Starting phenix.real_space_refine on Tue Aug 4 19:04:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9caj_45393/08_2026/9caj_45393_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9caj_45393/08_2026/9caj_45393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9caj_45393/08_2026/9caj_45393_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9caj_45393/08_2026/9caj_45393_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9caj_45393/08_2026/9caj_45393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9caj_45393/08_2026/9caj_45393.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.020 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 9 5.49 5 S 39 5.16 5 C 3918 2.51 5 N 1079 2.21 5 O 1199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6245 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4840 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.22, per 1000 atoms: 0.20 Number of scatterers: 6245 At special positions: 0 Unit cell: (76.36, 87.15, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 39 16.00 P 9 15.00 O 1199 8.00 N 1079 7.00 C 3918 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: 0.39 Conformation dependent library (CDL) restraints added in 238.3 milliseconds 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 41.1% alpha, 14.9% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 4.105A pdb=" N ILE A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 4.336A pdb=" N SER A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 157 through 165 removed outlier: 4.549A pdb=" N CYS A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 201 removed outlier: 3.706A pdb=" N SER A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.563A pdb=" N LEU A 207 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.708A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 3.682A pdb=" N ALA A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.714A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.718A pdb=" N TYR A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 495 through 507 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 551 Processing helix chain 'A' and resid 552 through 556 removed outlier: 3.899A pdb=" N VAL A 556 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 removed outlier: 3.645A pdb=" N SER A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 600 removed outlier: 3.576A pdb=" N ASP A 598 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.967A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 32 through 43 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.232A pdb=" N LYS A 2 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS A 53 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 41 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.232A pdb=" N LYS A 2 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS A 53 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET A 6 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N TRP A 115 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 7 " --> pdb=" O TRP A 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=AA6, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.939A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS A 424 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 294 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A 426 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU A 292 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN A 428 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG A 290 " --> pdb=" O GLN A 428 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 430 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR A 288 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 432 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 530 Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.646A pdb=" N ASP B 134 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N LEU B 140 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 126 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.49 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: 2011 1.34 - 1.45: 886 1.45 - 1.57: 3415 1.57 - 1.69: 17 1.69 - 1.81: 61 Bond restraints: 6390 Sorted by residual: bond pdb=" O3' DA C -1 " pdb=" P DC C 0 " ideal model delta sigma weight residual 1.607 1.579 0.028 1.20e-02 6.94e+03 5.56e+00 bond pdb=" O3' DT C 4 " pdb=" P DA C 5 " ideal model delta sigma weight residual 1.607 1.580 0.027 1.20e-02 6.94e+03 5.24e+00 bond pdb=" N LYS A 10 " pdb=" CA LYS A 10 " ideal model delta sigma weight residual 1.453 1.480 -0.027 1.18e-02 7.18e+03 5.18e+00 bond pdb=" N ARG A 338 " pdb=" CA ARG A 338 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.46e-02 4.69e+03 4.75e+00 bond pdb=" N GLU A 340 " pdb=" CA GLU A 340 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.61e-02 3.86e+03 3.77e+00 ... (remaining 6385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 8421 1.67 - 3.33: 207 3.33 - 5.00: 41 5.00 - 6.67: 11 6.67 - 8.34: 3 Bond angle restraints: 8683 Sorted by residual: angle pdb=" C LYS A 10 " pdb=" N PRO A 11 " pdb=" CA PRO A 11 " ideal model delta sigma weight residual 119.84 124.02 -4.18 1.25e+00 6.40e-01 1.12e+01 angle pdb=" C CYS A 109 " pdb=" N ASP A 110 " pdb=" CA ASP A 110 " ideal model delta sigma weight residual 121.54 127.52 -5.98 1.91e+00 2.74e-01 9.80e+00 angle pdb=" N GLY B 60 " pdb=" CA GLY B 60 " pdb=" C GLY B 60 " ideal model delta sigma weight residual 114.25 118.20 -3.95 1.30e+00 5.92e-01 9.23e+00 angle pdb=" C4' DA C -1 " pdb=" O4' DA C -1 " pdb=" C1' DA C -1 " ideal model delta sigma weight residual 110.10 107.18 2.92 1.00e+00 1.00e+00 8.51e+00 angle pdb=" O5' DT C 4 " pdb=" C5' DT C 4 " pdb=" C4' DT C 4 " ideal model delta sigma weight residual 109.40 111.72 -2.32 8.00e-01 1.56e+00 8.44e+00 ... (remaining 8678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3408 17.97 - 35.94: 345 35.94 - 53.91: 76 53.91 - 71.88: 24 71.88 - 89.85: 9 Dihedral angle restraints: 3862 sinusoidal: 1628 harmonic: 2234 Sorted by residual: dihedral pdb=" CA VAL A 113 " pdb=" C VAL A 113 " pdb=" N LEU A 114 " pdb=" CA LEU A 114 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TYR A 111 " pdb=" C TYR A 111 " pdb=" N ILE A 112 " pdb=" CA ILE A 112 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ASP A 552 " pdb=" C ASP A 552 " pdb=" N ALA A 553 " pdb=" CA ALA A 553 " ideal model delta harmonic sigma weight residual 180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 752 0.047 - 0.093: 181 0.093 - 0.139: 38 0.139 - 0.186: 2 0.186 - 0.232: 1 Chirality restraints: 974 Sorted by residual: chirality pdb=" CB ILE A 435 " pdb=" CA ILE A 435 " pdb=" CG1 ILE A 435 " pdb=" CG2 ILE A 435 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA VAL A 4 " pdb=" N VAL A 4 " pdb=" C VAL A 4 " pdb=" CB VAL A 4 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA LEU A 134 " pdb=" N LEU A 134 " pdb=" C LEU A 134 " pdb=" CB LEU A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 971 not shown) Planarity restraints: 1091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 436 " -0.055 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO A 437 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 456 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 457 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 53 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO B 54 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.023 5.00e-02 4.00e+02 ... (remaining 1088 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 83 2.65 - 3.21: 5753 3.21 - 3.78: 9333 3.78 - 4.34: 12421 4.34 - 4.90: 20680 Nonbonded interactions: 48270 Sorted by model distance: nonbonded pdb=" OE2 GLU A 9 " pdb=" OD2 ASP A 117 " model vdw 2.088 3.040 nonbonded pdb=" OE2 GLU A 9 " pdb="MN MN A 701 " model vdw 2.124 2.320 nonbonded pdb=" OP1 DA C 5 " pdb="MN MN A 701 " model vdw 2.151 2.320 nonbonded pdb=" OG SER A 289 " pdb=" OG1 THR A 430 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 204 " pdb=" OD1 ASP A 604 " model vdw 2.296 3.040 ... (remaining 48265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 0.065 6390 Z= 0.189 Angle : 0.658 8.336 8683 Z= 0.363 Chirality : 0.042 0.232 974 Planarity : 0.005 0.085 1091 Dihedral : 15.919 89.853 2420 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.45 % Allowed : 0.60 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.31), residues: 769 helix: 1.05 (0.30), residues: 293 sheet: -0.50 (0.45), residues: 148 loop : -1.07 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 338 TYR 0.014 0.001 TYR A 240 PHE 0.011 0.001 PHE B 52 TRP 0.007 0.001 TRP A 458 HIS 0.007 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 ( 6390) covalent geometry : angle 0.65845 / 0.36 ( 8683) hydrogen bonds : bond 0.08452 / 5.77 ( 258) hydrogen bonds : angle 4.86236 / 3.31 ( 732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7068 (mm) cc_final: 0.6853 (mm) REVERT: A 40 GLU cc_start: 0.7154 (mp0) cc_final: 0.6867 (mp0) REVERT: A 164 MET cc_start: 0.6093 (mpp) cc_final: 0.5564 (mpp) REVERT: A 185 ASP cc_start: 0.7013 (t70) cc_final: 0.6665 (t0) REVERT: A 198 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7618 (mtmm) REVERT: A 243 LEU cc_start: 0.8216 (tp) cc_final: 0.7955 (tt) REVERT: A 282 GLU cc_start: 0.6430 (mp0) cc_final: 0.5844 (mp0) REVERT: A 380 LYS cc_start: 0.7601 (mppt) cc_final: 0.7380 (mppt) REVERT: A 386 ASP cc_start: 0.6972 (t70) cc_final: 0.6567 (t70) REVERT: B 33 VAL cc_start: 0.8196 (t) cc_final: 0.7853 (m) outliers start: 3 outliers final: 0 residues processed: 171 average time/residue: 0.0648 time to fit residues: 14.3226 Evaluate side-chains 156 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0030 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 HIS A 162 ASN A 172 HIS A 357 GLN ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110564 restraints weight = 9715.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113868 restraints weight = 4285.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.115925 restraints weight = 2291.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117200 restraints weight = 1398.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118013 restraints weight = 950.938| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6390 Z= 0.180 Angle : 0.613 11.363 8683 Z= 0.310 Chirality : 0.042 0.153 974 Planarity : 0.005 0.063 1091 Dihedral : 12.204 86.451 932 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 0.45 % Allowed : 12.13 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.31), residues: 769 helix: 0.94 (0.30), residues: 298 sheet: -0.60 (0.44), residues: 151 loop : -1.09 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.014 0.001 TYR A 240 PHE 0.012 0.002 PHE A 593 TRP 0.010 0.001 TRP B 14 HIS 0.005 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 6390) covalent geometry : angle 0.61252 / 0.31 ( 8683) hydrogen bonds : bond 0.03826 / 2.64 ( 258) hydrogen bonds : angle 4.50873 / 3.11 ( 732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7094 (mm) cc_final: 0.6836 (mm) REVERT: A 40 GLU cc_start: 0.7265 (mp0) cc_final: 0.6858 (mp0) REVERT: A 198 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7621 (mtmm) REVERT: A 231 LYS cc_start: 0.7921 (ttmm) cc_final: 0.7712 (mtmm) REVERT: A 327 ARG cc_start: 0.6317 (tmt170) cc_final: 0.6061 (tmt170) REVERT: A 380 LYS cc_start: 0.7630 (mppt) cc_final: 0.7394 (mppt) REVERT: A 386 ASP cc_start: 0.6770 (t70) cc_final: 0.6508 (t70) REVERT: A 438 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7052 (mm-30) outliers start: 3 outliers final: 1 residues processed: 173 average time/residue: 0.0686 time to fit residues: 15.2840 Evaluate side-chains 163 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 HIS A 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110178 restraints weight = 9538.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113313 restraints weight = 4159.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115287 restraints weight = 2234.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116494 restraints weight = 1378.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117272 restraints weight = 949.199| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6390 Z= 0.204 Angle : 0.608 7.822 8683 Z= 0.310 Chirality : 0.043 0.161 974 Planarity : 0.005 0.044 1091 Dihedral : 12.044 86.618 932 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 1.95 % Allowed : 14.52 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.31), residues: 769 helix: 0.90 (0.30), residues: 298 sheet: -0.70 (0.44), residues: 151 loop : -1.13 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.012 0.001 TYR A 578 PHE 0.022 0.002 PHE A 45 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 6390) covalent geometry : angle 0.60778 / 0.31 ( 8683) hydrogen bonds : bond 0.03868 / 2.67 ( 258) hydrogen bonds : angle 4.51365 / 3.14 ( 732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7116 (mm) cc_final: 0.6892 (mm) REVERT: A 40 GLU cc_start: 0.7332 (mp0) cc_final: 0.6921 (mp0) REVERT: A 185 ASP cc_start: 0.6951 (t70) cc_final: 0.6722 (t70) REVERT: A 198 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7621 (mtmm) REVERT: A 243 LEU cc_start: 0.8232 (tp) cc_final: 0.7929 (tt) REVERT: A 251 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5875 (pttt) REVERT: A 327 ARG cc_start: 0.6299 (tmt170) cc_final: 0.6010 (tmt170) REVERT: A 386 ASP cc_start: 0.6681 (t70) cc_final: 0.6472 (t70) outliers start: 13 outliers final: 7 residues processed: 169 average time/residue: 0.0685 time to fit residues: 15.1349 Evaluate side-chains 165 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 72 optimal weight: 0.0060 chunk 13 optimal weight: 0.0270 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 HIS A 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110672 restraints weight = 9603.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113944 restraints weight = 4277.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115963 restraints weight = 2315.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117226 restraints weight = 1431.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118055 restraints weight = 979.724| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6390 Z= 0.129 Angle : 0.575 7.715 8683 Z= 0.290 Chirality : 0.040 0.157 974 Planarity : 0.004 0.039 1091 Dihedral : 11.876 86.283 932 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.41 % Rotamer: Outliers : 2.40 % Allowed : 15.27 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.31), residues: 769 helix: 0.99 (0.30), residues: 299 sheet: -0.69 (0.44), residues: 151 loop : -1.03 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.011 0.001 TYR A 411 PHE 0.030 0.002 PHE A 45 TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6390) covalent geometry : angle 0.57495 / 0.29 ( 8683) hydrogen bonds : bond 0.03323 / 2.30 ( 258) hydrogen bonds : angle 4.37380 / 3.05 ( 732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7132 (mm) cc_final: 0.6851 (mm) REVERT: A 40 GLU cc_start: 0.7339 (mp0) cc_final: 0.6872 (mp0) REVERT: A 185 ASP cc_start: 0.6972 (t70) cc_final: 0.6745 (t70) REVERT: A 198 LYS cc_start: 0.8009 (mtmm) cc_final: 0.7644 (mtmm) REVERT: A 243 LEU cc_start: 0.8216 (tp) cc_final: 0.7865 (tt) REVERT: A 251 LYS cc_start: 0.6242 (OUTLIER) cc_final: 0.5805 (pttt) REVERT: A 327 ARG cc_start: 0.6324 (tmt170) cc_final: 0.6013 (tmt170) REVERT: A 386 ASP cc_start: 0.6774 (t70) cc_final: 0.6513 (t70) REVERT: A 552 ASP cc_start: 0.7302 (t0) cc_final: 0.7049 (t0) outliers start: 16 outliers final: 10 residues processed: 168 average time/residue: 0.0728 time to fit residues: 15.7364 Evaluate side-chains 164 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108580 restraints weight = 9800.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111843 restraints weight = 4359.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113865 restraints weight = 2359.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115111 restraints weight = 1457.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115966 restraints weight = 1003.247| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6390 Z= 0.193 Angle : 0.594 8.230 8683 Z= 0.301 Chirality : 0.042 0.158 974 Planarity : 0.004 0.059 1091 Dihedral : 11.884 86.195 932 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.59 % Favored : 94.28 % Rotamer: Outliers : 3.59 % Allowed : 15.72 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.31), residues: 769 helix: 0.95 (0.30), residues: 298 sheet: -0.74 (0.44), residues: 151 loop : -1.06 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 290 TYR 0.011 0.001 TYR A 578 PHE 0.018 0.002 PHE A 45 TRP 0.008 0.001 TRP A 458 HIS 0.002 0.000 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 6390) covalent geometry : angle 0.59406 / 0.30 ( 8683) hydrogen bonds : bond 0.03656 / 2.51 ( 258) hydrogen bonds : angle 4.47520 / 3.13 ( 732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 12 SER cc_start: 0.7542 (m) cc_final: 0.7238 (p) REVERT: A 40 GLU cc_start: 0.7347 (mp0) cc_final: 0.6868 (mp0) REVERT: A 185 ASP cc_start: 0.6921 (t70) cc_final: 0.6652 (t70) REVERT: A 198 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7659 (mtmm) REVERT: A 243 LEU cc_start: 0.8212 (tp) cc_final: 0.7869 (tt) REVERT: A 251 LYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5826 (pttt) REVERT: A 327 ARG cc_start: 0.6332 (tmt170) cc_final: 0.5995 (tmt170) REVERT: A 386 ASP cc_start: 0.6758 (t70) cc_final: 0.6513 (t70) REVERT: A 552 ASP cc_start: 0.7315 (t0) cc_final: 0.7053 (t0) outliers start: 24 outliers final: 15 residues processed: 167 average time/residue: 0.0673 time to fit residues: 14.3832 Evaluate side-chains 171 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 19 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.0020 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 0.0170 chunk 67 optimal weight: 1.9990 overall best weight: 0.2404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109926 restraints weight = 9664.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113212 restraints weight = 4319.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115218 restraints weight = 2337.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.116494 restraints weight = 1446.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.117306 restraints weight = 986.930| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6390 Z= 0.121 Angle : 0.581 8.835 8683 Z= 0.293 Chirality : 0.040 0.146 974 Planarity : 0.004 0.053 1091 Dihedral : 11.789 85.982 932 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 2.99 % Allowed : 16.62 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.31), residues: 769 helix: 1.05 (0.30), residues: 297 sheet: -0.78 (0.44), residues: 151 loop : -0.96 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 93 TYR 0.012 0.001 TYR A 199 PHE 0.015 0.001 PHE A 45 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.000 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6390) covalent geometry : angle 0.58079 / 0.29 ( 8683) hydrogen bonds : bond 0.03328 / 2.28 ( 258) hydrogen bonds : angle 4.37789 / 3.08 ( 732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 29 HIS cc_start: 0.7195 (t-170) cc_final: 0.6876 (t-170) REVERT: A 40 GLU cc_start: 0.7321 (mp0) cc_final: 0.6848 (mp0) REVERT: A 185 ASP cc_start: 0.6895 (t70) cc_final: 0.6629 (t70) REVERT: A 198 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7618 (mtmm) REVERT: A 243 LEU cc_start: 0.8214 (tp) cc_final: 0.7858 (tt) REVERT: A 251 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5902 (pttt) REVERT: A 327 ARG cc_start: 0.6317 (tmt170) cc_final: 0.5979 (tmt170) REVERT: A 386 ASP cc_start: 0.6774 (t70) cc_final: 0.6516 (t70) REVERT: A 552 ASP cc_start: 0.7257 (t0) cc_final: 0.6992 (t0) outliers start: 20 outliers final: 15 residues processed: 162 average time/residue: 0.0684 time to fit residues: 14.3095 Evaluate side-chains 166 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 chunk 72 optimal weight: 0.0270 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN B 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110162 restraints weight = 9698.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113456 restraints weight = 4336.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115488 restraints weight = 2340.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116749 restraints weight = 1441.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117580 restraints weight = 985.302| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6390 Z= 0.124 Angle : 0.582 9.595 8683 Z= 0.292 Chirality : 0.040 0.192 974 Planarity : 0.004 0.049 1091 Dihedral : 11.726 85.973 932 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.20 % Favored : 94.67 % Rotamer: Outliers : 2.99 % Allowed : 17.96 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.31), residues: 769 helix: 1.05 (0.30), residues: 298 sheet: -0.78 (0.44), residues: 151 loop : -0.93 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 290 TYR 0.010 0.001 TYR A 411 PHE 0.013 0.001 PHE A 45 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.000 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 6390) covalent geometry : angle 0.58241 / 0.29 ( 8683) hydrogen bonds : bond 0.03229 / 2.21 ( 258) hydrogen bonds : angle 4.37613 / 3.08 ( 732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 HIS cc_start: 0.7179 (t-170) cc_final: 0.6841 (t-170) REVERT: A 40 GLU cc_start: 0.7311 (mp0) cc_final: 0.6850 (mp0) REVERT: A 185 ASP cc_start: 0.6883 (t70) cc_final: 0.6613 (t70) REVERT: A 198 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7590 (mtmm) REVERT: A 243 LEU cc_start: 0.8232 (tp) cc_final: 0.7850 (tt) REVERT: A 251 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5900 (pttt) REVERT: A 280 GLU cc_start: 0.7089 (tp30) cc_final: 0.6856 (tp30) REVERT: A 386 ASP cc_start: 0.6784 (t70) cc_final: 0.6525 (t70) REVERT: A 503 MET cc_start: 0.7960 (mtt) cc_final: 0.7756 (mtt) REVERT: A 552 ASP cc_start: 0.7243 (t0) cc_final: 0.6995 (t0) outliers start: 20 outliers final: 15 residues processed: 164 average time/residue: 0.0679 time to fit residues: 14.2999 Evaluate side-chains 174 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 76 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN B 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109319 restraints weight = 9735.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112568 restraints weight = 4370.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114569 restraints weight = 2372.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115755 restraints weight = 1472.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116679 restraints weight = 1028.475| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6390 Z= 0.164 Angle : 0.592 10.056 8683 Z= 0.297 Chirality : 0.041 0.189 974 Planarity : 0.004 0.046 1091 Dihedral : 11.740 86.150 932 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 3.14 % Allowed : 18.41 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.32), residues: 769 helix: 1.04 (0.30), residues: 298 sheet: -0.81 (0.44), residues: 158 loop : -0.86 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 290 TYR 0.013 0.001 TYR A 41 PHE 0.011 0.001 PHE B 52 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.000 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 6390) covalent geometry : angle 0.59229 / 0.30 ( 8683) hydrogen bonds : bond 0.03395 / 2.33 ( 258) hydrogen bonds : angle 4.41319 / 3.11 ( 732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 12 SER cc_start: 0.7500 (m) cc_final: 0.7219 (p) REVERT: A 29 HIS cc_start: 0.7217 (t-170) cc_final: 0.6886 (t-170) REVERT: A 40 GLU cc_start: 0.7333 (mp0) cc_final: 0.6850 (mp0) REVERT: A 185 ASP cc_start: 0.6855 (t70) cc_final: 0.6583 (t70) REVERT: A 198 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7607 (mtmm) REVERT: A 243 LEU cc_start: 0.8224 (tp) cc_final: 0.7856 (tt) REVERT: A 251 LYS cc_start: 0.6238 (OUTLIER) cc_final: 0.5918 (pttt) REVERT: A 280 GLU cc_start: 0.7091 (tp30) cc_final: 0.6804 (tp30) REVERT: A 327 ARG cc_start: 0.6343 (tmt170) cc_final: 0.5982 (tmt170) REVERT: A 386 ASP cc_start: 0.6781 (t70) cc_final: 0.6523 (t70) REVERT: A 552 ASP cc_start: 0.7259 (t0) cc_final: 0.7027 (t0) REVERT: A 554 GLU cc_start: 0.7835 (pt0) cc_final: 0.7622 (pp20) outliers start: 21 outliers final: 16 residues processed: 169 average time/residue: 0.0630 time to fit residues: 13.7683 Evaluate side-chains 171 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 7 optimal weight: 0.0670 chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110041 restraints weight = 9738.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113219 restraints weight = 4399.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115244 restraints weight = 2412.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.116538 restraints weight = 1498.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117338 restraints weight = 1028.056| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6390 Z= 0.131 Angle : 0.602 10.536 8683 Z= 0.299 Chirality : 0.041 0.203 974 Planarity : 0.004 0.045 1091 Dihedral : 11.700 86.137 932 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 3.29 % Allowed : 19.01 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.31), residues: 769 helix: 1.13 (0.30), residues: 294 sheet: -0.57 (0.45), residues: 145 loop : -0.88 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.037 0.001 TYR A 41 PHE 0.037 0.002 PHE A 45 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.000 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6390) covalent geometry : angle 0.60179 / 0.30 ( 8683) hydrogen bonds : bond 0.03240 / 2.24 ( 258) hydrogen bonds : angle 4.45721 / 3.13 ( 732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.7484 (m) cc_final: 0.7213 (p) REVERT: A 40 GLU cc_start: 0.7277 (mp0) cc_final: 0.6818 (mp0) REVERT: A 185 ASP cc_start: 0.6845 (t70) cc_final: 0.6594 (t70) REVERT: A 198 LYS cc_start: 0.7895 (mtmm) cc_final: 0.7504 (mtmm) REVERT: A 243 LEU cc_start: 0.8230 (tp) cc_final: 0.7848 (tt) REVERT: A 251 LYS cc_start: 0.6240 (OUTLIER) cc_final: 0.5923 (pttt) REVERT: A 280 GLU cc_start: 0.7083 (tp30) cc_final: 0.6737 (tp30) REVERT: A 386 ASP cc_start: 0.6811 (t70) cc_final: 0.6555 (t70) REVERT: B 95 LEU cc_start: 0.7813 (mp) cc_final: 0.7601 (mt) outliers start: 22 outliers final: 17 residues processed: 166 average time/residue: 0.0691 time to fit residues: 14.8506 Evaluate side-chains 170 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 52 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN B 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110509 restraints weight = 9647.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113718 restraints weight = 4399.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115681 restraints weight = 2413.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116938 restraints weight = 1514.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117768 restraints weight = 1042.735| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6390 Z= 0.136 Angle : 0.620 11.642 8683 Z= 0.306 Chirality : 0.041 0.221 974 Planarity : 0.004 0.069 1091 Dihedral : 11.653 86.177 932 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 2.84 % Allowed : 20.06 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.31), residues: 769 helix: 1.10 (0.30), residues: 294 sheet: -0.54 (0.45), residues: 145 loop : -0.87 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.070 0.002 TYR A 41 PHE 0.035 0.002 PHE A 45 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6390) covalent geometry : angle 0.61966 / 0.31 ( 8683) hydrogen bonds : bond 0.03284 / 2.28 ( 258) hydrogen bonds : angle 4.52001 / 3.17 ( 732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.7502 (m) cc_final: 0.7237 (p) REVERT: A 29 HIS cc_start: 0.7137 (t-170) cc_final: 0.6743 (t70) REVERT: A 40 GLU cc_start: 0.7136 (mp0) cc_final: 0.6726 (mp0) REVERT: A 185 ASP cc_start: 0.6827 (t70) cc_final: 0.6570 (t70) REVERT: A 198 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7485 (mtmm) REVERT: A 243 LEU cc_start: 0.8215 (tp) cc_final: 0.7832 (tt) REVERT: A 251 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5896 (pttt) REVERT: A 280 GLU cc_start: 0.7047 (tp30) cc_final: 0.6717 (tp30) REVERT: A 386 ASP cc_start: 0.6782 (t70) cc_final: 0.6538 (t70) outliers start: 19 outliers final: 16 residues processed: 158 average time/residue: 0.0654 time to fit residues: 13.4636 Evaluate side-chains 163 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.0370 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110540 restraints weight = 9740.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113876 restraints weight = 4345.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115942 restraints weight = 2355.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117239 restraints weight = 1458.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118039 restraints weight = 999.268| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6390 Z= 0.130 Angle : 0.608 11.424 8683 Z= 0.300 Chirality : 0.041 0.189 974 Planarity : 0.004 0.067 1091 Dihedral : 11.653 86.293 932 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.69 % Allowed : 20.06 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.31), residues: 769 helix: 1.09 (0.30), residues: 294 sheet: -0.53 (0.46), residues: 145 loop : -0.86 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.059 0.002 TYR A 41 PHE 0.009 0.001 PHE A 66 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6390) covalent geometry : angle 0.60786 / 0.30 ( 8683) hydrogen bonds : bond 0.03222 / 2.24 ( 258) hydrogen bonds : angle 4.48818 / 3.16 ( 732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1034.51 seconds wall clock time: 18 minutes 34.59 seconds (1114.59 seconds total)