Starting phenix.real_space_refine on Tue Sep 24 08:44:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okd_16926/09_2024/8okd_16926.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okd_16926/09_2024/8okd_16926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okd_16926/09_2024/8okd_16926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okd_16926/09_2024/8okd_16926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okd_16926/09_2024/8okd_16926.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okd_16926/09_2024/8okd_16926.cif" } resolution = 3.1 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= 0.001 sd= 0.058 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 P 138 5.49 5 S 30 5.16 5 C 4392 2.51 5 N 1358 2.21 5 O 1830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7748 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2390 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 2 Chain: "B" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2390 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 2 Chain: "C" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1484 Classifications: {'RNA': 70} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 28, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 59} Chain breaks: 1 Chain: "X" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1484 Classifications: {'RNA': 70} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 58} Chain breaks: 1 Time building chain proxies: 4.99, per 1000 atoms: 0.64 Number of scatterers: 7748 At special positions: 0 Unit cell: (98.9, 162.54, 66.22, 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 30 16.00 P 138 15.00 O 1830 8.00 N 1358 7.00 C 4392 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: 1.99 Conformation dependent library (CDL) restraints added in 546.8 milliseconds 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 37.3% alpha, 21.0% beta 46 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.782A pdb=" N ALA A 59 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.718A pdb=" N LYS A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.954A pdb=" N SER A 109 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.862A pdb=" N VAL A 217 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.746A pdb=" N CYS A 281 " --> pdb=" O HIS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 removed outlier: 4.281A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 337 through 369 removed outlier: 3.842A pdb=" N LYS A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.909A pdb=" N ALA B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.827A pdb=" N LYS B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 4.038A pdb=" N SER B 109 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.660A pdb=" N ARG B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.731A pdb=" N CYS B 281 " --> pdb=" O HIS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 removed outlier: 4.333A pdb=" N GLU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 369 removed outlier: 3.801A pdb=" N LYS B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 removed outlier: 3.762A pdb=" N SER A 129 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 128 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 3.762A pdb=" N SER A 129 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 128 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 123 removed outlier: 7.098A pdb=" N SER A 122 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASP A 326 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR A 194 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 243 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.531A pdb=" N GLY A 218 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 241 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 239 " --> pdb=" O HIS A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 134 removed outlier: 7.798A pdb=" N HIS B 64 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 66 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP B 177 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ARG B 68 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 123 removed outlier: 6.824A pdb=" N SER B 122 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP B 326 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR B 194 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 269 " --> pdb=" O TYR B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 220 through 221 190 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 2.31 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: 1941 1.34 - 1.46: 2451 1.46 - 1.57: 3492 1.57 - 1.69: 274 1.69 - 1.81: 48 Bond restraints: 8206 Sorted by residual: bond pdb=" C GLU A 260 " pdb=" N PRO A 261 " ideal model delta sigma weight residual 1.334 1.345 -0.011 8.40e-03 1.42e+04 1.75e+00 bond pdb=" C GLU B 260 " pdb=" N PRO B 261 " ideal model delta sigma weight residual 1.334 1.344 -0.011 8.40e-03 1.42e+04 1.68e+00 bond pdb=" CB LYS A 307 " pdb=" CG LYS A 307 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.35e-01 bond pdb=" CG1 ILE A 69 " pdb=" CD1 ILE A 69 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.31e-01 bond pdb=" C3' U X 20 " pdb=" O3' U X 20 " ideal model delta sigma weight residual 1.417 1.428 -0.011 1.50e-02 4.44e+03 5.18e-01 ... (remaining 8201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 11572 1.66 - 3.31: 167 3.31 - 4.97: 21 4.97 - 6.63: 3 6.63 - 8.28: 3 Bond angle restraints: 11766 Sorted by residual: angle pdb=" N GLY A 233 " pdb=" CA GLY A 233 " pdb=" C GLY A 233 " ideal model delta sigma weight residual 113.18 121.06 -7.88 2.37e+00 1.78e-01 1.10e+01 angle pdb=" CB MET B 283 " pdb=" CG MET B 283 " pdb=" SD MET B 283 " ideal model delta sigma weight residual 112.70 120.98 -8.28 3.00e+00 1.11e-01 7.63e+00 angle pdb=" CA LYS A 307 " pdb=" CB LYS A 307 " pdb=" CG LYS A 307 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.98e+00 angle pdb=" C ALA B 118 " pdb=" N LYS B 119 " pdb=" CA LYS B 119 " ideal model delta sigma weight residual 120.90 124.51 -3.61 1.41e+00 5.03e-01 6.55e+00 angle pdb=" CA LEU B 303 " pdb=" CB LEU B 303 " pdb=" CG LEU B 303 " ideal model delta sigma weight residual 116.30 124.17 -7.87 3.50e+00 8.16e-02 5.05e+00 ... (remaining 11761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.81: 4606 32.81 - 65.63: 431 65.63 - 98.44: 58 98.44 - 131.25: 2 131.25 - 164.07: 1 Dihedral angle restraints: 5098 sinusoidal: 3384 harmonic: 1714 Sorted by residual: dihedral pdb=" O4' C X 48 " pdb=" C1' C X 48 " pdb=" N1 C X 48 " pdb=" C2 C X 48 " ideal model delta sinusoidal sigma weight residual -160.00 -54.00 -106.00 1 1.50e+01 4.44e-03 5.44e+01 dihedral pdb=" O4' C C 48 " pdb=" C1' C C 48 " pdb=" N1 C C 48 " pdb=" C2 C C 48 " ideal model delta sinusoidal sigma weight residual -160.00 -57.34 -102.66 1 1.50e+01 4.44e-03 5.20e+01 dihedral pdb=" O4' U X 20 " pdb=" C1' U X 20 " pdb=" N1 U X 20 " pdb=" C2 U X 20 " ideal model delta sinusoidal sigma weight residual -160.00 -78.93 -81.07 1 1.50e+01 4.44e-03 3.60e+01 ... (remaining 5095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1177 0.042 - 0.083: 169 0.083 - 0.125: 54 0.125 - 0.167: 5 0.167 - 0.208: 1 Chirality restraints: 1406 Sorted by residual: chirality pdb=" C1' U C 39 " pdb=" O4' U C 39 " pdb=" C2' U C 39 " pdb=" N1 U C 39 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA PHE A 320 " pdb=" N PHE A 320 " pdb=" C PHE A 320 " pdb=" CB PHE A 320 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1403 not shown) Planarity restraints: 996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 267 " -0.010 2.00e-02 2.50e+03 1.50e-02 3.94e+00 pdb=" CG PHE A 267 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 267 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 267 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 267 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 267 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 295 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 296 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 124 " 0.007 2.00e-02 2.50e+03 1.04e-02 1.88e+00 pdb=" CG PHE A 124 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 124 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 124 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 124 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 124 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 124 " -0.000 2.00e-02 2.50e+03 ... (remaining 993 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 947 2.75 - 3.28: 7297 3.28 - 3.82: 13914 3.82 - 4.36: 16028 4.36 - 4.90: 24623 Nonbonded interactions: 62809 Sorted by model distance: nonbonded pdb=" O2' A C 7 " pdb=" O2 C C 48 " model vdw 2.207 3.040 nonbonded pdb=" O2' A X 7 " pdb=" O2 C X 48 " model vdw 2.255 3.040 nonbonded pdb=" O2' A C 57 " pdb=" OP2 U C 59 " model vdw 2.294 3.040 nonbonded pdb=" ND2 ASN B 224 " pdb=" O LEU B 302 " model vdw 2.296 3.120 nonbonded pdb=" O GLY A 115 " pdb=" NE2 GLN A 126 " model vdw 2.306 3.120 ... (remaining 62804 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' } ncs_group { reference = chain 'C' selection = chain 'X' } 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=0.00 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: 1.530 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.710 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 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 : 0.003 0.028 8206 Z= 0.180 Angle : 0.509 8.284 11766 Z= 0.267 Chirality : 0.034 0.208 1406 Planarity : 0.003 0.036 996 Dihedral : 21.865 164.067 3986 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.39 % Allowed : 35.94 % Favored : 63.67 % 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: -0.76 (0.35), residues: 570 helix: 1.83 (0.43), residues: 146 sheet: -0.83 (0.51), residues: 100 loop : -1.57 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 352 HIS 0.002 0.001 HIS A 360 PHE 0.034 0.002 PHE A 267 TYR 0.007 0.001 TYR A 160 ARG 0.002 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.596 Fit side-chains REVERT: A 119 LYS cc_start: 0.6643 (pttt) cc_final: 0.6378 (ptmm) REVERT: A 228 MET cc_start: 0.6839 (mtm) cc_final: 0.6537 (mtp) REVERT: A 313 GLN cc_start: 0.5796 (tp-100) cc_final: 0.5578 (mt0) REVERT: A 316 MET cc_start: 0.5871 (ptp) cc_final: 0.5106 (ptt) REVERT: A 320 PHE cc_start: 0.6789 (p90) cc_final: 0.5657 (p90) REVERT: A 328 LYS cc_start: 0.5720 (ttmm) cc_final: 0.5416 (ttpt) REVERT: A 331 ASN cc_start: 0.7059 (m-40) cc_final: 0.6816 (m-40) REVERT: B 210 ASP cc_start: 0.6151 (t0) cc_final: 0.5945 (t0) REVERT: B 247 GLN cc_start: 0.6086 (pt0) cc_final: 0.5367 (pm20) REVERT: B 282 MET cc_start: 0.5447 (tpp) cc_final: 0.5172 (mtt) REVERT: B 347 HIS cc_start: 0.5805 (t70) cc_final: 0.5526 (t-170) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.2400 time to fit residues: 30.8157 Evaluate side-chains 65 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 238 GLN A 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8206 Z= 0.175 Angle : 0.532 8.542 11766 Z= 0.276 Chirality : 0.035 0.194 1406 Planarity : 0.004 0.034 996 Dihedral : 21.066 162.652 2821 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.12 % Allowed : 32.81 % Favored : 64.06 % 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: -0.61 (0.35), residues: 570 helix: 1.83 (0.42), residues: 146 sheet: -0.48 (0.50), residues: 90 loop : -1.49 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 352 HIS 0.003 0.001 HIS A 162 PHE 0.021 0.002 PHE A 320 TYR 0.008 0.001 TYR A 197 ARG 0.004 0.001 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.636 Fit side-chains REVERT: A 238 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6803 (mm-40) REVERT: A 304 ASN cc_start: 0.5515 (m-40) cc_final: 0.4817 (t0) REVERT: A 313 GLN cc_start: 0.5737 (tp-100) cc_final: 0.5503 (mt0) REVERT: A 316 MET cc_start: 0.6172 (ptp) cc_final: 0.5399 (ptt) REVERT: A 328 LYS cc_start: 0.5798 (ttmm) cc_final: 0.5455 (ttpt) REVERT: B 72 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6926 (ptp) REVERT: B 247 GLN cc_start: 0.5805 (pt0) cc_final: 0.4944 (pm20) REVERT: B 282 MET cc_start: 0.5343 (tpp) cc_final: 0.5063 (mtt) REVERT: B 303 LEU cc_start: 0.6554 (pp) cc_final: 0.6312 (mt) REVERT: B 347 HIS cc_start: 0.5836 (t70) cc_final: 0.5487 (t70) outliers start: 16 outliers final: 9 residues processed: 76 average time/residue: 0.1867 time to fit residues: 19.6656 Evaluate side-chains 71 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 361 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 22 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 126 GLN A 247 GLN B 64 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8206 Z= 0.300 Angle : 0.628 8.048 11766 Z= 0.326 Chirality : 0.040 0.256 1406 Planarity : 0.005 0.038 996 Dihedral : 21.143 158.832 2818 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 6.45 % Allowed : 28.32 % Favored : 65.23 % 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: -0.84 (0.34), residues: 570 helix: 1.33 (0.41), residues: 146 sheet: -0.54 (0.50), residues: 90 loop : -1.49 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.003 0.001 HIS A 355 PHE 0.028 0.002 PHE A 320 TYR 0.013 0.002 TYR A 76 ARG 0.004 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 56 time to evaluate : 0.648 Fit side-chains REVERT: A 181 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: A 238 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6627 (mm-40) REVERT: A 304 ASN cc_start: 0.5337 (m-40) cc_final: 0.4817 (t0) REVERT: A 313 GLN cc_start: 0.5745 (tp-100) cc_final: 0.5457 (mt0) REVERT: A 316 MET cc_start: 0.6775 (ptp) cc_final: 0.6225 (ptt) REVERT: A 328 LYS cc_start: 0.5802 (ttmm) cc_final: 0.5550 (ttpt) REVERT: A 366 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6751 (tt) REVERT: B 64 HIS cc_start: 0.6499 (OUTLIER) cc_final: 0.5607 (t-90) REVERT: B 82 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6182 (mt0) REVERT: B 156 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5866 (pt0) REVERT: B 303 LEU cc_start: 0.6388 (pp) cc_final: 0.6082 (mt) REVERT: B 316 MET cc_start: 0.5932 (ttp) cc_final: 0.5628 (ptm) REVERT: B 347 HIS cc_start: 0.6130 (t70) cc_final: 0.5801 (t70) REVERT: B 350 GLN cc_start: 0.5577 (OUTLIER) cc_final: 0.5121 (mt0) outliers start: 33 outliers final: 14 residues processed: 80 average time/residue: 0.1671 time to fit residues: 19.0958 Evaluate side-chains 69 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 48 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 361 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8206 Z= 0.279 Angle : 0.606 8.794 11766 Z= 0.315 Chirality : 0.039 0.252 1406 Planarity : 0.004 0.037 996 Dihedral : 21.063 157.818 2818 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 6.25 % Allowed : 27.15 % Favored : 66.60 % 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: -1.23 (0.34), residues: 570 helix: 0.74 (0.40), residues: 158 sheet: -0.71 (0.48), residues: 90 loop : -1.72 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.006 0.001 HIS B 64 PHE 0.026 0.002 PHE A 320 TYR 0.013 0.002 TYR A 195 ARG 0.004 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 48 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.5978 (OUTLIER) cc_final: 0.4675 (mp10) REVERT: A 198 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.5699 (m-80) REVERT: A 304 ASN cc_start: 0.5181 (m-40) cc_final: 0.4732 (t0) REVERT: A 313 GLN cc_start: 0.5745 (tp-100) cc_final: 0.5439 (mt0) REVERT: A 316 MET cc_start: 0.6762 (ptp) cc_final: 0.6379 (ptt) REVERT: A 328 LYS cc_start: 0.5779 (ttmm) cc_final: 0.5537 (ttpt) REVERT: A 366 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6714 (tt) REVERT: B 82 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6184 (mt0) REVERT: B 156 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5864 (pt0) REVERT: B 282 MET cc_start: 0.6097 (OUTLIER) cc_final: 0.5716 (tpp) REVERT: B 303 LEU cc_start: 0.6339 (pp) cc_final: 0.5920 (mt) REVERT: B 314 TYR cc_start: 0.6455 (OUTLIER) cc_final: 0.5758 (p90) REVERT: B 316 MET cc_start: 0.5892 (ttp) cc_final: 0.5489 (ptm) REVERT: B 347 HIS cc_start: 0.6097 (t70) cc_final: 0.5742 (t70) outliers start: 32 outliers final: 20 residues processed: 72 average time/residue: 0.1719 time to fit residues: 17.6174 Evaluate side-chains 72 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 45 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8206 Z= 0.142 Angle : 0.494 7.398 11766 Z= 0.258 Chirality : 0.034 0.193 1406 Planarity : 0.003 0.031 996 Dihedral : 20.799 154.468 2818 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.12 % Allowed : 30.08 % Favored : 66.80 % 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: -0.76 (0.34), residues: 570 helix: 1.49 (0.42), residues: 146 sheet: -0.52 (0.49), residues: 90 loop : -1.48 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 352 HIS 0.002 0.001 HIS B 347 PHE 0.022 0.001 PHE A 320 TYR 0.007 0.001 TYR A 195 ARG 0.005 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.611 Fit side-chains REVERT: A 304 ASN cc_start: 0.4761 (m-40) cc_final: 0.4350 (t0) REVERT: A 311 LYS cc_start: 0.6127 (ptpp) cc_final: 0.5618 (pttt) REVERT: A 313 GLN cc_start: 0.5851 (tp-100) cc_final: 0.5156 (mt0) REVERT: A 316 MET cc_start: 0.6495 (ptp) cc_final: 0.5865 (ptt) REVERT: A 328 LYS cc_start: 0.5802 (ttmm) cc_final: 0.5536 (ttpt) REVERT: B 64 HIS cc_start: 0.6260 (OUTLIER) cc_final: 0.5329 (t-90) REVERT: B 82 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6121 (mp10) REVERT: B 156 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5847 (pt0) REVERT: B 303 LEU cc_start: 0.6499 (pp) cc_final: 0.6102 (mt) REVERT: B 316 MET cc_start: 0.5898 (ttp) cc_final: 0.5472 (ptm) REVERT: B 347 HIS cc_start: 0.6071 (t70) cc_final: 0.5792 (t70) REVERT: B 350 GLN cc_start: 0.5647 (OUTLIER) cc_final: 0.5246 (mt0) outliers start: 16 outliers final: 9 residues processed: 66 average time/residue: 0.1800 time to fit residues: 16.7895 Evaluate side-chains 62 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 0.0370 chunk 40 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- 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: 0.6060 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8206 Z= 0.277 Angle : 0.595 8.260 11766 Z= 0.308 Chirality : 0.039 0.245 1406 Planarity : 0.004 0.039 996 Dihedral : 20.962 155.239 2818 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 5.66 % Allowed : 27.34 % Favored : 66.99 % 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: -0.96 (0.34), residues: 570 helix: 1.18 (0.42), residues: 146 sheet: -0.59 (0.49), residues: 90 loop : -1.56 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.004 0.001 HIS A 162 PHE 0.029 0.002 PHE A 320 TYR 0.013 0.002 TYR A 195 ARG 0.006 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 49 time to evaluate : 0.578 Fit side-chains REVERT: A 77 GLN cc_start: 0.5965 (OUTLIER) cc_final: 0.4680 (mp10) REVERT: A 311 LYS cc_start: 0.6255 (ptpp) cc_final: 0.5766 (pttt) REVERT: A 313 GLN cc_start: 0.5840 (tp-100) cc_final: 0.5141 (mt0) REVERT: A 316 MET cc_start: 0.6840 (ptp) cc_final: 0.6191 (ptt) REVERT: A 328 LYS cc_start: 0.5836 (ttmm) cc_final: 0.5578 (ttpt) REVERT: A 366 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6718 (tt) REVERT: B 82 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6171 (mp10) REVERT: B 92 LYS cc_start: 0.6257 (OUTLIER) cc_final: 0.5789 (mttm) REVERT: B 156 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5810 (pt0) REVERT: B 303 LEU cc_start: 0.6227 (pp) cc_final: 0.5885 (mt) REVERT: B 316 MET cc_start: 0.5963 (ttp) cc_final: 0.5463 (ptm) REVERT: B 347 HIS cc_start: 0.6176 (t70) cc_final: 0.5902 (t70) REVERT: B 350 GLN cc_start: 0.5503 (OUTLIER) cc_final: 0.5057 (mt0) outliers start: 29 outliers final: 18 residues processed: 72 average time/residue: 0.1765 time to fit residues: 17.9739 Evaluate side-chains 72 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 48 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8206 Z= 0.196 Angle : 0.532 7.781 11766 Z= 0.277 Chirality : 0.036 0.222 1406 Planarity : 0.004 0.034 996 Dihedral : 20.856 154.522 2818 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.86 % Allowed : 26.95 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.35), residues: 570 helix: 0.98 (0.42), residues: 158 sheet: -0.46 (0.50), residues: 90 loop : -1.50 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 352 HIS 0.005 0.001 HIS A 162 PHE 0.026 0.002 PHE A 320 TYR 0.010 0.001 TYR A 195 ARG 0.006 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 49 time to evaluate : 0.630 Fit side-chains REVERT: A 77 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.4602 (mp10) REVERT: A 311 LYS cc_start: 0.6297 (ptpp) cc_final: 0.5797 (pttt) REVERT: A 313 GLN cc_start: 0.5923 (tp-100) cc_final: 0.5209 (mt0) REVERT: A 316 MET cc_start: 0.6665 (ptp) cc_final: 0.6016 (ptt) REVERT: A 328 LYS cc_start: 0.5839 (ttmm) cc_final: 0.5568 (ttpt) REVERT: A 366 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6640 (tt) REVERT: B 53 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6334 (ppt170) REVERT: B 64 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.5709 (t-90) REVERT: B 82 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6145 (mp10) REVERT: B 92 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.6040 (mmtt) REVERT: B 156 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5834 (pt0) REVERT: B 282 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5697 (tpp) REVERT: B 303 LEU cc_start: 0.6239 (pp) cc_final: 0.5917 (mt) REVERT: B 316 MET cc_start: 0.5922 (ttp) cc_final: 0.5439 (ptm) REVERT: B 347 HIS cc_start: 0.6124 (t70) cc_final: 0.5840 (t70) REVERT: B 350 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.5202 (mt0) REVERT: B 361 MET cc_start: 0.5135 (OUTLIER) cc_final: 0.4432 (ttm) outliers start: 30 outliers final: 17 residues processed: 73 average time/residue: 0.1836 time to fit residues: 18.6086 Evaluate side-chains 75 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 48 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS B 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8206 Z= 0.236 Angle : 0.564 7.999 11766 Z= 0.292 Chirality : 0.037 0.234 1406 Planarity : 0.004 0.037 996 Dihedral : 20.909 155.031 2818 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 6.25 % Allowed : 25.78 % Favored : 67.97 % 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: -1.03 (0.35), residues: 570 helix: 0.84 (0.42), residues: 158 sheet: -0.50 (0.50), residues: 90 loop : -1.58 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 177 HIS 0.005 0.001 HIS B 64 PHE 0.027 0.002 PHE A 320 TYR 0.011 0.001 TYR A 195 ARG 0.005 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 49 time to evaluate : 0.627 Fit side-chains REVERT: A 77 GLN cc_start: 0.5964 (OUTLIER) cc_final: 0.4605 (mp10) REVERT: A 311 LYS cc_start: 0.6304 (ptpp) cc_final: 0.5835 (pttt) REVERT: A 313 GLN cc_start: 0.5910 (tp-100) cc_final: 0.5137 (mt0) REVERT: A 316 MET cc_start: 0.6756 (ptp) cc_final: 0.6125 (ptt) REVERT: A 328 LYS cc_start: 0.5849 (ttmm) cc_final: 0.5579 (ttpt) REVERT: A 366 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6587 (tt) REVERT: B 53 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6329 (ppt170) REVERT: B 64 HIS cc_start: 0.6334 (OUTLIER) cc_final: 0.5729 (t-90) REVERT: B 82 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6166 (mp10) REVERT: B 92 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.6021 (mmtt) REVERT: B 156 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5864 (pt0) REVERT: B 282 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5689 (tpp) REVERT: B 303 LEU cc_start: 0.6319 (pp) cc_final: 0.5938 (mt) REVERT: B 316 MET cc_start: 0.5939 (ttp) cc_final: 0.5512 (ptm) REVERT: B 347 HIS cc_start: 0.6153 (t70) cc_final: 0.5888 (t70) REVERT: B 350 GLN cc_start: 0.5533 (OUTLIER) cc_final: 0.5094 (mt0) REVERT: B 361 MET cc_start: 0.5052 (OUTLIER) cc_final: 0.4430 (ttm) outliers start: 32 outliers final: 21 residues processed: 74 average time/residue: 0.1829 time to fit residues: 18.9162 Evaluate side-chains 79 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 48 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8206 Z= 0.251 Angle : 0.573 8.064 11766 Z= 0.297 Chirality : 0.038 0.241 1406 Planarity : 0.004 0.037 996 Dihedral : 20.934 155.728 2818 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 6.64 % Allowed : 25.59 % Favored : 67.77 % 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: -1.06 (0.35), residues: 570 helix: 0.79 (0.42), residues: 158 sheet: -0.50 (0.50), residues: 90 loop : -1.59 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 177 HIS 0.005 0.001 HIS A 162 PHE 0.028 0.002 PHE A 320 TYR 0.012 0.001 TYR A 195 ARG 0.005 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 47 time to evaluate : 0.630 Fit side-chains REVERT: A 77 GLN cc_start: 0.5955 (OUTLIER) cc_final: 0.4596 (mp10) REVERT: A 311 LYS cc_start: 0.6360 (ptpp) cc_final: 0.5898 (pttt) REVERT: A 313 GLN cc_start: 0.5878 (tp-100) cc_final: 0.5078 (mt0) REVERT: A 316 MET cc_start: 0.6722 (ptp) cc_final: 0.6103 (ptt) REVERT: A 328 LYS cc_start: 0.5848 (ttmm) cc_final: 0.5581 (ttpt) REVERT: A 366 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6678 (tt) REVERT: B 53 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6221 (ppt170) REVERT: B 64 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5422 (t-90) REVERT: B 82 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6188 (mp10) REVERT: B 92 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.6023 (mmtt) REVERT: B 156 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.5792 (pt0) REVERT: B 282 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5670 (tpp) REVERT: B 316 MET cc_start: 0.5939 (ttp) cc_final: 0.5512 (ptm) REVERT: B 347 HIS cc_start: 0.6136 (t70) cc_final: 0.5840 (t70) REVERT: B 350 GLN cc_start: 0.5691 (OUTLIER) cc_final: 0.5259 (mt0) REVERT: B 361 MET cc_start: 0.5128 (OUTLIER) cc_final: 0.4495 (ttm) outliers start: 34 outliers final: 23 residues processed: 72 average time/residue: 0.1827 time to fit residues: 18.4541 Evaluate side-chains 79 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 46 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 0.0020 chunk 71 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8206 Z= 0.187 Angle : 0.539 9.571 11766 Z= 0.278 Chirality : 0.036 0.218 1406 Planarity : 0.004 0.035 996 Dihedral : 20.870 155.302 2818 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.66 % Allowed : 26.37 % Favored : 67.97 % 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: -0.99 (0.35), residues: 570 helix: 0.82 (0.42), residues: 160 sheet: -0.47 (0.51), residues: 90 loop : -1.55 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 177 HIS 0.004 0.001 HIS B 64 PHE 0.025 0.002 PHE A 320 TYR 0.009 0.001 TYR A 195 ARG 0.006 0.000 ARG B 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 48 time to evaluate : 0.635 Fit side-chains REVERT: A 77 GLN cc_start: 0.5960 (OUTLIER) cc_final: 0.4597 (mp10) REVERT: A 311 LYS cc_start: 0.6369 (ptpp) cc_final: 0.5886 (pttt) REVERT: A 313 GLN cc_start: 0.5811 (tp-100) cc_final: 0.4980 (mt0) REVERT: A 316 MET cc_start: 0.6630 (ptp) cc_final: 0.6011 (ptt) REVERT: A 328 LYS cc_start: 0.5840 (ttmm) cc_final: 0.5568 (ttpt) REVERT: A 366 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6658 (tt) REVERT: B 64 HIS cc_start: 0.6239 (OUTLIER) cc_final: 0.5746 (t-90) REVERT: B 82 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6191 (mp10) REVERT: B 92 LYS cc_start: 0.6253 (OUTLIER) cc_final: 0.6043 (mmtt) REVERT: B 156 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5846 (pt0) REVERT: B 282 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5694 (tpp) REVERT: B 316 MET cc_start: 0.5894 (ttp) cc_final: 0.5458 (ptm) REVERT: B 347 HIS cc_start: 0.6133 (t70) cc_final: 0.5852 (t70) REVERT: B 350 GLN cc_start: 0.5754 (OUTLIER) cc_final: 0.5307 (mt0) outliers start: 29 outliers final: 20 residues processed: 70 average time/residue: 0.1707 time to fit residues: 17.0575 Evaluate side-chains 75 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 47 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 15 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.0170 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.198191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.163383 restraints weight = 8881.383| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.49 r_work: 0.3860 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8206 Z= 0.124 Angle : 0.486 9.434 11766 Z= 0.251 Chirality : 0.033 0.167 1406 Planarity : 0.003 0.031 996 Dihedral : 20.730 153.367 2818 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.93 % Allowed : 29.10 % Favored : 67.97 % 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: -0.66 (0.35), residues: 570 helix: 1.18 (0.42), residues: 158 sheet: -0.28 (0.51), residues: 90 loop : -1.37 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 352 HIS 0.011 0.001 HIS B 64 PHE 0.020 0.001 PHE A 320 TYR 0.006 0.001 TYR A 160 ARG 0.007 0.000 ARG B 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1577.70 seconds wall clock time: 28 minutes 48.59 seconds (1728.59 seconds total)