Starting phenix.real_space_refine on Thu Oct 22 22:22:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25vk_80405/10_2026/25vk_80405.cif Found real_map, /net/cci-nas-00/data/ceres_data/25vk_80405/10_2026/25vk_80405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/25vk_80405/10_2026/25vk_80405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25vk_80405/10_2026/25vk_80405.map" model { file = "/net/cci-nas-00/data/ceres_data/25vk_80405/10_2026/25vk_80405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25vk_80405/10_2026/25vk_80405.cif" } resolution = 2.91 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= 0.003 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 Fe 2 7.16 5 P 1 5.49 5 S 32 5.16 5 C 4234 2.51 5 N 1051 2.21 5 O 1097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6417 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6281 Classifications: {'peptide': 786} Link IDs: {'PTRANS': 27, 'TRANS': 758} Chain breaks: 1 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'HEM': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.50, per 1000 atoms: 0.23 Number of scatterers: 6417 At special positions: 0 Unit cell: (95.3375, 85.4224, 103.727, 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) Fe 2 26.01 S 32 16.00 P 1 15.00 O 1097 8.00 N 1051 7.00 C 4234 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 348.1 milliseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 3 sheets defined 69.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 9 through 35 Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.746A pdb=" N ALA A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 65 Processing helix chain 'A' and resid 66 through 73 removed outlier: 6.089A pdb=" N PHE A 70 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 73 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 98 Processing helix chain 'A' and resid 200 through 224 removed outlier: 3.564A pdb=" N MET A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.735A pdb=" N LYS A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.880A pdb=" N GLY A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 360 through 365 removed outlier: 3.548A pdb=" N VAL A 364 " --> pdb=" O TRP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 removed outlier: 3.500A pdb=" N ALA A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 389 through 410 Processing helix chain 'A' and resid 439 through 463 removed outlier: 4.864A pdb=" N MET A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 489 through 503 Processing helix chain 'A' and resid 503 through 529 removed outlier: 3.624A pdb=" N TRP A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 564 Processing helix chain 'A' and resid 566 through 569 Processing helix chain 'A' and resid 570 through 589 Processing helix chain 'A' and resid 594 through 617 removed outlier: 3.881A pdb=" N ALA A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 617 " --> pdb=" O LEU A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 662 Processing helix chain 'A' and resid 667 through 708 removed outlier: 3.849A pdb=" N PHE A 673 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 706 " --> pdb=" O ILE A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 733 Processing helix chain 'A' and resid 744 through 770 removed outlier: 3.897A pdb=" N ILE A 756 " --> pdb=" O SER A 752 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 757 " --> pdb=" O VAL A 753 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 758 " --> pdb=" O VAL A 754 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 767 " --> pdb=" O TRP A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 810 removed outlier: 3.522A pdb=" N ARG A 805 " --> pdb=" O LEU A 801 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.687A pdb=" N SER A 149 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP A 135 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A 155 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU A 133 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LYS A 157 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL A 131 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP A 112 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 10.999A pdb=" N PHE A 129 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N THR A 110 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 111 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ARG A 106 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ARG A 113 " --> pdb=" O HIS A 104 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS A 104 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY A 192 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE A 186 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 194 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 198 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 290 Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 342 434 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 2236 1.38 - 1.56: 4290 1.56 - 1.74: 2 1.74 - 1.92: 58 1.92 - 2.11: 6 Bond restraints: 6592 Sorted by residual: bond pdb=" C3B HEM A 902 " pdb=" CAB HEM A 902 " ideal model delta sigma weight residual 1.544 1.462 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C3C HEM A 902 " pdb=" CAC HEM A 902 " ideal model delta sigma weight residual 1.544 1.464 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C3C HEM A 901 " pdb=" CAC HEM A 901 " ideal model delta sigma weight residual 1.544 1.466 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" N HIS A 774 " pdb=" CA HIS A 774 " ideal model delta sigma weight residual 1.459 1.503 -0.043 1.20e-02 6.94e+03 1.31e+01 bond pdb=" C3B HEM A 901 " pdb=" CAB HEM A 901 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 8761 2.42 - 4.84: 164 4.84 - 7.26: 26 7.26 - 9.68: 3 9.68 - 12.10: 3 Bond angle restraints: 8957 Sorted by residual: angle pdb=" CA HIS A 774 " pdb=" CB HIS A 774 " pdb=" CG HIS A 774 " ideal model delta sigma weight residual 113.80 123.79 -9.99 1.00e+00 1.00e+00 9.98e+01 angle pdb=" N LEU A 739 " pdb=" CA LEU A 739 " pdb=" C LEU A 739 " ideal model delta sigma weight residual 112.90 103.39 9.51 1.31e+00 5.83e-01 5.27e+01 angle pdb=" C HIS A 81 " pdb=" CA HIS A 81 " pdb=" CB HIS A 81 " ideal model delta sigma weight residual 110.85 122.95 -12.10 1.70e+00 3.46e-01 5.07e+01 angle pdb=" N PRO A 738 " pdb=" CA PRO A 738 " pdb=" CB PRO A 738 " ideal model delta sigma weight residual 103.25 96.97 6.28 1.05e+00 9.07e-01 3.58e+01 angle pdb=" CA HIS A 81 " pdb=" CB HIS A 81 " pdb=" CG HIS A 81 " ideal model delta sigma weight residual 113.80 119.48 -5.68 1.00e+00 1.00e+00 3.23e+01 ... (remaining 8952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 3597 20.83 - 41.67: 171 41.67 - 62.50: 35 62.50 - 83.34: 9 83.34 - 104.17: 3 Dihedral angle restraints: 3815 sinusoidal: 1543 harmonic: 2272 Sorted by residual: dihedral pdb=" C2C HEM A 902 " pdb=" C3C HEM A 902 " pdb=" CAC HEM A 902 " pdb=" CBC HEM A 902 " ideal model delta sinusoidal sigma weight residual 0.00 -51.24 51.24 2 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" C2B HEM A 902 " pdb=" C3B HEM A 902 " pdb=" CAB HEM A 902 " pdb=" CBB HEM A 902 " ideal model delta sinusoidal sigma weight residual 0.00 48.96 -48.96 2 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" C HIS A 81 " pdb=" N HIS A 81 " pdb=" CA HIS A 81 " pdb=" CB HIS A 81 " ideal model delta harmonic sigma weight residual -122.60 -135.28 12.68 0 2.50e+00 1.60e-01 2.57e+01 ... (remaining 3812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 827 0.056 - 0.111: 126 0.111 - 0.167: 15 0.167 - 0.222: 3 0.222 - 0.278: 2 Chirality restraints: 973 Sorted by residual: chirality pdb=" CA HIS A 81 " pdb=" N HIS A 81 " pdb=" C HIS A 81 " pdb=" CB HIS A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU A 739 " pdb=" N LEU A 739 " pdb=" C LEU A 739 " pdb=" CB LEU A 739 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ILE A 737 " pdb=" N ILE A 737 " pdb=" C ILE A 737 " pdb=" CB ILE A 737 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 970 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 228 " -0.308 9.50e-02 1.11e+02 1.38e-01 1.18e+01 pdb=" NE ARG A 228 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 228 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 228 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 228 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 779 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C THR A 779 " -0.048 2.00e-02 2.50e+03 pdb=" O THR A 779 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 780 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 80 " 0.018 2.00e-02 2.50e+03 1.63e-02 4.66e+00 pdb=" CG PHE A 80 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 80 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 80 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 80 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 80 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 80 " 0.002 2.00e-02 2.50e+03 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1466 2.80 - 3.32: 6289 3.32 - 3.85: 10747 3.85 - 4.37: 12270 4.37 - 4.90: 21588 Nonbonded interactions: 52360 Sorted by model distance: nonbonded pdb=" NE2 HIS A 81 " pdb="FE HEM A 901 " model vdw 2.271 3.080 nonbonded pdb=" NE2 HIS A 774 " pdb="FE HEM A 902 " model vdw 2.276 3.080 nonbonded pdb=" O LEU A 784 " pdb=" N TRP A 787 " model vdw 2.444 3.120 nonbonded pdb=" CAA HEM A 901 " pdb=" O1A HEM A 901 " model vdw 2.479 2.752 nonbonded pdb=" O GLU A 159 " pdb=" OD1 ASN A 160 " model vdw 2.491 3.040 ... (remaining 52355 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.190 Find NCS groups from input model: 0.150 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:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 0.231 6594 Z= 0.308 Angle : 0.795 12.101 8957 Z= 0.455 Chirality : 0.042 0.278 973 Planarity : 0.006 0.138 1098 Dihedral : 13.077 104.171 2363 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.40 % Cbeta Deviations : 0.14 % 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: 2.15 (0.30), residues: 782 helix: 2.63 (0.22), residues: 493 sheet: -0.42 (0.73), residues: 53 loop : -0.80 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 228 TYR 0.030 0.002 TYR A 311 PHE 0.038 0.002 PHE A 80 TRP 0.012 0.001 TRP A 789 HIS 0.014 0.002 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.31 ( 6592) covalent geometry : angle 0.79511 / 0.45 ( 8957) hydrogen bonds : bond 0.12247 / 8.24 ( 434) hydrogen bonds : angle 5.36142 / 3.88 ( 1269) Misc. bond : bond 0.07153 / 3.48 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.262 Fit side-chains REVERT: A 11 ILE cc_start: 0.8927 (mp) cc_final: 0.8727 (tp) REVERT: A 139 LYS cc_start: 0.9123 (mttp) cc_final: 0.8922 (mtpm) REVERT: A 200 ASP cc_start: 0.7379 (t0) cc_final: 0.7136 (t0) REVERT: A 204 MET cc_start: 0.8111 (ttt) cc_final: 0.7817 (ttp) REVERT: A 322 ASP cc_start: 0.7931 (m-30) cc_final: 0.7721 (m-30) REVERT: A 346 LYS cc_start: 0.9116 (tppp) cc_final: 0.8911 (tptt) REVERT: A 350 GLN cc_start: 0.9049 (tt0) cc_final: 0.8773 (tp40) REVERT: A 617 ASN cc_start: 0.8527 (t0) cc_final: 0.7831 (p0) outliers start: 2 outliers final: 1 residues processed: 135 average time/residue: 0.5372 time to fit residues: 76.0650 Evaluate side-chains 80 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 739 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN A 280 HIS A 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082334 restraints weight = 10811.429| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.12 r_work: 0.2945 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6594 Z= 0.115 Angle : 0.568 13.887 8957 Z= 0.275 Chirality : 0.039 0.149 973 Planarity : 0.004 0.039 1098 Dihedral : 8.277 70.569 920 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.81 % Allowed : 11.30 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.47 (0.30), residues: 782 helix: 2.82 (0.22), residues: 497 sheet: -0.24 (0.69), residues: 53 loop : -0.61 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 565 TYR 0.019 0.001 TYR A 776 PHE 0.028 0.001 PHE A 80 TRP 0.012 0.001 TRP A 789 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6592) covalent geometry : angle 0.56844 / 0.27 ( 8957) hydrogen bonds : bond 0.03938 / 2.70 ( 434) hydrogen bonds : angle 4.10844 / 2.98 ( 1269) Misc. bond : bond 0.05831 / 2.78 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.237 Fit side-chains REVERT: A 11 ILE cc_start: 0.8623 (mp) cc_final: 0.8387 (tp) REVERT: A 139 LYS cc_start: 0.9059 (mttp) cc_final: 0.8762 (mtpp) REVERT: A 200 ASP cc_start: 0.7278 (t0) cc_final: 0.6787 (t0) REVERT: A 204 MET cc_start: 0.7707 (ttt) cc_final: 0.7397 (ttp) REVERT: A 322 ASP cc_start: 0.7886 (m-30) cc_final: 0.7680 (m-30) REVERT: A 346 LYS cc_start: 0.9080 (tppp) cc_final: 0.8708 (tptt) REVERT: A 347 ASP cc_start: 0.8748 (t0) cc_final: 0.8453 (t0) REVERT: A 350 GLN cc_start: 0.9300 (tt0) cc_final: 0.8752 (tp40) outliers start: 12 outliers final: 4 residues processed: 104 average time/residue: 0.4115 time to fit residues: 45.6382 Evaluate side-chains 86 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 699 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: [15, 67, 34, 33, 1, 49, 50, 25, 3, 77, 20] chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 56 GLN A 617 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080691 restraints weight = 10802.672| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.02 r_work: 0.2910 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 6594 Z= 0.122 Angle : 0.563 17.032 8957 Z= 0.265 Chirality : 0.038 0.150 973 Planarity : 0.004 0.040 1098 Dihedral : 8.015 72.764 918 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.11 % Allowed : 13.70 % Favored : 84.19 % 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: 2.65 (0.30), residues: 782 helix: 2.96 (0.22), residues: 496 sheet: -0.04 (0.70), residues: 53 loop : -0.55 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 565 TYR 0.017 0.001 TYR A 776 PHE 0.026 0.001 PHE A 80 TRP 0.010 0.001 TRP A 720 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.12 ( 6592) covalent geometry : angle 0.56281 / 0.27 ( 8957) hydrogen bonds : bond 0.03866 / 2.64 ( 434) hydrogen bonds : angle 3.91290 / 2.84 ( 1269) Misc. bond : bond 0.07430 / 3.54 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.260 Fit side-chains REVERT: A 11 ILE cc_start: 0.8636 (mp) cc_final: 0.8432 (tp) REVERT: A 139 LYS cc_start: 0.9059 (mttp) cc_final: 0.8752 (mtpp) REVERT: A 171 ASN cc_start: 0.9266 (t0) cc_final: 0.8759 (p0) REVERT: A 200 ASP cc_start: 0.7219 (t0) cc_final: 0.6968 (t0) REVERT: A 322 ASP cc_start: 0.7907 (m-30) cc_final: 0.7694 (m-30) REVERT: A 346 LYS cc_start: 0.9093 (tppp) cc_final: 0.8692 (tptt) REVERT: A 347 ASP cc_start: 0.8828 (t0) cc_final: 0.8512 (t0) REVERT: A 350 GLN cc_start: 0.9290 (tt0) cc_final: 0.8719 (tp40) REVERT: A 520 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7620 (mp) REVERT: A 801 LEU cc_start: 0.8339 (mp) cc_final: 0.8079 (tt) outliers start: 14 outliers final: 3 residues processed: 90 average time/residue: 0.4218 time to fit residues: 40.5867 Evaluate side-chains 82 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 520 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: [58, 53, 30, 16, 14, 31, 50, 33, 72, 67, 60] chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN A 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083024 restraints weight = 10817.488| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.03 r_work: 0.2945 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 6594 Z= 0.098 Angle : 0.522 15.600 8957 Z= 0.245 Chirality : 0.037 0.136 973 Planarity : 0.004 0.047 1098 Dihedral : 7.774 70.521 918 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.41 % Allowed : 13.86 % Favored : 83.73 % 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: 2.82 (0.30), residues: 782 helix: 3.09 (0.22), residues: 496 sheet: 0.20 (0.71), residues: 53 loop : -0.54 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 565 TYR 0.024 0.001 TYR A 311 PHE 0.023 0.001 PHE A 80 TRP 0.010 0.001 TRP A 789 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 6592) covalent geometry : angle 0.52201 / 0.24 ( 8957) hydrogen bonds : bond 0.03490 / 2.38 ( 434) hydrogen bonds : angle 3.74635 / 2.73 ( 1269) Misc. bond : bond 0.07644 / 3.68 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.228 Fit side-chains REVERT: A 139 LYS cc_start: 0.9069 (mttp) cc_final: 0.8799 (mtpm) REVERT: A 171 ASN cc_start: 0.9285 (t0) cc_final: 0.8766 (p0) REVERT: A 198 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7731 (p) REVERT: A 200 ASP cc_start: 0.7261 (t0) cc_final: 0.6999 (t0) REVERT: A 204 MET cc_start: 0.7848 (ttt) cc_final: 0.7638 (ttt) REVERT: A 322 ASP cc_start: 0.7912 (m-30) cc_final: 0.7700 (m-30) REVERT: A 346 LYS cc_start: 0.9074 (tppp) cc_final: 0.8578 (tptp) REVERT: A 347 ASP cc_start: 0.8837 (t0) cc_final: 0.8510 (t0) REVERT: A 350 GLN cc_start: 0.9278 (tt0) cc_final: 0.8678 (tp40) REVERT: A 520 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7582 (mp) REVERT: A 801 LEU cc_start: 0.8341 (mp) cc_final: 0.8092 (tt) outliers start: 16 outliers final: 6 residues processed: 93 average time/residue: 0.4238 time to fit residues: 42.1018 Evaluate side-chains 81 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: [73, 10, 72, 48, 54, 23, 18, 24, 74, 49, 70] chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 0.0470 chunk 74 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 70 optimal weight: 0.0770 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.078318 restraints weight = 11126.468| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.07 r_work: 0.2860 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 6594 Z= 0.145 Angle : 0.555 15.849 8957 Z= 0.264 Chirality : 0.039 0.158 973 Planarity : 0.004 0.053 1098 Dihedral : 7.809 72.223 918 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.71 % Allowed : 15.66 % Favored : 81.63 % 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: 2.86 (0.30), residues: 782 helix: 3.13 (0.22), residues: 496 sheet: 0.18 (0.70), residues: 53 loop : -0.54 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 565 TYR 0.027 0.001 TYR A 311 PHE 0.026 0.001 PHE A 80 TRP 0.010 0.001 TRP A 720 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.14 ( 6592) covalent geometry : angle 0.55481 / 0.26 ( 8957) hydrogen bonds : bond 0.03891 / 2.66 ( 434) hydrogen bonds : angle 3.85154 / 2.80 ( 1269) Misc. bond : bond 0.08593 / 4.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.250 Fit side-chains REVERT: A 104 HIS cc_start: 0.8835 (t-170) cc_final: 0.8632 (t-90) REVERT: A 171 ASN cc_start: 0.9294 (t0) cc_final: 0.8731 (p0) REVERT: A 200 ASP cc_start: 0.7352 (t0) cc_final: 0.7036 (t0) REVERT: A 204 MET cc_start: 0.7927 (ttt) cc_final: 0.7670 (ttt) REVERT: A 322 ASP cc_start: 0.7977 (m-30) cc_final: 0.7757 (m-30) REVERT: A 346 LYS cc_start: 0.9087 (tppp) cc_final: 0.8704 (tptt) REVERT: A 347 ASP cc_start: 0.8858 (t0) cc_final: 0.8557 (t0) REVERT: A 350 GLN cc_start: 0.9276 (tt0) cc_final: 0.8746 (tp40) REVERT: A 520 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7616 (mp) REVERT: A 801 LEU cc_start: 0.8347 (mp) cc_final: 0.8089 (tt) outliers start: 18 outliers final: 10 residues processed: 87 average time/residue: 0.4169 time to fit residues: 38.7245 Evaluate side-chains 77 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 737 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: [42, 7, 45, 12, 38, 56, 34, 29, 41, 25, 32] chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 614 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 = 0.3369 r_free = 0.3369 target = 0.101947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.077672 restraints weight = 10988.252| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.04 r_work: 0.2835 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 6594 Z= 0.164 Angle : 0.573 15.964 8957 Z= 0.273 Chirality : 0.039 0.169 973 Planarity : 0.004 0.042 1098 Dihedral : 7.845 72.113 918 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.86 % Allowed : 15.96 % Favored : 81.17 % 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: 2.81 (0.30), residues: 782 helix: 3.10 (0.22), residues: 496 sheet: 0.03 (0.69), residues: 53 loop : -0.55 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 565 TYR 0.022 0.001 TYR A 311 PHE 0.027 0.001 PHE A 80 TRP 0.014 0.001 TRP A 789 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.16 ( 6592) covalent geometry : angle 0.57347 / 0.27 ( 8957) hydrogen bonds : bond 0.04050 / 2.78 ( 434) hydrogen bonds : angle 3.88360 / 2.83 ( 1269) Misc. bond : bond 0.09438 / 4.56 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.184 Fit side-chains REVERT: A 171 ASN cc_start: 0.9303 (t0) cc_final: 0.8744 (p0) REVERT: A 200 ASP cc_start: 0.7417 (t0) cc_final: 0.7087 (t0) REVERT: A 204 MET cc_start: 0.8002 (ttt) cc_final: 0.7735 (ttt) REVERT: A 322 ASP cc_start: 0.8048 (m-30) cc_final: 0.7824 (m-30) REVERT: A 346 LYS cc_start: 0.9088 (tppp) cc_final: 0.8701 (tptt) REVERT: A 347 ASP cc_start: 0.8853 (t0) cc_final: 0.8559 (t0) REVERT: A 350 GLN cc_start: 0.9288 (tt0) cc_final: 0.8779 (tp40) REVERT: A 520 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7611 (mp) REVERT: A 789 TRP cc_start: 0.7740 (m100) cc_final: 0.7512 (m100) REVERT: A 801 LEU cc_start: 0.8338 (mp) cc_final: 0.8103 (tt) outliers start: 19 outliers final: 9 residues processed: 84 average time/residue: 0.4057 time to fit residues: 36.4903 Evaluate side-chains 77 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 737 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: [62, 21, 16, 3, 18, 44, 23, 60, 38, 1, 75] chunk 62 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.074229 restraints weight = 11317.677| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.09 r_work: 0.2784 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 6594 Z= 0.230 Angle : 0.640 15.393 8957 Z= 0.303 Chirality : 0.041 0.191 973 Planarity : 0.004 0.050 1098 Dihedral : 8.106 73.411 918 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.41 % Allowed : 16.27 % Favored : 81.33 % 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: 2.58 (0.30), residues: 782 helix: 2.90 (0.22), residues: 498 sheet: -0.14 (0.71), residues: 53 loop : -0.58 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 565 TYR 0.023 0.002 TYR A 311 PHE 0.029 0.002 PHE A 80 TRP 0.011 0.001 TRP A 465 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.23 ( 6592) covalent geometry : angle 0.63976 / 0.30 ( 8957) hydrogen bonds : bond 0.04512 / 3.11 ( 434) hydrogen bonds : angle 4.06370 / 2.95 ( 1269) Misc. bond : bond 0.12481 / 6.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.226 Fit side-chains REVERT: A 171 ASN cc_start: 0.9296 (t0) cc_final: 0.8716 (p0) REVERT: A 175 GLU cc_start: 0.8474 (tt0) cc_final: 0.8232 (tt0) REVERT: A 200 ASP cc_start: 0.7565 (t0) cc_final: 0.7271 (t0) REVERT: A 204 MET cc_start: 0.8021 (ttt) cc_final: 0.7747 (ttt) REVERT: A 212 PHE cc_start: 0.7510 (t80) cc_final: 0.6677 (m-10) REVERT: A 322 ASP cc_start: 0.8065 (m-30) cc_final: 0.7835 (m-30) REVERT: A 346 LYS cc_start: 0.9093 (tppp) cc_final: 0.8684 (tptt) REVERT: A 347 ASP cc_start: 0.8872 (t0) cc_final: 0.8582 (t0) REVERT: A 350 GLN cc_start: 0.9291 (tt0) cc_final: 0.8788 (tp40) REVERT: A 520 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7692 (mp) REVERT: A 801 LEU cc_start: 0.8345 (mp) cc_final: 0.8109 (tt) outliers start: 16 outliers final: 8 residues processed: 82 average time/residue: 0.3885 time to fit residues: 34.3551 Evaluate side-chains 73 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 737 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: [27, 20, 41, 48, 55, 15, 46, 77, 4, 1, 30] chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN A 614 ASN A 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.104568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.080685 restraints weight = 10983.669| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.98 r_work: 0.2911 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 6594 Z= 0.106 Angle : 0.550 16.086 8957 Z= 0.255 Chirality : 0.038 0.176 973 Planarity : 0.004 0.048 1098 Dihedral : 7.725 72.635 918 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.11 % Allowed : 17.62 % 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: 2.82 (0.31), residues: 782 helix: 3.12 (0.22), residues: 497 sheet: -0.01 (0.73), residues: 53 loop : -0.57 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 565 TYR 0.016 0.001 TYR A 311 PHE 0.022 0.001 PHE A 80 TRP 0.017 0.001 TRP A 789 HIS 0.002 0.000 HIS A 635 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6592) covalent geometry : angle 0.55010 / 0.26 ( 8957) hydrogen bonds : bond 0.03594 / 2.45 ( 434) hydrogen bonds : angle 3.74767 / 2.74 ( 1269) Misc. bond : bond 0.09427 / 4.50 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.217 Fit side-chains REVERT: A 171 ASN cc_start: 0.9267 (t0) cc_final: 0.8728 (OUTLIER) REVERT: A 175 GLU cc_start: 0.8543 (tt0) cc_final: 0.8280 (tt0) REVERT: A 198 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7935 (p) REVERT: A 200 ASP cc_start: 0.7415 (t0) cc_final: 0.7121 (t0) REVERT: A 204 MET cc_start: 0.8106 (ttt) cc_final: 0.7810 (ttt) REVERT: A 322 ASP cc_start: 0.8088 (m-30) cc_final: 0.7857 (m-30) REVERT: A 346 LYS cc_start: 0.9055 (tppp) cc_final: 0.8668 (tptt) REVERT: A 347 ASP cc_start: 0.8842 (t0) cc_final: 0.8550 (t0) REVERT: A 350 GLN cc_start: 0.9270 (tt0) cc_final: 0.8782 (tp40) REVERT: A 520 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7689 (mp) REVERT: A 737 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9059 (pp) REVERT: A 801 LEU cc_start: 0.8435 (mp) cc_final: 0.8166 (tt) outliers start: 14 outliers final: 7 residues processed: 84 average time/residue: 0.4117 time to fit residues: 36.9344 Evaluate side-chains 79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 737 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: [29, 33, 3, 17, 6, 45, 23, 0, 55, 2, 28] chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.081724 restraints weight = 11350.309| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.15 r_work: 0.2909 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 6594 Z= 0.105 Angle : 0.566 14.695 8957 Z= 0.262 Chirality : 0.038 0.155 973 Planarity : 0.004 0.054 1098 Dihedral : 7.579 71.645 918 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.56 % Allowed : 17.02 % Favored : 80.42 % 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: 2.91 (0.31), residues: 782 helix: 3.20 (0.22), residues: 497 sheet: 0.09 (0.74), residues: 53 loop : -0.57 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 565 TYR 0.016 0.001 TYR A 311 PHE 0.020 0.001 PHE A 593 TRP 0.029 0.001 TRP A 789 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 ( 6592) covalent geometry : angle 0.56577 / 0.26 ( 8957) hydrogen bonds : bond 0.03513 / 2.40 ( 434) hydrogen bonds : angle 3.68147 / 2.68 ( 1269) Misc. bond : bond 0.09090 / 4.36 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.196 Fit side-chains REVERT: A 175 GLU cc_start: 0.8503 (tt0) cc_final: 0.8242 (tt0) REVERT: A 198 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.7813 (p) REVERT: A 200 ASP cc_start: 0.7278 (t0) cc_final: 0.6981 (t0) REVERT: A 204 MET cc_start: 0.7983 (ttt) cc_final: 0.7679 (ttt) REVERT: A 315 LYS cc_start: 0.7220 (mttt) cc_final: 0.6908 (mtpp) REVERT: A 322 ASP cc_start: 0.8013 (m-30) cc_final: 0.7801 (m-30) REVERT: A 346 LYS cc_start: 0.9056 (tppp) cc_final: 0.8545 (tptp) REVERT: A 347 ASP cc_start: 0.8868 (t0) cc_final: 0.8580 (t0) REVERT: A 350 GLN cc_start: 0.9261 (tt0) cc_final: 0.8736 (tp40) REVERT: A 400 GLU cc_start: 0.8461 (tt0) cc_final: 0.8116 (tp30) REVERT: A 520 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7593 (mp) REVERT: A 621 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 737 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8998 (pp) REVERT: A 801 LEU cc_start: 0.8332 (mp) cc_final: 0.8078 (tt) outliers start: 17 outliers final: 5 residues processed: 86 average time/residue: 0.4078 time to fit residues: 37.6106 Evaluate side-chains 79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 737 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: [15, 7, 6, 23, 72, 70, 76, 48, 30, 53, 75] chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 72 optimal weight: 0.0270 chunk 70 optimal weight: 0.0970 chunk 76 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.082056 restraints weight = 10954.154| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.95 r_work: 0.2928 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 6594 Z= 0.110 Angle : 0.562 12.881 8957 Z= 0.262 Chirality : 0.038 0.138 973 Planarity : 0.004 0.052 1098 Dihedral : 7.539 71.808 918 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.66 % Allowed : 18.22 % Favored : 80.12 % 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: 2.97 (0.31), residues: 782 helix: 3.21 (0.22), residues: 497 sheet: 0.33 (0.76), residues: 53 loop : -0.54 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 565 TYR 0.016 0.001 TYR A 311 PHE 0.022 0.001 PHE A 80 TRP 0.034 0.001 TRP A 789 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 6592) covalent geometry : angle 0.56216 / 0.26 ( 8957) hydrogen bonds : bond 0.03499 / 2.39 ( 434) hydrogen bonds : angle 3.67305 / 2.67 ( 1269) Misc. bond : bond 0.08623 / 4.15 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.254 Fit side-chains REVERT: A 172 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8995 (mmmm) REVERT: A 175 GLU cc_start: 0.8493 (tt0) cc_final: 0.8236 (tt0) REVERT: A 198 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.7920 (p) REVERT: A 200 ASP cc_start: 0.7346 (t0) cc_final: 0.7074 (t0) REVERT: A 204 MET cc_start: 0.8135 (ttt) cc_final: 0.7840 (ttt) REVERT: A 315 LYS cc_start: 0.7305 (mttt) cc_final: 0.7057 (mtpp) REVERT: A 322 ASP cc_start: 0.8068 (m-30) cc_final: 0.7853 (m-30) REVERT: A 346 LYS cc_start: 0.9082 (tppp) cc_final: 0.8699 (tptt) REVERT: A 347 ASP cc_start: 0.8884 (t0) cc_final: 0.8588 (t0) REVERT: A 350 GLN cc_start: 0.9235 (tt0) cc_final: 0.8768 (tp40) REVERT: A 400 GLU cc_start: 0.8550 (tt0) cc_final: 0.8326 (tp30) REVERT: A 520 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7698 (mp) REVERT: A 737 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9040 (pp) REVERT: A 801 LEU cc_start: 0.8439 (mp) cc_final: 0.8168 (tt) outliers start: 11 outliers final: 8 residues processed: 86 average time/residue: 0.4069 time to fit residues: 37.4014 Evaluate side-chains 86 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 737 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: [63, 14, 27, 30, 3, 2, 37, 19, 24, 45, 20] chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 45 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.107522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082826 restraints weight = 11150.924| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.08 r_work: 0.2939 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 6594 Z= 0.103 Angle : 0.561 12.776 8957 Z= 0.260 Chirality : 0.037 0.130 973 Planarity : 0.004 0.078 1098 Dihedral : 7.477 72.373 918 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.51 % Allowed : 18.37 % Favored : 80.12 % 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: 3.00 (0.31), residues: 782 helix: 3.24 (0.22), residues: 497 sheet: 0.30 (0.77), residues: 53 loop : -0.51 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 565 TYR 0.015 0.001 TYR A 311 PHE 0.021 0.001 PHE A 593 TRP 0.034 0.001 TRP A 789 HIS 0.002 0.000 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 6592) covalent geometry : angle 0.56109 / 0.26 ( 8957) hydrogen bonds : bond 0.03356 / 2.28 ( 434) hydrogen bonds : angle 3.62176 / 2.64 ( 1269) Misc. bond : bond 0.08070 / 3.92 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1852.71 seconds wall clock time: 32 minutes 23.42 seconds (1943.42 seconds total)