Starting phenix.real_space_refine on Thu Jul 2 03:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9caj_45393/07_2026/9caj_45393_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9caj_45393/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9caj_45393/07_2026/9caj_45393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9caj_45393/07_2026/9caj_45393.map" model { file = "/net/cci-nas-00/data/ceres_data/9caj_45393/07_2026/9caj_45393_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9caj_45393/07_2026/9caj_45393_neut.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.18, per 1000 atoms: 0.19 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: 0.36 Conformation dependent library (CDL) restraints added in 228.6 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: 0.61 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: 0.98 Time building geometry restraints manager: 0.51 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=" 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 bond pdb=" O3' DA C -1 " pdb=" P DC C 0 " ideal model delta sigma weight residual 1.607 1.579 0.028 1.50e-02 4.44e+03 3.56e+00 bond pdb=" O3' DT C 4 " pdb=" P DA C 5 " ideal model delta sigma weight residual 1.607 1.580 0.027 1.50e-02 4.44e+03 3.36e+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 3.060 nonbonded pdb=" OP1 DA C 5 " pdb="MN MN A 701 " model vdw 2.151 3.060 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: 3.250 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.720 Find NCS groups from input model: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.360 ------------------------------------------------------------------------------- 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= 0.186 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 0.65800 / 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 : 0.224 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7068 (mm) cc_final: 0.6852 (mm) REVERT: A 40 GLU cc_start: 0.7154 (mp0) cc_final: 0.6868 (mp0) REVERT: A 164 MET cc_start: 0.6093 (mpp) cc_final: 0.5565 (mpp) REVERT: A 185 ASP cc_start: 0.7013 (t70) cc_final: 0.6666 (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: 0.6572 (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: 0.0813 time to fit residues: 18.0075 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 : 0.148 ------------------------------------------------------------------------------- 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: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 HIS A 162 ASN A 172 HIS ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108472 restraints weight = 9635.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111699 restraints weight = 4212.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113741 restraints weight = 2259.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115005 restraints weight = 1382.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115835 restraints weight = 939.118| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 6390 Z= 0.246 Angle : 0.647 11.615 8683 Z= 0.329 Chirality : 0.044 0.162 974 Planarity : 0.005 0.064 1091 Dihedral : 12.189 86.620 932 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.22 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: -0.45 (0.31), residues: 769 helix: 0.86 (0.30), residues: 298 sheet: -0.64 (0.44), residues: 151 loop : -1.18 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 290 TYR 0.017 0.002 TYR A 240 PHE 0.012 0.002 PHE A 265 TRP 0.008 0.001 TRP A 458 HIS 0.005 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 ( 6390) covalent geometry : angle 0.64654 / 0.33 ( 8683) hydrogen bonds : bond 0.04223 / 2.90 ( 258) hydrogen bonds : angle 4.61087 / 3.18 ( 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 174 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7148 (mm) cc_final: 0.6887 (mm) REVERT: A 40 GLU cc_start: 0.7307 (mp0) cc_final: 0.6874 (mp0) REVERT: A 198 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7675 (mtmm) REVERT: A 231 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7710 (mtmm) REVERT: A 327 ARG cc_start: 0.6312 (tmt170) cc_final: 0.6036 (tmt170) REVERT: A 380 LYS cc_start: 0.7653 (mppt) cc_final: 0.7415 (mppt) REVERT: A 386 ASP cc_start: 0.6828 (t70) cc_final: 0.6565 (t70) REVERT: A 438 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7037 (mm-30) REVERT: A 552 ASP cc_start: 0.7408 (t0) cc_final: 0.7086 (t70) REVERT: B 57 ILE cc_start: 0.8153 (tp) cc_final: 0.7944 (tp) outliers start: 3 outliers final: 2 residues processed: 173 average time/residue: 0.0929 time to fit residues: 20.7269 Evaluate side-chains 166 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS 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: 0.6980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.120357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109613 restraints weight = 9568.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112751 restraints weight = 4179.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.114730 restraints weight = 2245.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.115924 restraints weight = 1380.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116691 restraints weight = 949.278| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6390 Z= 0.212 Angle : 0.613 8.677 8683 Z= 0.314 Chirality : 0.043 0.164 974 Planarity : 0.005 0.045 1091 Dihedral : 11.941 86.562 932 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 2.40 % Allowed : 14.52 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.46 (0.31), residues: 769 helix: 0.85 (0.30), residues: 298 sheet: -0.68 (0.44), residues: 151 loop : -1.16 (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 0.013 0.002 PHE A 152 TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 ( 6390) covalent geometry : angle 0.61349 / 0.31 ( 8683) hydrogen bonds : bond 0.03929 / 2.71 ( 258) hydrogen bonds : angle 4.56113 / 3.17 ( 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 181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7150 (mm) cc_final: 0.6909 (mm) REVERT: A 40 GLU cc_start: 0.7354 (mp0) cc_final: 0.6950 (mp0) REVERT: A 198 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7689 (mtmm) REVERT: A 243 LEU cc_start: 0.8248 (tp) cc_final: 0.7929 (tt) REVERT: A 251 LYS cc_start: 0.6199 (OUTLIER) cc_final: 0.5887 (pttt) REVERT: A 327 ARG cc_start: 0.6293 (tmt170) cc_final: 0.5988 (tmt170) REVERT: A 386 ASP cc_start: 0.6734 (t70) cc_final: 0.6521 (t70) REVERT: A 552 ASP cc_start: 0.7277 (t0) cc_final: 0.7020 (t0) outliers start: 16 outliers final: 8 residues processed: 172 average time/residue: 0.0913 time to fit residues: 20.2941 Evaluate side-chains 166 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 GLN 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: 0.9990 chunk 49 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0000 overall best weight: 0.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 HIS A 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109850 restraints weight = 9612.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113017 restraints weight = 4280.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115067 restraints weight = 2335.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116347 restraints weight = 1441.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117171 restraints weight = 976.973| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6390 Z= 0.140 Angle : 0.598 7.677 8683 Z= 0.301 Chirality : 0.041 0.157 974 Planarity : 0.004 0.039 1091 Dihedral : 11.789 86.132 932 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.59 % Favored : 94.28 % Rotamer: Outliers : 2.54 % Allowed : 15.57 % Favored : 81.89 % 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: -0.41 (0.31), residues: 769 helix: 0.86 (0.30), residues: 299 sheet: -0.69 (0.44), residues: 151 loop : -1.07 (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 0.012 0.001 PHE B 52 TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6390) covalent geometry : angle 0.59772 / 0.30 ( 8683) hydrogen bonds : bond 0.03506 / 2.44 ( 258) hydrogen bonds : angle 4.47117 / 3.13 ( 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 177 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7175 (mm) cc_final: 0.6921 (mm) REVERT: A 40 GLU cc_start: 0.7345 (mp0) cc_final: 0.6896 (mp0) REVERT: A 198 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7672 (mtmm) REVERT: A 243 LEU cc_start: 0.8231 (tp) cc_final: 0.7879 (tt) REVERT: A 251 LYS cc_start: 0.6287 (OUTLIER) cc_final: 0.5961 (pttt) REVERT: A 327 ARG cc_start: 0.6321 (tmt170) cc_final: 0.6001 (tmt170) REVERT: A 386 ASP cc_start: 0.6785 (t70) cc_final: 0.6524 (t70) REVERT: A 552 ASP cc_start: 0.7303 (t0) cc_final: 0.7049 (t0) outliers start: 17 outliers final: 10 residues processed: 166 average time/residue: 0.0900 time to fit residues: 19.2660 Evaluate side-chains 171 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 184 LEU 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 523 GLN 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: 0.9990 chunk 51 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108586 restraints weight = 9789.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111835 restraints weight = 4371.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113859 restraints weight = 2371.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115099 restraints weight = 1465.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115923 restraints weight = 1007.217| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6390 Z= 0.178 Angle : 0.598 7.969 8683 Z= 0.304 Chirality : 0.041 0.162 974 Planarity : 0.004 0.037 1091 Dihedral : 11.775 85.964 932 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 2.99 % Allowed : 16.02 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.37 (0.31), residues: 769 helix: 0.90 (0.30), residues: 299 sheet: -0.71 (0.45), residues: 149 loop : -1.05 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 290 TYR 0.010 0.001 TYR A 578 PHE 0.017 0.002 PHE A 127 TRP 0.008 0.001 TRP A 458 HIS 0.007 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 6390) covalent geometry : angle 0.59817 / 0.30 ( 8683) hydrogen bonds : bond 0.03631 / 2.51 ( 258) hydrogen bonds : angle 4.46395 / 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 181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7366 (mp0) cc_final: 0.6908 (mp0) REVERT: A 198 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7682 (mtmm) REVERT: A 243 LEU cc_start: 0.8218 (tp) cc_final: 0.7878 (tt) REVERT: A 282 GLU cc_start: 0.6218 (mp0) cc_final: 0.6005 (mp0) REVERT: A 386 ASP cc_start: 0.6787 (t70) cc_final: 0.6529 (t70) REVERT: A 552 ASP cc_start: 0.7290 (t0) cc_final: 0.7068 (t0) REVERT: A 554 GLU cc_start: 0.7866 (pt0) cc_final: 0.7630 (pp20) outliers start: 20 outliers final: 15 residues processed: 171 average time/residue: 0.0980 time to fit residues: 21.3973 Evaluate side-chains 174 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 447 VAL Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain B residue 141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 0.0270 chunk 67 optimal weight: 0.9980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.120600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109705 restraints weight = 9689.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112938 restraints weight = 4341.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114913 restraints weight = 2357.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116166 restraints weight = 1465.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116828 restraints weight = 1005.940| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1665 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= 0.137 Angle : 0.581 7.931 8683 Z= 0.294 Chirality : 0.040 0.153 974 Planarity : 0.004 0.061 1091 Dihedral : 11.627 85.743 932 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 2.99 % Allowed : 16.32 % 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: -0.27 (0.31), residues: 769 helix: 0.98 (0.30), residues: 299 sheet: -0.80 (0.44), residues: 158 loop : -0.88 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 93 TYR 0.010 0.001 TYR A 411 PHE 0.013 0.001 PHE A 127 TRP 0.010 0.001 TRP A 458 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 6390) covalent geometry : angle 0.58052 / 0.29 ( 8683) hydrogen bonds : bond 0.03355 / 2.33 ( 258) hydrogen bonds : angle 4.40607 / 3.10 ( 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 186 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7118 (mm) cc_final: 0.6915 (mm) REVERT: A 29 HIS cc_start: 0.7208 (t-170) cc_final: 0.6896 (t-170) REVERT: A 40 GLU cc_start: 0.7354 (mp0) cc_final: 0.6873 (mp0) REVERT: A 198 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7655 (mtmm) REVERT: A 243 LEU cc_start: 0.8216 (tp) cc_final: 0.7851 (tt) REVERT: A 386 ASP cc_start: 0.6804 (t70) cc_final: 0.6545 (t70) REVERT: A 552 ASP cc_start: 0.7246 (t0) cc_final: 0.7032 (t0) REVERT: A 554 GLU cc_start: 0.7849 (pt0) cc_final: 0.7618 (pp20) REVERT: B 93 ARG cc_start: 0.8464 (ttp80) cc_final: 0.7864 (ttp80) REVERT: B 94 MET cc_start: 0.7639 (ttm) cc_final: 0.7354 (ttm) outliers start: 20 outliers final: 16 residues processed: 174 average time/residue: 0.0988 time to fit residues: 21.8754 Evaluate side-chains 177 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 251 LYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 571 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 0.0270 chunk 19 optimal weight: 0.6980 chunk 72 optimal weight: 0.0870 chunk 48 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 16 optimal weight: 0.0010 chunk 41 optimal weight: 0.6980 overall best weight: 0.0578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112284 restraints weight = 9674.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115578 restraints weight = 4322.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117605 restraints weight = 2323.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118872 restraints weight = 1427.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119623 restraints weight = 973.303| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6390 Z= 0.107 Angle : 0.571 8.503 8683 Z= 0.289 Chirality : 0.040 0.151 974 Planarity : 0.004 0.057 1091 Dihedral : 11.485 84.718 932 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 2.69 % Allowed : 18.11 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.14 (0.31), residues: 769 helix: 1.09 (0.30), residues: 299 sheet: -0.66 (0.45), residues: 151 loop : -0.86 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.011 0.001 TYR A 411 PHE 0.014 0.001 PHE A 127 TRP 0.009 0.001 TRP A 458 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 6390) covalent geometry : angle 0.57105 / 0.29 ( 8683) hydrogen bonds : bond 0.02903 / 2.03 ( 258) hydrogen bonds : angle 4.29321 / 3.02 ( 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 184 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.6997 (mm) cc_final: 0.6792 (mm) REVERT: A 40 GLU cc_start: 0.7310 (mp0) cc_final: 0.7016 (mp0) REVERT: A 148 PHE cc_start: 0.8147 (m-80) cc_final: 0.7938 (m-10) REVERT: A 198 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7509 (mtmm) REVERT: A 251 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5936 (pttt) REVERT: A 386 ASP cc_start: 0.6786 (t70) cc_final: 0.6527 (t70) REVERT: A 552 ASP cc_start: 0.7221 (t0) cc_final: 0.6976 (t0) outliers start: 18 outliers final: 11 residues processed: 175 average time/residue: 0.0920 time to fit residues: 20.6270 Evaluate side-chains 173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 251 LYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 525 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107864 restraints weight = 9784.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111094 restraints weight = 4414.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113119 restraints weight = 2416.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114379 restraints weight = 1503.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115152 restraints weight = 1034.529| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6390 Z= 0.237 Angle : 0.648 8.547 8683 Z= 0.326 Chirality : 0.043 0.169 974 Planarity : 0.004 0.066 1091 Dihedral : 11.659 85.443 932 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.20 % Favored : 94.67 % Rotamer: Outliers : 3.14 % Allowed : 19.46 % Favored : 77.40 % 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: 1.01 (0.31), residues: 299 sheet: -0.68 (0.45), residues: 149 loop : -0.99 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 472 TYR 0.017 0.002 TYR A 41 PHE 0.035 0.003 PHE A 45 TRP 0.006 0.001 TRP A 458 HIS 0.004 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 ( 6390) covalent geometry : angle 0.64805 / 0.33 ( 8683) hydrogen bonds : bond 0.03896 / 2.68 ( 258) hydrogen bonds : angle 4.46377 / 3.14 ( 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 189 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7162 (mm) cc_final: 0.6945 (mm) REVERT: A 29 HIS cc_start: 0.7238 (t-170) cc_final: 0.6957 (t-170) REVERT: A 40 GLU cc_start: 0.7299 (mp0) cc_final: 0.6916 (mp0) REVERT: A 51 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7434 (ttm-80) REVERT: A 198 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7661 (mtmm) REVERT: A 243 LEU cc_start: 0.8217 (tp) cc_final: 0.7909 (tt) REVERT: A 386 ASP cc_start: 0.6815 (t70) cc_final: 0.6554 (t70) REVERT: A 552 ASP cc_start: 0.7268 (t0) cc_final: 0.7008 (t0) REVERT: B 64 LYS cc_start: 0.8081 (mppt) cc_final: 0.7817 (mppt) REVERT: B 93 ARG cc_start: 0.8432 (ttp80) cc_final: 0.7938 (ttp-170) outliers start: 21 outliers final: 16 residues processed: 175 average time/residue: 0.0904 time to fit residues: 20.2721 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 : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU 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 231 LYS 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 262 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 523 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 57 optimal weight: 0.0010 chunk 18 optimal weight: 0.0970 chunk 69 optimal weight: 0.0070 overall best weight: 0.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112162 restraints weight = 9702.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115463 restraints weight = 4359.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117543 restraints weight = 2382.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118839 restraints weight = 1472.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119694 restraints weight = 1004.964| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6390 Z= 0.115 Angle : 0.612 8.333 8683 Z= 0.309 Chirality : 0.040 0.191 974 Planarity : 0.004 0.062 1091 Dihedral : 11.514 85.198 932 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 2.10 % Allowed : 21.26 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.16 (0.31), residues: 769 helix: 1.05 (0.30), residues: 299 sheet: -0.73 (0.46), residues: 145 loop : -0.81 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.036 0.001 TYR A 41 PHE 0.041 0.002 PHE A 45 TRP 0.010 0.001 TRP A 458 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 6390) covalent geometry : angle 0.61210 / 0.31 ( 8683) hydrogen bonds : bond 0.03046 / 2.11 ( 258) hydrogen bonds : angle 4.41705 / 3.10 ( 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 174 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.6844 (mtt) cc_final: 0.6500 (mtt) REVERT: A 29 HIS cc_start: 0.7150 (t-170) cc_final: 0.6748 (t-170) REVERT: A 40 GLU cc_start: 0.7236 (mp0) cc_final: 0.6974 (mp0) REVERT: A 51 ARG cc_start: 0.7596 (ttm-80) cc_final: 0.7301 (ttm-80) REVERT: A 198 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7510 (mtmm) REVERT: A 386 ASP cc_start: 0.6846 (t70) cc_final: 0.6583 (t70) REVERT: B 52 PHE cc_start: 0.6850 (t80) cc_final: 0.6594 (t80) REVERT: B 114 MET cc_start: 0.7522 (mmp) cc_final: 0.7268 (mmm) outliers start: 14 outliers final: 8 residues processed: 167 average time/residue: 0.0784 time to fit residues: 16.8868 Evaluate side-chains 166 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU 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 251 LYS Chi-restraints excluded: chain A residue 376 ASN 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 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 7 optimal weight: 0.1980 chunk 52 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111201 restraints weight = 9687.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114473 restraints weight = 4365.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116540 restraints weight = 2379.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117793 restraints weight = 1470.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118626 restraints weight = 1012.910| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6390 Z= 0.138 Angle : 0.639 8.717 8683 Z= 0.317 Chirality : 0.041 0.180 974 Planarity : 0.004 0.061 1091 Dihedral : 11.463 85.440 932 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.20 % Favored : 94.67 % Rotamer: Outliers : 1.35 % Allowed : 22.60 % Favored : 76.05 % 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: 1.14 (0.30), residues: 299 sheet: -0.69 (0.45), residues: 151 loop : -0.85 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 379 TYR 0.035 0.001 TYR A 41 PHE 0.039 0.002 PHE A 45 TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6390) covalent geometry : angle 0.63927 / 0.32 ( 8683) hydrogen bonds : bond 0.03194 / 2.21 ( 258) hydrogen bonds : angle 4.38798 / 3.08 ( 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 171 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 HIS cc_start: 0.7177 (t-170) cc_final: 0.6744 (t70) REVERT: A 40 GLU cc_start: 0.7254 (mp0) cc_final: 0.7033 (mp0) REVERT: A 51 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7347 (ttm-80) REVERT: A 198 LYS cc_start: 0.7905 (mtmm) cc_final: 0.7510 (mtmm) REVERT: A 243 LEU cc_start: 0.8231 (tp) cc_final: 0.7905 (tt) REVERT: A 251 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5930 (pttt) REVERT: A 386 ASP cc_start: 0.6838 (t70) cc_final: 0.6577 (t70) REVERT: A 503 MET cc_start: 0.7763 (mmm) cc_final: 0.7494 (mtt) REVERT: B 52 PHE cc_start: 0.6850 (t80) cc_final: 0.6631 (t80) REVERT: B 114 MET cc_start: 0.7529 (mmp) cc_final: 0.7241 (mmm) outliers start: 9 outliers final: 7 residues processed: 165 average time/residue: 0.0883 time to fit residues: 18.6420 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 : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU 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 251 LYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 104 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.3980 chunk 73 optimal weight: 0.0970 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 0.0070 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110181 restraints weight = 9767.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113472 restraints weight = 4386.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115534 restraints weight = 2387.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116812 restraints weight = 1477.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117684 restraints weight = 1011.736| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6390 Z= 0.148 Angle : 0.635 8.328 8683 Z= 0.316 Chirality : 0.041 0.153 974 Planarity : 0.005 0.069 1091 Dihedral : 11.505 85.987 932 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.94 % Favored : 94.93 % Rotamer: Outliers : 1.65 % Allowed : 21.86 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.13 (0.31), residues: 769 helix: 1.12 (0.30), residues: 299 sheet: -0.65 (0.45), residues: 151 loop : -0.89 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 93 TYR 0.067 0.002 TYR A 41 PHE 0.016 0.001 PHE A 127 TRP 0.008 0.001 TRP A 458 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6390) covalent geometry : angle 0.63514 / 0.32 ( 8683) hydrogen bonds : bond 0.03305 / 2.30 ( 258) hydrogen bonds : angle 4.44214 / 3.12 ( 732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1328.06 seconds wall clock time: 23 minutes 41.88 seconds (1421.88 seconds total)