Planarity : 0.004 0.037 1128 Dihedral : 4.236 24.913 908 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.99 % Allowed : 11.22 % Favored : 87.78 % 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: 1.28 (0.29), residues: 886 helix: 1.69 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -3.37 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 311 HIS 0.003 0.001 HIS A 65 PHE 0.008 0.001 PHE A 100 TYR 0.005 0.001 TYR A 187 ARG 0.001 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 512) hydrogen bonds : angle 3.84234 ( 1536) covalent geometry : bond 0.00282 ( 6840) covalent geometry : angle 0.56126 ( 9326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7504 (mpp) cc_final: 0.7180 (mpp) REVERT: A 247 MET cc_start: 0.7671 (mmm) cc_final: 0.7363 (mmm) REVERT: B 131 MET cc_start: 0.7480 (mpp) cc_final: 0.7181 (mpp) REVERT: B 427 VAL cc_start: 0.6617 (OUTLIER) cc_final: 0.6295 (p) outliers start: 7 outliers final: 6 residues processed: 113 average time/residue: 0.6179 time to fit residues: 103.5347 Evaluate side-chains 112 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.129215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096896 restraints weight = 39901.855| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.62 r_work: 0.3232 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6840 Z= 0.150 Angle : 0.569 10.965 9326 Z= 0.289 Chirality : 0.081 1.728 1158 Planarity : 0.004 0.037 1128 Dihedral : 4.242 25.272 908 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.99 % Allowed : 11.93 % Favored : 87.07 % 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: 1.24 (0.29), residues: 886 helix: 1.67 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -3.41 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.004 0.001 HIS B 65 PHE 0.010 0.001 PHE B 98 TYR 0.008 0.001 TYR B 187 ARG 0.001 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 512) hydrogen bonds : angle 3.86118 ( 1536) covalent geometry : bond 0.00329 ( 6840) covalent geometry : angle 0.56942 ( 9326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7697 (mmm) cc_final: 0.7390 (mmm) REVERT: A 427 VAL cc_start: 0.6452 (OUTLIER) cc_final: 0.6150 (p) REVERT: B 131 MET cc_start: 0.7476 (mpp) cc_final: 0.7195 (mpp) REVERT: B 427 VAL cc_start: 0.6653 (OUTLIER) cc_final: 0.6337 (p) outliers start: 7 outliers final: 5 residues processed: 111 average time/residue: 0.4871 time to fit residues: 79.6507 Evaluate side-chains 112 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 0.1980 chunk 17 optimal weight: 10.0000 chunk 57 optimal weight: 0.0770 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.130753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097875 restraints weight = 40112.282| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.74 r_work: 0.3250 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6840 Z= 0.107 Angle : 0.560 11.066 9326 Z= 0.279 Chirality : 0.080 1.706 1158 Planarity : 0.004 0.036 1128 Dihedral : 4.224 25.586 908 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.14 % Allowed : 12.22 % Favored : 86.65 % 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: 1.40 (0.29), residues: 886 helix: 1.78 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -3.35 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 311 HIS 0.003 0.001 HIS B 65 PHE 0.007 0.001 PHE A 396 TYR 0.013 0.001 TYR A 187 ARG 0.004 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 512) hydrogen bonds : angle 3.75914 ( 1536) covalent geometry : bond 0.00231 ( 6840) covalent geometry : angle 0.55962 ( 9326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8740.67 seconds wall clock time: 157 minutes 14.03 seconds (9434.03 seconds total)