Starting phenix.real_space_refine on Thu Jul 2 04:08:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh7_61474/07_2026/9jh7_61474.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh7_61474/07_2026/9jh7_61474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jh7_61474/07_2026/9jh7_61474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh7_61474/07_2026/9jh7_61474.map" model { file = "/net/cci-nas-00/data/ceres_data/9jh7_61474/07_2026/9jh7_61474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh7_61474/07_2026/9jh7_61474.cif" } resolution = 3.4 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= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 20 5.16 5 C 4052 2.51 5 N 1047 2.21 5 O 1223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 6357 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6039 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Time building chain proxies: 1.24, per 1000 atoms: 0.20 Number of scatterers: 6357 At special positions: 0 Unit cell: (77.08, 79.54, 106.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 15 15.00 O 1223 8.00 N 1047 7.00 C 4052 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: 0.38 Conformation dependent library (CDL) restraints added in 228.7 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 11 sheets defined 32.1% alpha, 19.3% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.276A pdb=" N SER A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.973A pdb=" N GLY A 244 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR A 245 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.626A pdb=" N ASN A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.779A pdb=" N GLN A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.564A pdb=" N TYR A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.203A pdb=" N TYR A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.887A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 712 Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'A' and resid 736 through 739 removed outlier: 3.672A pdb=" N ILE A 739 " --> pdb=" O ILE A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 736 through 739' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 3.750A pdb=" N ARG A 158 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 16 removed outlier: 4.720A pdb=" N ASN A 155 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LYS A 148 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.730A pdb=" N LYS A 30 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.819A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASN A 261 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 321 Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.783A pdb=" N SER A 663 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 673 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 637 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 609 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE A 638 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE A 611 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 640 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG A 613 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 558 " --> pdb=" O GLY A 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 353 Processing sheet with id=AB1, first strand: chain 'A' and resid 432 through 435 removed outlier: 6.301A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 383 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 570 through 571 removed outlier: 4.091A pdb=" N TYR A 570 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 745 " --> pdb=" O TYR A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 235 hydrogen bonds defined for protein. 660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 0.77 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: 1.21 - 1.33: 1727 1.33 - 1.45: 1247 1.45 - 1.57: 3482 1.57 - 1.69: 29 1.69 - 1.81: 35 Bond restraints: 6520 Sorted by residual: bond pdb=" C1' DT C 6 " pdb=" N1 DT C 6 " ideal model delta sigma weight residual 1.468 1.535 -0.067 1.40e-02 5.10e+03 2.26e+01 bond pdb=" C3' DA C 7 " pdb=" O3' DA C 7 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" C4' DG C 5 " pdb=" C3' DG C 5 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.00e-02 1.00e+04 1.17e+01 bond pdb=" C3' DG C 4 " pdb=" O3' DG C 4 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 9.15e+00 bond pdb=" N VAL A 378 " pdb=" CA VAL A 378 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.09e+00 ... (remaining 6515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 8182 1.83 - 3.66: 583 3.66 - 5.49: 65 5.49 - 7.31: 21 7.31 - 9.14: 6 Bond angle restraints: 8857 Sorted by residual: angle pdb=" O4' DG C 5 " pdb=" C4' DG C 5 " pdb=" C3' DG C 5 " ideal model delta sigma weight residual 106.00 102.16 3.84 6.00e-01 2.78e+00 4.09e+01 angle pdb=" N LYS A 88 " pdb=" CA LYS A 88 " pdb=" C LYS A 88 " ideal model delta sigma weight residual 110.35 118.59 -8.24 1.40e+00 5.10e-01 3.47e+01 angle pdb=" O4' DA C 3 " pdb=" C4' DA C 3 " pdb=" C3' DA C 3 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 angle pdb=" O4' DG C 4 " pdb=" C4' DG C 4 " pdb=" C3' DG C 4 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" C VAL A 87 " pdb=" N LYS A 88 " pdb=" CA LYS A 88 " ideal model delta sigma weight residual 121.31 127.91 -6.60 1.49e+00 4.50e-01 1.96e+01 ... (remaining 8852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.96: 3738 25.96 - 51.93: 151 51.93 - 77.89: 17 77.89 - 103.85: 2 103.85 - 129.82: 1 Dihedral angle restraints: 3909 sinusoidal: 1722 harmonic: 2187 Sorted by residual: dihedral pdb=" CA PHE A 86 " pdb=" C PHE A 86 " pdb=" N VAL A 87 " pdb=" CA VAL A 87 " ideal model delta harmonic sigma weight residual 180.00 -142.46 -37.54 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA ASN A 258 " pdb=" C ASN A 258 " pdb=" N ILE A 259 " pdb=" CA ILE A 259 " ideal model delta harmonic sigma weight residual -180.00 -147.59 -32.41 0 5.00e+00 4.00e-02 4.20e+01 dihedral pdb=" CA ALA A 257 " pdb=" C ALA A 257 " pdb=" N ASN A 258 " pdb=" CA ASN A 258 " ideal model delta harmonic sigma weight residual -180.00 -148.00 -32.00 0 5.00e+00 4.00e-02 4.10e+01 ... (remaining 3906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 636 0.050 - 0.100: 233 0.100 - 0.149: 72 0.149 - 0.199: 20 0.199 - 0.249: 3 Chirality restraints: 964 Sorted by residual: chirality pdb=" CB ILE A 582 " pdb=" CA ILE A 582 " pdb=" CG1 ILE A 582 " pdb=" CG2 ILE A 582 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL A 463 " pdb=" CA VAL A 463 " pdb=" CG1 VAL A 463 " pdb=" CG2 VAL A 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU A 383 " pdb=" CB LEU A 383 " pdb=" CD1 LEU A 383 " pdb=" CD2 LEU A 383 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 961 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 728 " -0.004 2.00e-02 2.50e+03 1.87e-02 7.01e+00 pdb=" CG TYR A 728 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 728 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 728 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 728 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 728 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 728 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 728 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 463 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO A 464 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 86 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C PHE A 86 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE A 86 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 87 " 0.014 2.00e-02 2.50e+03 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1773 2.80 - 3.33: 6087 3.33 - 3.85: 11128 3.85 - 4.38: 12737 4.38 - 4.90: 20674 Nonbonded interactions: 52399 Sorted by model distance: nonbonded pdb=" O LEU A 139 " pdb=" OH TYR A 306 " model vdw 2.278 3.040 nonbonded pdb=" NH1 ARG A 613 " pdb=" OE2 GLU A 639 " model vdw 2.312 3.120 nonbonded pdb=" O LYS A 50 " pdb=" OG SER A 53 " model vdw 2.321 3.040 nonbonded pdb=" OG SER A 650 " pdb=" OG1 THR A 657 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR A 125 " pdb=" OD2 ASP A 317 " model vdw 2.326 3.040 ... (remaining 52394 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 5.820 Find NCS groups from input model: 0.020 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.007 0.067 6520 Z= 0.401 Angle : 1.038 9.143 8857 Z= 0.642 Chirality : 0.059 0.249 964 Planarity : 0.006 0.061 1071 Dihedral : 13.421 129.817 2515 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.75 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.08 (0.27), residues: 743 helix: -2.27 (0.26), residues: 211 sheet: -1.60 (0.41), residues: 152 loop : -2.05 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 613 TYR 0.041 0.003 TYR A 728 PHE 0.028 0.003 PHE A 616 TRP 0.031 0.006 TRP A 623 HIS 0.024 0.005 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.40 ( 6520) covalent geometry : angle 1.03756 / 0.64 ( 8857) hydrogen bonds : bond 0.20452 / 12.42 ( 221) hydrogen bonds : angle 9.39035 / 6.84 ( 660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.9262 (m-30) cc_final: 0.8685 (p0) REVERT: A 112 LYS cc_start: 0.9592 (tppt) cc_final: 0.9167 (tptm) REVERT: A 167 ASN cc_start: 0.9484 (t0) cc_final: 0.8991 (t0) REVERT: A 176 LEU cc_start: 0.9394 (tp) cc_final: 0.9099 (tp) REVERT: A 191 MET cc_start: 0.9361 (mtp) cc_final: 0.9074 (mtm) REVERT: A 210 ILE cc_start: 0.8510 (mm) cc_final: 0.7962 (tp) REVERT: A 225 SER cc_start: 0.9551 (m) cc_final: 0.9085 (p) REVERT: A 226 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8854 (mm-30) REVERT: A 253 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8838 (tm-30) REVERT: A 259 ILE cc_start: 0.9635 (mt) cc_final: 0.9431 (mp) REVERT: A 269 TYR cc_start: 0.6193 (m-10) cc_final: 0.5830 (m-80) REVERT: A 289 ASP cc_start: 0.9051 (t0) cc_final: 0.8477 (t0) REVERT: A 295 GLU cc_start: 0.9766 (mm-30) cc_final: 0.9321 (tm-30) REVERT: A 296 ILE cc_start: 0.9869 (pt) cc_final: 0.9304 (pt) REVERT: A 304 MET cc_start: 0.9238 (mmt) cc_final: 0.8160 (mmp) REVERT: A 317 ASP cc_start: 0.8442 (m-30) cc_final: 0.8125 (m-30) REVERT: A 338 LYS cc_start: 0.9779 (mtpp) cc_final: 0.9546 (mmtm) REVERT: A 363 MET cc_start: 0.9008 (ttp) cc_final: 0.8619 (tmm) REVERT: A 364 GLN cc_start: 0.8859 (pt0) cc_final: 0.8624 (pt0) REVERT: A 444 LYS cc_start: 0.9644 (mttt) cc_final: 0.9329 (mttt) REVERT: A 453 TYR cc_start: 0.9178 (m-80) cc_final: 0.8835 (m-80) REVERT: A 495 LYS cc_start: 0.9679 (tttt) cc_final: 0.9357 (mtpp) REVERT: A 498 GLU cc_start: 0.9644 (mt-10) cc_final: 0.9421 (mt-10) REVERT: A 595 LEU cc_start: 0.9576 (mt) cc_final: 0.9285 (tp) REVERT: A 614 ASP cc_start: 0.9363 (t0) cc_final: 0.8786 (m-30) REVERT: A 626 ASN cc_start: 0.9809 (t0) cc_final: 0.9536 (p0) REVERT: A 639 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8422 (mm-30) REVERT: A 652 ASN cc_start: 0.9273 (t0) cc_final: 0.9042 (t0) REVERT: A 696 ASP cc_start: 0.9628 (t0) cc_final: 0.9413 (t0) REVERT: A 705 GLN cc_start: 0.8836 (mt0) cc_final: 0.8309 (mt0) REVERT: A 711 GLN cc_start: 0.9303 (mm-40) cc_final: 0.9028 (mm-40) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.0649 time to fit residues: 18.1486 Evaluate side-chains 153 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.0090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN A 368 ASN A 490 GLN ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.062805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.048564 restraints weight = 25663.915| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 6.85 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6520 Z= 0.200 Angle : 0.851 10.324 8857 Z= 0.461 Chirality : 0.052 0.315 964 Planarity : 0.005 0.055 1071 Dihedral : 14.512 127.641 974 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.34 % Favored : 91.52 % Rotamer: Outliers : 3.44 % Allowed : 12.56 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.37 (0.30), residues: 743 helix: -1.34 (0.31), residues: 215 sheet: -1.47 (0.39), residues: 164 loop : -1.68 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 613 TYR 0.054 0.002 TYR A 554 PHE 0.026 0.002 PHE A 616 TRP 0.020 0.003 TRP A 623 HIS 0.023 0.003 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 ( 6520) covalent geometry : angle 0.85111 / 0.46 ( 8857) hydrogen bonds : bond 0.05942 / 3.69 ( 221) hydrogen bonds : angle 7.06107 / 5.08 ( 660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.8928 (mmtt) REVERT: A 50 LYS cc_start: 0.9692 (mmtt) cc_final: 0.9254 (mttt) REVERT: A 106 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8743 (tm-30) REVERT: A 112 LYS cc_start: 0.9576 (tppt) cc_final: 0.9182 (tptm) REVERT: A 167 ASN cc_start: 0.9484 (t0) cc_final: 0.9084 (t0) REVERT: A 176 LEU cc_start: 0.9337 (tp) cc_final: 0.9003 (tp) REVERT: A 181 ASP cc_start: 0.9292 (OUTLIER) cc_final: 0.8232 (p0) REVERT: A 225 SER cc_start: 0.9590 (m) cc_final: 0.9235 (p) REVERT: A 226 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8855 (mm-30) REVERT: A 242 ASN cc_start: 0.9618 (m-40) cc_final: 0.9083 (p0) REVERT: A 243 GLN cc_start: 0.9550 (mt0) cc_final: 0.9338 (mt0) REVERT: A 289 ASP cc_start: 0.8945 (t0) cc_final: 0.8485 (t0) REVERT: A 295 GLU cc_start: 0.9759 (mm-30) cc_final: 0.9194 (tm-30) REVERT: A 296 ILE cc_start: 0.9893 (pt) cc_final: 0.9653 (pt) REVERT: A 363 MET cc_start: 0.9005 (ttp) cc_final: 0.8519 (tmm) REVERT: A 364 GLN cc_start: 0.8942 (pt0) cc_final: 0.8667 (pt0) REVERT: A 444 LYS cc_start: 0.9656 (mttt) cc_final: 0.9382 (mttt) REVERT: A 453 TYR cc_start: 0.9223 (m-80) cc_final: 0.8837 (m-80) REVERT: A 495 LYS cc_start: 0.9727 (tttt) cc_final: 0.9472 (ttpp) REVERT: A 614 ASP cc_start: 0.9368 (t0) cc_final: 0.8790 (m-30) REVERT: A 618 ARG cc_start: 0.9444 (mtm110) cc_final: 0.9013 (ptp-110) REVERT: A 626 ASN cc_start: 0.9760 (t0) cc_final: 0.9502 (p0) REVERT: A 640 VAL cc_start: 0.9482 (t) cc_final: 0.8690 (m) REVERT: A 696 ASP cc_start: 0.9680 (t0) cc_final: 0.9456 (t0) outliers start: 23 outliers final: 13 residues processed: 187 average time/residue: 0.0589 time to fit residues: 15.0707 Evaluate side-chains 160 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN A 741 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.046670 restraints weight = 25810.178| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 6.60 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6520 Z= 0.246 Angle : 0.817 10.027 8857 Z= 0.447 Chirality : 0.052 0.261 964 Planarity : 0.004 0.042 1071 Dihedral : 14.332 122.759 974 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.29 % Favored : 90.58 % Rotamer: Outliers : 4.19 % Allowed : 15.55 % Favored : 80.27 % 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: -2.09 (0.30), residues: 743 helix: -0.88 (0.30), residues: 215 sheet: -1.50 (0.38), residues: 167 loop : -1.55 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 141 TYR 0.053 0.002 TYR A 554 PHE 0.018 0.002 PHE A 616 TRP 0.012 0.002 TRP A 623 HIS 0.026 0.004 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.25 ( 6520) covalent geometry : angle 0.81695 / 0.45 ( 8857) hydrogen bonds : bond 0.04976 / 3.07 ( 221) hydrogen bonds : angle 6.56974 / 4.72 ( 660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9714 (mmtt) cc_final: 0.9312 (mttt) REVERT: A 106 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8814 (tm-30) REVERT: A 112 LYS cc_start: 0.9587 (tppt) cc_final: 0.9217 (tptm) REVERT: A 122 TYR cc_start: 0.7862 (t80) cc_final: 0.7585 (t80) REVERT: A 144 LYS cc_start: 0.9253 (mmtt) cc_final: 0.8996 (mmmt) REVERT: A 167 ASN cc_start: 0.9479 (t0) cc_final: 0.9058 (t0) REVERT: A 176 LEU cc_start: 0.9351 (tp) cc_final: 0.9002 (tp) REVERT: A 181 ASP cc_start: 0.9387 (OUTLIER) cc_final: 0.8413 (p0) REVERT: A 225 SER cc_start: 0.9568 (m) cc_final: 0.9190 (p) REVERT: A 226 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8751 (mm-30) REVERT: A 242 ASN cc_start: 0.9665 (m-40) cc_final: 0.9131 (p0) REVERT: A 289 ASP cc_start: 0.9016 (t0) cc_final: 0.8573 (t0) REVERT: A 295 GLU cc_start: 0.9739 (mm-30) cc_final: 0.9451 (tm-30) REVERT: A 296 ILE cc_start: 0.9915 (pt) cc_final: 0.9593 (pt) REVERT: A 363 MET cc_start: 0.9042 (ttp) cc_final: 0.8672 (tmm) REVERT: A 364 GLN cc_start: 0.9065 (pt0) cc_final: 0.8774 (pt0) REVERT: A 453 TYR cc_start: 0.9139 (m-80) cc_final: 0.8802 (m-80) REVERT: A 495 LYS cc_start: 0.9794 (tttt) cc_final: 0.9560 (mtpp) REVERT: A 498 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9219 (mp0) REVERT: A 513 HIS cc_start: 0.9201 (m-70) cc_final: 0.8909 (m90) REVERT: A 626 ASN cc_start: 0.9730 (t0) cc_final: 0.9473 (p0) REVERT: A 703 LEU cc_start: 0.9602 (mt) cc_final: 0.8991 (tt) outliers start: 28 outliers final: 18 residues processed: 165 average time/residue: 0.0564 time to fit residues: 12.5993 Evaluate side-chains 155 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 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 = 0.3260 r_free = 0.3260 target = 0.062781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.048929 restraints weight = 25434.007| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 6.58 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6520 Z= 0.155 Angle : 0.753 8.348 8857 Z= 0.402 Chirality : 0.049 0.218 964 Planarity : 0.004 0.040 1071 Dihedral : 14.195 124.798 974 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.29 % Allowed : 17.94 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.77 (0.30), residues: 743 helix: -0.57 (0.31), residues: 218 sheet: -1.04 (0.43), residues: 148 loop : -1.56 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 504 TYR 0.036 0.002 TYR A 554 PHE 0.013 0.002 PHE A 591 TRP 0.011 0.001 TRP A 623 HIS 0.022 0.003 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6520) covalent geometry : angle 0.75261 / 0.40 ( 8857) hydrogen bonds : bond 0.04255 / 2.67 ( 221) hydrogen bonds : angle 6.08418 / 4.37 ( 660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9653 (mmtt) cc_final: 0.9287 (mttt) REVERT: A 51 MET cc_start: 0.9635 (mmm) cc_final: 0.9293 (tpp) REVERT: A 79 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8504 (pp) REVERT: A 106 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8770 (tm-30) REVERT: A 112 LYS cc_start: 0.9554 (tppt) cc_final: 0.9183 (tptm) REVERT: A 122 TYR cc_start: 0.7819 (t80) cc_final: 0.7136 (t80) REVERT: A 144 LYS cc_start: 0.9203 (mmtt) cc_final: 0.8810 (mmmt) REVERT: A 149 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8947 (mtpp) REVERT: A 167 ASN cc_start: 0.9455 (t0) cc_final: 0.9044 (t0) REVERT: A 176 LEU cc_start: 0.9319 (tp) cc_final: 0.8965 (tp) REVERT: A 181 ASP cc_start: 0.9405 (OUTLIER) cc_final: 0.8452 (p0) REVERT: A 225 SER cc_start: 0.9580 (m) cc_final: 0.9232 (p) REVERT: A 226 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8850 (mm-30) REVERT: A 242 ASN cc_start: 0.9655 (m-40) cc_final: 0.9380 (m110) REVERT: A 289 ASP cc_start: 0.8995 (t0) cc_final: 0.8532 (t0) REVERT: A 295 GLU cc_start: 0.9753 (mm-30) cc_final: 0.9484 (tm-30) REVERT: A 296 ILE cc_start: 0.9897 (pt) cc_final: 0.9573 (pt) REVERT: A 363 MET cc_start: 0.9036 (ttp) cc_final: 0.8599 (tmm) REVERT: A 453 TYR cc_start: 0.9135 (m-80) cc_final: 0.8780 (m-80) REVERT: A 495 LYS cc_start: 0.9782 (tttt) cc_final: 0.9445 (mtpp) REVERT: A 504 ARG cc_start: 0.9606 (tpm170) cc_final: 0.8335 (mmp80) REVERT: A 625 GLU cc_start: 0.9390 (pt0) cc_final: 0.9078 (pp20) REVERT: A 626 ASN cc_start: 0.9769 (t0) cc_final: 0.9561 (t0) outliers start: 22 outliers final: 12 residues processed: 161 average time/residue: 0.0555 time to fit residues: 12.2164 Evaluate side-chains 147 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 693 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.057416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.043958 restraints weight = 27376.735| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 6.44 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 6520 Z= 0.426 Angle : 0.909 8.587 8857 Z= 0.495 Chirality : 0.052 0.208 964 Planarity : 0.005 0.040 1071 Dihedral : 14.181 126.285 974 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 31.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.29 % Favored : 90.44 % Rotamer: Outliers : 5.53 % Allowed : 17.04 % Favored : 77.43 % 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: -1.88 (0.30), residues: 743 helix: -0.68 (0.31), residues: 217 sheet: -1.34 (0.40), residues: 167 loop : -1.46 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 126 TYR 0.043 0.003 TYR A 554 PHE 0.041 0.003 PHE A 388 TRP 0.018 0.003 TRP A 623 HIS 0.025 0.004 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00860 / 0.43 ( 6520) covalent geometry : angle 0.90911 / 0.50 ( 8857) hydrogen bonds : bond 0.04849 / 3.02 ( 221) hydrogen bonds : angle 6.36704 / 4.54 ( 660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9732 (mmtt) cc_final: 0.9337 (mttt) REVERT: A 51 MET cc_start: 0.9656 (mmm) cc_final: 0.9251 (tpp) REVERT: A 106 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8901 (tm-30) REVERT: A 112 LYS cc_start: 0.9592 (tppt) cc_final: 0.9247 (tptm) REVERT: A 126 ARG cc_start: 0.9116 (ttm-80) cc_final: 0.8892 (mtp-110) REVERT: A 176 LEU cc_start: 0.9344 (tp) cc_final: 0.9039 (tp) REVERT: A 181 ASP cc_start: 0.9490 (OUTLIER) cc_final: 0.8573 (p0) REVERT: A 242 ASN cc_start: 0.9703 (m-40) cc_final: 0.9488 (m110) REVERT: A 243 GLN cc_start: 0.9597 (mt0) cc_final: 0.9207 (mt0) REVERT: A 289 ASP cc_start: 0.8949 (t0) cc_final: 0.8509 (t0) REVERT: A 295 GLU cc_start: 0.9759 (mm-30) cc_final: 0.9480 (tm-30) REVERT: A 296 ILE cc_start: 0.9905 (pt) cc_final: 0.9307 (pt) REVERT: A 363 MET cc_start: 0.9116 (ttp) cc_final: 0.8728 (tmm) REVERT: A 453 TYR cc_start: 0.9211 (m-80) cc_final: 0.8851 (m-80) REVERT: A 491 MET cc_start: 0.8858 (mpp) cc_final: 0.8460 (pmm) REVERT: A 495 LYS cc_start: 0.9828 (tttt) cc_final: 0.9596 (ttmm) REVERT: A 498 GLU cc_start: 0.9651 (mt-10) cc_final: 0.9289 (mp0) REVERT: A 502 ASN cc_start: 0.9589 (OUTLIER) cc_final: 0.9328 (p0) REVERT: A 589 GLU cc_start: 0.9621 (tt0) cc_final: 0.9267 (tm-30) REVERT: A 625 GLU cc_start: 0.9421 (pt0) cc_final: 0.9186 (pp20) REVERT: A 646 LEU cc_start: 0.8778 (mp) cc_final: 0.8359 (tt) REVERT: A 673 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8368 (ptp) REVERT: A 703 LEU cc_start: 0.9645 (mm) cc_final: 0.8753 (tt) outliers start: 37 outliers final: 23 residues processed: 155 average time/residue: 0.0553 time to fit residues: 11.8132 Evaluate side-chains 155 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.061491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.047491 restraints weight = 26042.625| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 6.64 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6520 Z= 0.170 Angle : 0.774 8.722 8857 Z= 0.413 Chirality : 0.049 0.186 964 Planarity : 0.004 0.041 1071 Dihedral : 14.146 127.768 974 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.44 % Allowed : 20.18 % Favored : 76.38 % 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: -1.72 (0.30), residues: 743 helix: -0.46 (0.31), residues: 218 sheet: -1.16 (0.43), residues: 145 loop : -1.50 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 618 TYR 0.023 0.002 TYR A 554 PHE 0.019 0.002 PHE A 366 TRP 0.011 0.002 TRP A 623 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 6520) covalent geometry : angle 0.77363 / 0.41 ( 8857) hydrogen bonds : bond 0.03990 / 2.46 ( 221) hydrogen bonds : angle 5.96287 / 4.29 ( 660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9691 (mmtt) cc_final: 0.9286 (mttt) REVERT: A 51 MET cc_start: 0.9592 (mmm) cc_final: 0.9239 (tpp) REVERT: A 79 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8591 (pp) REVERT: A 106 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8687 (tm-30) REVERT: A 112 LYS cc_start: 0.9552 (tppt) cc_final: 0.9176 (tptm) REVERT: A 126 ARG cc_start: 0.9109 (ttm-80) cc_final: 0.8889 (mtp-110) REVERT: A 167 ASN cc_start: 0.9412 (t0) cc_final: 0.9015 (t0) REVERT: A 176 LEU cc_start: 0.9302 (tp) cc_final: 0.8960 (tp) REVERT: A 181 ASP cc_start: 0.9444 (OUTLIER) cc_final: 0.8463 (p0) REVERT: A 226 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8844 (mm-30) REVERT: A 242 ASN cc_start: 0.9673 (m-40) cc_final: 0.9447 (m110) REVERT: A 243 GLN cc_start: 0.9565 (mt0) cc_final: 0.9185 (mt0) REVERT: A 289 ASP cc_start: 0.9017 (t0) cc_final: 0.8627 (t0) REVERT: A 296 ILE cc_start: 0.9875 (pt) cc_final: 0.9136 (pt) REVERT: A 298 GLN cc_start: 0.9055 (pm20) cc_final: 0.8730 (pp30) REVERT: A 363 MET cc_start: 0.9033 (ttp) cc_final: 0.8635 (tmm) REVERT: A 364 GLN cc_start: 0.9081 (pt0) cc_final: 0.8822 (pt0) REVERT: A 453 TYR cc_start: 0.9122 (m-80) cc_final: 0.8779 (m-80) REVERT: A 495 LYS cc_start: 0.9794 (tttt) cc_final: 0.9548 (ttmm) REVERT: A 498 GLU cc_start: 0.9606 (mt-10) cc_final: 0.9217 (mp0) REVERT: A 502 ASN cc_start: 0.9551 (m110) cc_final: 0.9334 (p0) REVERT: A 625 GLU cc_start: 0.9383 (pt0) cc_final: 0.9117 (pp20) REVERT: A 646 LEU cc_start: 0.8706 (mp) cc_final: 0.8284 (tt) REVERT: A 703 LEU cc_start: 0.9642 (mm) cc_final: 0.8889 (tt) REVERT: A 705 GLN cc_start: 0.9387 (mt0) cc_final: 0.9061 (mm-40) outliers start: 23 outliers final: 16 residues processed: 153 average time/residue: 0.0583 time to fit residues: 12.2191 Evaluate side-chains 150 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 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 = 0.3219 r_free = 0.3219 target = 0.060897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.047130 restraints weight = 25699.955| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 6.59 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6520 Z= 0.195 Angle : 0.773 9.647 8857 Z= 0.409 Chirality : 0.049 0.221 964 Planarity : 0.004 0.037 1071 Dihedral : 14.023 129.286 974 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.59 % Allowed : 22.12 % Favored : 74.29 % 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: -1.77 (0.30), residues: 743 helix: -0.58 (0.31), residues: 218 sheet: -1.08 (0.43), residues: 145 loop : -1.54 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 126 TYR 0.021 0.002 TYR A 554 PHE 0.018 0.002 PHE A 388 TRP 0.010 0.001 TRP A 623 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 6520) covalent geometry : angle 0.77277 / 0.41 ( 8857) hydrogen bonds : bond 0.03902 / 2.43 ( 221) hydrogen bonds : angle 5.98365 / 4.28 ( 660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9692 (mmtt) cc_final: 0.9285 (mttt) REVERT: A 51 MET cc_start: 0.9623 (mmm) cc_final: 0.9290 (tpp) REVERT: A 106 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8760 (tm-30) REVERT: A 112 LYS cc_start: 0.9556 (tppt) cc_final: 0.9170 (tptm) REVERT: A 126 ARG cc_start: 0.9123 (ttm-80) cc_final: 0.8875 (mtp-110) REVERT: A 167 ASN cc_start: 0.9430 (t0) cc_final: 0.9020 (t0) REVERT: A 176 LEU cc_start: 0.9312 (tp) cc_final: 0.8967 (tp) REVERT: A 181 ASP cc_start: 0.9461 (OUTLIER) cc_final: 0.8531 (p0) REVERT: A 226 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8830 (mm-30) REVERT: A 242 ASN cc_start: 0.9671 (m-40) cc_final: 0.9451 (m110) REVERT: A 243 GLN cc_start: 0.9569 (mt0) cc_final: 0.9184 (mt0) REVERT: A 289 ASP cc_start: 0.8953 (t0) cc_final: 0.8488 (t0) REVERT: A 363 MET cc_start: 0.9025 (ttp) cc_final: 0.8617 (tmm) REVERT: A 364 GLN cc_start: 0.9054 (pt0) cc_final: 0.8826 (pt0) REVERT: A 453 TYR cc_start: 0.9099 (m-80) cc_final: 0.8737 (m-80) REVERT: A 495 LYS cc_start: 0.9795 (tttt) cc_final: 0.9510 (ttmm) REVERT: A 502 ASN cc_start: 0.9583 (OUTLIER) cc_final: 0.9367 (p0) REVERT: A 562 ASP cc_start: 0.8557 (t70) cc_final: 0.8034 (p0) REVERT: A 625 GLU cc_start: 0.9368 (pt0) cc_final: 0.9102 (pp20) REVERT: A 646 LEU cc_start: 0.8701 (mp) cc_final: 0.8259 (tt) REVERT: A 652 ASN cc_start: 0.9331 (t0) cc_final: 0.9052 (t0) REVERT: A 673 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7798 (ptp) REVERT: A 703 LEU cc_start: 0.9617 (mm) cc_final: 0.8734 (tt) outliers start: 24 outliers final: 17 residues processed: 144 average time/residue: 0.0616 time to fit residues: 12.1937 Evaluate side-chains 147 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 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 = 0.3236 r_free = 0.3236 target = 0.061520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.047822 restraints weight = 25534.849| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 6.47 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6520 Z= 0.175 Angle : 0.770 10.342 8857 Z= 0.408 Chirality : 0.049 0.249 964 Planarity : 0.004 0.041 1071 Dihedral : 13.954 130.418 974 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.14 % Allowed : 21.82 % Favored : 75.04 % 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: -1.67 (0.30), residues: 743 helix: -0.42 (0.31), residues: 218 sheet: -1.06 (0.42), residues: 147 loop : -1.51 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 618 TYR 0.018 0.002 TYR A 554 PHE 0.020 0.002 PHE A 366 TRP 0.009 0.001 TRP A 623 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 6520) covalent geometry : angle 0.77026 / 0.41 ( 8857) hydrogen bonds : bond 0.03774 / 2.34 ( 221) hydrogen bonds : angle 5.87705 / 4.21 ( 660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9693 (mmtt) cc_final: 0.9278 (mttt) REVERT: A 51 MET cc_start: 0.9619 (mmm) cc_final: 0.9229 (tpp) REVERT: A 106 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8713 (tm-30) REVERT: A 112 LYS cc_start: 0.9566 (tppt) cc_final: 0.9132 (tptm) REVERT: A 126 ARG cc_start: 0.9148 (ttm-80) cc_final: 0.8885 (mtp-110) REVERT: A 167 ASN cc_start: 0.9420 (t0) cc_final: 0.9034 (t0) REVERT: A 176 LEU cc_start: 0.9290 (tp) cc_final: 0.8957 (tp) REVERT: A 181 ASP cc_start: 0.9457 (OUTLIER) cc_final: 0.8537 (p0) REVERT: A 226 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8843 (mm-30) REVERT: A 242 ASN cc_start: 0.9669 (m-40) cc_final: 0.9441 (m110) REVERT: A 243 GLN cc_start: 0.9554 (mt0) cc_final: 0.9181 (mt0) REVERT: A 289 ASP cc_start: 0.9029 (t0) cc_final: 0.8433 (t0) REVERT: A 363 MET cc_start: 0.9043 (ttp) cc_final: 0.8671 (tmm) REVERT: A 453 TYR cc_start: 0.9072 (m-80) cc_final: 0.8730 (m-80) REVERT: A 495 LYS cc_start: 0.9788 (tttt) cc_final: 0.9489 (ttmm) REVERT: A 502 ASN cc_start: 0.9576 (m110) cc_final: 0.9362 (p0) REVERT: A 562 ASP cc_start: 0.8448 (t70) cc_final: 0.8056 (p0) REVERT: A 589 GLU cc_start: 0.9594 (tt0) cc_final: 0.9125 (tm-30) REVERT: A 590 ILE cc_start: 0.9728 (pt) cc_final: 0.9120 (pt) REVERT: A 595 LEU cc_start: 0.9498 (tp) cc_final: 0.9232 (pp) REVERT: A 625 GLU cc_start: 0.9349 (pt0) cc_final: 0.9084 (pp20) REVERT: A 646 LEU cc_start: 0.8751 (mp) cc_final: 0.8335 (tt) REVERT: A 652 ASN cc_start: 0.9314 (t0) cc_final: 0.9078 (t0) REVERT: A 703 LEU cc_start: 0.9613 (mm) cc_final: 0.8907 (tt) outliers start: 21 outliers final: 15 residues processed: 145 average time/residue: 0.0589 time to fit residues: 11.7529 Evaluate side-chains 145 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** 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 = 0.3262 r_free = 0.3262 target = 0.062846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.048970 restraints weight = 25539.025| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 6.61 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6520 Z= 0.156 Angle : 0.787 10.948 8857 Z= 0.413 Chirality : 0.049 0.248 964 Planarity : 0.004 0.045 1071 Dihedral : 13.895 131.181 974 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.69 % Allowed : 22.72 % Favored : 74.59 % 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: -1.70 (0.30), residues: 743 helix: -0.44 (0.31), residues: 218 sheet: -1.02 (0.42), residues: 147 loop : -1.55 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 618 TYR 0.023 0.002 TYR A 108 PHE 0.020 0.002 PHE A 61 TRP 0.009 0.001 TRP A 623 HIS 0.006 0.002 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 6520) covalent geometry : angle 0.78728 / 0.41 ( 8857) hydrogen bonds : bond 0.03675 / 2.31 ( 221) hydrogen bonds : angle 5.85921 / 4.19 ( 660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.9512 (m-10) cc_final: 0.9266 (m-80) REVERT: A 50 LYS cc_start: 0.9677 (mmtt) cc_final: 0.9224 (mttt) REVERT: A 51 MET cc_start: 0.9614 (mmm) cc_final: 0.9207 (tpp) REVERT: A 106 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8682 (tm-30) REVERT: A 112 LYS cc_start: 0.9562 (tppt) cc_final: 0.9179 (tptm) REVERT: A 122 TYR cc_start: 0.7524 (t80) cc_final: 0.7266 (t80) REVERT: A 167 ASN cc_start: 0.9411 (t0) cc_final: 0.9036 (t0) REVERT: A 176 LEU cc_start: 0.9248 (tp) cc_final: 0.8901 (tp) REVERT: A 181 ASP cc_start: 0.9465 (OUTLIER) cc_final: 0.8553 (p0) REVERT: A 226 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8878 (mm-30) REVERT: A 242 ASN cc_start: 0.9651 (m-40) cc_final: 0.9422 (m110) REVERT: A 243 GLN cc_start: 0.9536 (mt0) cc_final: 0.9168 (mt0) REVERT: A 289 ASP cc_start: 0.8885 (t0) cc_final: 0.8464 (t0) REVERT: A 304 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7584 (mmt) REVERT: A 363 MET cc_start: 0.9005 (ttp) cc_final: 0.8628 (tmm) REVERT: A 453 TYR cc_start: 0.9051 (m-80) cc_final: 0.8714 (m-80) REVERT: A 495 LYS cc_start: 0.9785 (tttt) cc_final: 0.9483 (ttmm) REVERT: A 589 GLU cc_start: 0.9588 (tt0) cc_final: 0.9142 (tm-30) REVERT: A 590 ILE cc_start: 0.9720 (pt) cc_final: 0.9072 (pt) REVERT: A 595 LEU cc_start: 0.9481 (tp) cc_final: 0.9202 (pp) REVERT: A 625 GLU cc_start: 0.9347 (pt0) cc_final: 0.9071 (pp20) REVERT: A 646 LEU cc_start: 0.8704 (mp) cc_final: 0.8297 (tt) REVERT: A 652 ASN cc_start: 0.9301 (t0) cc_final: 0.9064 (t0) REVERT: A 669 ASN cc_start: 0.9393 (m-40) cc_final: 0.8872 (t0) REVERT: A 703 LEU cc_start: 0.9621 (mm) cc_final: 0.8948 (tt) REVERT: A 705 GLN cc_start: 0.9435 (mt0) cc_final: 0.9134 (mm-40) outliers start: 18 outliers final: 14 residues processed: 144 average time/residue: 0.0536 time to fit residues: 10.8558 Evaluate side-chains 143 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.0370 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.064294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.050290 restraints weight = 24906.223| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 6.65 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6520 Z= 0.156 Angle : 0.819 16.863 8857 Z= 0.424 Chirality : 0.049 0.257 964 Planarity : 0.004 0.043 1071 Dihedral : 13.840 131.291 974 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.24 % Allowed : 23.77 % Favored : 73.99 % 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: -1.70 (0.30), residues: 743 helix: -0.43 (0.31), residues: 224 sheet: -1.01 (0.42), residues: 147 loop : -1.59 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 618 TYR 0.016 0.001 TYR A 306 PHE 0.020 0.002 PHE A 61 TRP 0.009 0.001 TRP A 623 HIS 0.006 0.002 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 6520) covalent geometry : angle 0.81870 / 0.42 ( 8857) hydrogen bonds : bond 0.03504 / 2.23 ( 221) hydrogen bonds : angle 5.93164 / 4.20 ( 660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9675 (mmtt) cc_final: 0.9291 (mttt) REVERT: A 51 MET cc_start: 0.9638 (mmm) cc_final: 0.9250 (tpp) REVERT: A 106 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8644 (tm-30) REVERT: A 112 LYS cc_start: 0.9543 (tppt) cc_final: 0.9131 (tptm) REVERT: A 122 TYR cc_start: 0.7558 (t80) cc_final: 0.7284 (t80) REVERT: A 146 GLU cc_start: 0.9123 (tp30) cc_final: 0.8449 (tm-30) REVERT: A 149 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8773 (mmmt) REVERT: A 167 ASN cc_start: 0.9411 (t0) cc_final: 0.9024 (t0) REVERT: A 176 LEU cc_start: 0.9242 (tp) cc_final: 0.8836 (tp) REVERT: A 181 ASP cc_start: 0.9443 (OUTLIER) cc_final: 0.8536 (p0) REVERT: A 226 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8899 (mm-30) REVERT: A 242 ASN cc_start: 0.9640 (m-40) cc_final: 0.9416 (m110) REVERT: A 243 GLN cc_start: 0.9528 (mt0) cc_final: 0.9175 (mt0) REVERT: A 304 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7518 (mmt) REVERT: A 363 MET cc_start: 0.9031 (ttp) cc_final: 0.8602 (tmm) REVERT: A 368 ASN cc_start: 0.9329 (m-40) cc_final: 0.9025 (m110) REVERT: A 453 TYR cc_start: 0.9089 (m-80) cc_final: 0.8751 (m-80) REVERT: A 495 LYS cc_start: 0.9779 (tttt) cc_final: 0.9552 (ttmm) REVERT: A 498 GLU cc_start: 0.9617 (mt-10) cc_final: 0.9232 (mp0) REVERT: A 589 GLU cc_start: 0.9591 (tt0) cc_final: 0.9147 (tm-30) REVERT: A 590 ILE cc_start: 0.9722 (pt) cc_final: 0.9075 (pt) REVERT: A 625 GLU cc_start: 0.9334 (pt0) cc_final: 0.9053 (pp20) REVERT: A 646 LEU cc_start: 0.8711 (mp) cc_final: 0.8282 (tt) REVERT: A 652 ASN cc_start: 0.9331 (t0) cc_final: 0.9091 (t0) REVERT: A 669 ASN cc_start: 0.9377 (m-40) cc_final: 0.8820 (t0) REVERT: A 703 LEU cc_start: 0.9574 (mm) cc_final: 0.8908 (tt) REVERT: A 705 GLN cc_start: 0.9486 (mt0) cc_final: 0.9173 (mm-40) outliers start: 15 outliers final: 13 residues processed: 144 average time/residue: 0.0589 time to fit residues: 11.8606 Evaluate side-chains 147 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** 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 = 0.3305 r_free = 0.3305 target = 0.064461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.050484 restraints weight = 25502.518| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 6.67 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6520 Z= 0.150 Angle : 0.814 14.459 8857 Z= 0.420 Chirality : 0.049 0.246 964 Planarity : 0.004 0.052 1071 Dihedral : 13.787 131.259 974 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.39 % Allowed : 24.22 % Favored : 73.39 % 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: -1.69 (0.30), residues: 743 helix: -0.35 (0.32), residues: 223 sheet: -0.94 (0.42), residues: 148 loop : -1.65 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 618 TYR 0.030 0.002 TYR A 371 PHE 0.019 0.002 PHE A 61 TRP 0.009 0.001 TRP A 623 HIS 0.006 0.002 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6520) covalent geometry : angle 0.81395 / 0.42 ( 8857) hydrogen bonds : bond 0.03503 / 2.20 ( 221) hydrogen bonds : angle 5.91223 / 4.17 ( 660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 975.79 seconds wall clock time: 17 minutes 43.11 seconds (1063.11 seconds total)