Starting phenix.real_space_refine on Sat Jul 4 00:47:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m5x_23684/07_2026/7m5x_23684_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m5x_23684/07_2026/7m5x_23684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m5x_23684/07_2026/7m5x_23684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m5x_23684/07_2026/7m5x_23684.map" model { file = "/net/cci-nas-00/data/ceres_data/7m5x_23684/07_2026/7m5x_23684_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m5x_23684/07_2026/7m5x_23684_trim.cif" } resolution = 2.7 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= 0.002 sd= 0.023 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: 9 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 50 5.16 5 Be 1 3.05 5 C 5215 2.51 5 N 1270 2.21 5 O 1388 1.98 5 F 3 1.80 5 H 7545 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 15476 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 15007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 15007 Classifications: {'peptide': 1000} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 930} Chain breaks: 11 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 13, 'TRP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 178 Chain: "A" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 469 Unusual residues: {' MG': 1, 'BEF': 1, 'C14': 1, 'CLR': 4, 'D10': 10, 'D12': 1, 'EUJ': 1, 'LMT': 1, 'NAG': 1, 'SPK': 1, 'Y01': 3} Classifications: {'undetermined': 25, 'water': 11} Link IDs: {None: 35} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.65, per 1000 atoms: 0.17 Number of scatterers: 15476 At special positions: 0 Unit cell: (75.53, 97.94, 137.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 50 16.00 P 3 15.00 Mg 1 11.99 F 3 9.00 O 1388 8.00 N 1270 7.00 C 5215 6.00 Be 1 4.00 H 7545 1.00 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=1, symmetry=0 Links applied NAG-ASN " NAG A1223 " - " ASN A1033 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 431.7 milliseconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 50.4% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.639A pdb=" N ALA A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 66 removed outlier: 3.507A pdb=" N LEU A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.635A pdb=" N SER A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.553A pdb=" N GLY A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 290 removed outlier: 3.614A pdb=" N ALA A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.982A pdb=" N LYS A 427 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 428 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 450 Processing helix chain 'A' and resid 453 through 469 removed outlier: 3.618A pdb=" N VAL A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 490 removed outlier: 4.313A pdb=" N CYS A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR A 481 " --> pdb=" O MET A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.844A pdb=" N GLY A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 506' Processing helix chain 'A' and resid 549 through 558 Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 672 through 682 removed outlier: 4.073A pdb=" N TYR A 680 " --> pdb=" O MET A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 826 through 837 removed outlier: 3.580A pdb=" N GLY A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 847 removed outlier: 3.604A pdb=" N GLN A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 869 removed outlier: 3.692A pdb=" N THR A 860 " --> pdb=" O PRO A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 889 Processing helix chain 'A' and resid 914 through 953 removed outlier: 3.921A pdb=" N MET A 918 " --> pdb=" O GLU A 914 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 968 Processing helix chain 'A' and resid 968 through 978 Processing helix chain 'A' and resid 998 through 1024 Processing helix chain 'A' and resid 1038 through 1042 Processing helix chain 'A' and resid 1044 through 1066 removed outlier: 3.620A pdb=" N PHE A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1098 Processing helix chain 'A' and resid 1113 through 1149 Proline residue: A1143 - end of helix Processing helix chain 'A' and resid 1157 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110 removed outlier: 3.574A pdb=" N GLU A 110 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 163 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG A 164 " --> pdb=" O TRP A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 297 Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 320 removed outlier: 4.691A pdb=" N VAL A 391 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 392 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASP A 330 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.582A pdb=" N MET A 339 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA A 383 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU A 337 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 495 removed outlier: 7.160A pdb=" N VAL A 873 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE A 893 " --> pdb=" O VAL A 873 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET A 875 " --> pdb=" O ILE A 893 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR A 849 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU A 823 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE A 851 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU A 825 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 774 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 524 through 530 removed outlier: 6.952A pdb=" N VAL A 723 " --> pdb=" O MET A 526 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 528 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU A 721 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LEU A 719 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 690 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU A 721 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL A 688 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A 723 " --> pdb=" O ARG A 686 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG A 686 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA A 642 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL A 624 " --> pdb=" O ALA A 642 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1182 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: 3.47 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7519 1.03 - 1.22: 30 1.22 - 1.42: 3032 1.42 - 1.62: 4965 1.62 - 1.81: 74 Bond restraints: 15620 Sorted by residual: bond pdb=" O3 EUJ A1225 " pdb=" P3 EUJ A1225 " ideal model delta sigma weight residual 1.727 1.568 0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" F2 BEF A1202 " pdb="BE BEF A1202 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CAI Y01 A1203 " pdb=" CAK Y01 A1203 " ideal model delta sigma weight residual 1.492 1.407 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CAI Y01 A1208 " pdb=" CAK Y01 A1208 " ideal model delta sigma weight residual 1.492 1.408 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" CAI Y01 A1205 " pdb=" CAK Y01 A1205 " ideal model delta sigma weight residual 1.492 1.409 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 27795 2.55 - 5.10: 256 5.10 - 7.65: 61 7.65 - 10.20: 11 10.20 - 12.75: 10 Bond angle restraints: 28133 Sorted by residual: angle pdb=" CA THR A 750 " pdb=" C THR A 750 " pdb=" O THR A 750 " ideal model delta sigma weight residual 121.11 114.74 6.37 1.17e+00 7.31e-01 2.96e+01 angle pdb=" CA TYR A 940 " pdb=" C TYR A 940 " pdb=" O TYR A 940 " ideal model delta sigma weight residual 120.92 115.43 5.49 1.12e+00 7.97e-01 2.40e+01 angle pdb=" C VAL A 749 " pdb=" N THR A 750 " pdb=" CA THR A 750 " ideal model delta sigma weight residual 122.62 129.70 -7.08 1.56e+00 4.11e-01 2.06e+01 angle pdb=" N VAL A 334 " pdb=" CA VAL A 334 " pdb=" C VAL A 334 " ideal model delta sigma weight residual 113.53 109.34 4.19 9.80e-01 1.04e+00 1.83e+01 angle pdb=" O3 EUJ A1225 " pdb=" P3 EUJ A1225 " pdb=" O31 EUJ A1225 " ideal model delta sigma weight residual 100.72 87.97 12.75 3.00e+00 1.11e-01 1.81e+01 ... (remaining 28128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.90: 7538 30.90 - 61.80: 308 61.80 - 92.70: 23 92.70 - 123.61: 17 123.61 - 154.51: 1 Dihedral angle restraints: 7887 sinusoidal: 4621 harmonic: 3266 Sorted by residual: dihedral pdb=" C1 EUJ A1225 " pdb=" O1 EUJ A1225 " pdb=" P1 EUJ A1225 " pdb=" O11 EUJ A1225 " ideal model delta sinusoidal sigma weight residual 50.66 -154.83 -154.51 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA THR A 750 " pdb=" C THR A 750 " pdb=" N GLY A 751 " pdb=" CA GLY A 751 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" C10 CLR A1206 " pdb=" C1 CLR A1206 " pdb=" C2 CLR A1206 " pdb=" C3 CLR A1206 " ideal model delta sinusoidal sigma weight residual -56.83 60.45 -117.28 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 7884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 1348 0.965 - 1.930: 0 1.930 - 2.894: 0 2.894 - 3.859: 0 3.859 - 4.824: 1 Chirality restraints: 1349 Sorted by residual: chirality pdb=" C4 EUJ A1225 " pdb=" C3 EUJ A1225 " pdb=" C5 EUJ A1225 " pdb=" O4 EUJ A1225 " both_signs ideal model delta sigma weight residual False 2.45 -2.37 4.82 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C2 NAG A1223 " pdb=" C1 NAG A1223 " pdb=" C3 NAG A1223 " pdb=" N2 NAG A1223 " both_signs ideal model delta sigma weight residual False -2.49 -2.86 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C1' LMT A1204 " pdb=" C2' LMT A1204 " pdb=" O1' LMT A1204 " pdb=" O5' LMT A1204 " both_signs ideal model delta sigma weight residual False 2.31 2.65 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 1346 not shown) Planarity restraints: 2238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A EUJ A1225 " 0.060 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C2A EUJ A1225 " -0.017 2.00e-02 2.50e+03 pdb=" O1A EUJ A1225 " -0.022 2.00e-02 2.50e+03 pdb=" O2C EUJ A1225 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 939 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C LEU A 939 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A 939 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 940 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 939 " -0.012 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" N TYR A 940 " 0.038 2.00e-02 2.50e+03 pdb=" CA TYR A 940 " -0.010 2.00e-02 2.50e+03 pdb=" H TYR A 940 " -0.016 2.00e-02 2.50e+03 ... (remaining 2235 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 2648 2.29 - 2.87: 34808 2.87 - 3.44: 39741 3.44 - 4.02: 53497 4.02 - 4.60: 82546 Nonbonded interactions: 213240 Sorted by model distance: nonbonded pdb=" OE1 GLU A 658 " pdb=" H GLU A 658 " model vdw 1.712 2.450 nonbonded pdb=" O THR A 440 " pdb=" HG SER A 443 " model vdw 1.716 2.450 nonbonded pdb=" HZ1 LYS A 277 " pdb=" O3' LMT A1204 " model vdw 1.718 2.450 nonbonded pdb=" HH TYR A 240 " pdb=" O PRO A 470 " model vdw 1.726 2.450 nonbonded pdb=" O ARG A 192 " pdb=" H TYR A 364 " model vdw 1.726 2.450 ... (remaining 213235 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 0.267 8077 Z= 0.424 Angle : 0.991 12.752 10996 Z= 0.428 Chirality : 0.141 4.824 1349 Planarity : 0.005 0.035 1317 Dihedral : 16.396 154.508 3446 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.27), residues: 976 helix: 1.28 (0.25), residues: 453 sheet: -1.26 (0.41), residues: 152 loop : -1.06 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 636 TYR 0.013 0.002 TYR A1020 PHE 0.010 0.001 PHE A 945 TRP 0.005 0.001 TRP A 643 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.30 ( 8075) covalent geometry : angle 0.99021 / 0.43 (10993) hydrogen bonds : bond 0.15265 / 10.35 ( 412) hydrogen bonds : angle 6.49306 / 4.47 ( 1182) Misc. bond : bond 0.26680 / 14.04 ( 1) link_NAG-ASN : bond 0.00687 / 0.36 ( 1) link_NAG-ASN : angle 1.76003 / 0.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.345 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.7711 time to fit residues: 51.4686 Evaluate side-chains 40 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1044 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.068717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059068 restraints weight = 99357.355| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.04 r_work: 0.3120 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8077 Z= 0.119 Angle : 0.566 5.622 10996 Z= 0.272 Chirality : 0.041 0.217 1349 Planarity : 0.004 0.045 1317 Dihedral : 13.117 155.476 1788 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.63 % Allowed : 5.03 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.28), residues: 976 helix: 1.79 (0.24), residues: 466 sheet: -1.23 (0.40), residues: 162 loop : -0.81 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 991 TYR 0.014 0.001 TYR A 936 PHE 0.008 0.001 PHE A1128 TRP 0.004 0.000 TRP A 258 HIS 0.003 0.000 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8075) covalent geometry : angle 0.56465 / 0.27 (10993) hydrogen bonds : bond 0.04022 / 2.74 ( 412) hydrogen bonds : angle 4.86024 / 3.38 ( 1182) Misc. bond : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : bond 0.00453 / 0.24 ( 1) link_NAG-ASN : angle 2.46042 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.321 Fit side-chains REVERT: A 676 MET cc_start: 0.8842 (tpp) cc_final: 0.8284 (mmm) REVERT: A 910 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8155 (pp-130) outliers start: 5 outliers final: 1 residues processed: 48 average time/residue: 0.6584 time to fit residues: 35.3442 Evaluate side-chains 44 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1061 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.067963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.058340 restraints weight = 100530.317| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.05 r_work: 0.3106 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8077 Z= 0.112 Angle : 0.532 7.659 10996 Z= 0.252 Chirality : 0.040 0.227 1349 Planarity : 0.004 0.045 1317 Dihedral : 11.475 154.055 1788 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.63 % Allowed : 6.04 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.28), residues: 976 helix: 1.93 (0.25), residues: 467 sheet: -1.07 (0.40), residues: 156 loop : -0.67 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 991 TYR 0.013 0.001 TYR A 936 PHE 0.007 0.001 PHE A1128 TRP 0.004 0.000 TRP A 258 HIS 0.002 0.000 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8075) covalent geometry : angle 0.53031 / 0.25 (10993) hydrogen bonds : bond 0.03538 / 2.40 ( 412) hydrogen bonds : angle 4.49131 / 3.11 ( 1182) Misc. bond : bond 0.00026 / 0.01 ( 1) link_NAG-ASN : bond 0.00537 / 0.28 ( 1) link_NAG-ASN : angle 2.52270 / 1.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 676 MET cc_start: 0.8908 (tpp) cc_final: 0.8425 (mmm) REVERT: A 899 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7563 (tp30) REVERT: A 910 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8119 (ppp) outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.6792 time to fit residues: 33.9987 Evaluate side-chains 45 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1061 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 626 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 = 0.3496 r_free = 0.3496 target = 0.067994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.058354 restraints weight = 99789.122| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.03 r_work: 0.3110 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8077 Z= 0.099 Angle : 0.512 7.858 10996 Z= 0.242 Chirality : 0.040 0.202 1349 Planarity : 0.004 0.043 1317 Dihedral : 10.291 153.129 1788 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.50 % Allowed : 6.92 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.28), residues: 976 helix: 1.97 (0.24), residues: 473 sheet: -0.90 (0.40), residues: 150 loop : -0.85 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 980 TYR 0.013 0.001 TYR A 936 PHE 0.006 0.001 PHE A1159 TRP 0.004 0.000 TRP A 258 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 8075) covalent geometry : angle 0.51029 / 0.24 (10993) hydrogen bonds : bond 0.03227 / 2.20 ( 412) hydrogen bonds : angle 4.28522 / 2.98 ( 1182) Misc. bond : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : bond 0.00490 / 0.26 ( 1) link_NAG-ASN : angle 2.64614 / 1.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 676 MET cc_start: 0.8890 (tpp) cc_final: 0.8368 (mmm) REVERT: A 899 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7510 (tp30) REVERT: A 910 MET cc_start: 0.8548 (pp-130) cc_final: 0.8012 (ppp) outliers start: 4 outliers final: 1 residues processed: 44 average time/residue: 0.6712 time to fit residues: 32.8507 Evaluate side-chains 42 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 85 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.067817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.058235 restraints weight = 99974.847| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.08 r_work: 0.3109 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8077 Z= 0.096 Angle : 0.491 5.905 10996 Z= 0.234 Chirality : 0.040 0.202 1349 Planarity : 0.004 0.038 1317 Dihedral : 9.525 153.112 1788 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.38 % Allowed : 7.42 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.28), residues: 976 helix: 2.05 (0.24), residues: 474 sheet: -0.94 (0.40), residues: 158 loop : -0.72 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 627 TYR 0.013 0.001 TYR A 936 PHE 0.006 0.001 PHE A1159 TRP 0.004 0.000 TRP A 258 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 8075) covalent geometry : angle 0.48856 / 0.23 (10993) hydrogen bonds : bond 0.03104 / 2.11 ( 412) hydrogen bonds : angle 4.13047 / 2.87 ( 1182) Misc. bond : bond 0.00020 / 0.01 ( 1) link_NAG-ASN : bond 0.00484 / 0.25 ( 1) link_NAG-ASN : angle 2.82697 / 1.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 676 MET cc_start: 0.8881 (tpp) cc_final: 0.8489 (tpp) REVERT: A 899 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7525 (tp30) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.6498 time to fit residues: 34.1282 Evaluate side-chains 44 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.067530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.058050 restraints weight = 98821.042| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.00 r_work: 0.3107 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8077 Z= 0.095 Angle : 0.483 6.276 10996 Z= 0.230 Chirality : 0.039 0.204 1349 Planarity : 0.004 0.036 1317 Dihedral : 9.241 154.680 1788 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.38 % Allowed : 8.30 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.28), residues: 976 helix: 2.15 (0.24), residues: 474 sheet: -0.83 (0.40), residues: 158 loop : -0.69 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 980 TYR 0.012 0.001 TYR A 936 PHE 0.006 0.001 PHE A1159 TRP 0.004 0.000 TRP A 258 HIS 0.001 0.000 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 8075) covalent geometry : angle 0.48111 / 0.23 (10993) hydrogen bonds : bond 0.03027 / 2.06 ( 412) hydrogen bonds : angle 4.05409 / 2.82 ( 1182) Misc. bond : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : bond 0.00475 / 0.25 ( 1) link_NAG-ASN : angle 2.94359 / 1.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 637 MET cc_start: 0.6864 (tmm) cc_final: 0.6525 (ttt) REVERT: A 676 MET cc_start: 0.8885 (tpp) cc_final: 0.8513 (tpp) REVERT: A 899 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7394 (tp30) REVERT: A 910 MET cc_start: 0.8439 (pp-130) cc_final: 0.7902 (ppp) REVERT: A 940 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8981 (t80) outliers start: 3 outliers final: 1 residues processed: 47 average time/residue: 0.7294 time to fit residues: 38.0826 Evaluate side-chains 42 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 940 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.065456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055904 restraints weight = 100411.130| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.95 r_work: 0.3041 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8077 Z= 0.241 Angle : 0.578 6.755 10996 Z= 0.285 Chirality : 0.042 0.195 1349 Planarity : 0.004 0.029 1317 Dihedral : 9.657 158.640 1788 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.50 % Allowed : 8.43 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.28), residues: 976 helix: 2.05 (0.24), residues: 470 sheet: -0.82 (0.40), residues: 160 loop : -0.82 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1073 TYR 0.016 0.002 TYR A 936 PHE 0.013 0.001 PHE A 934 TRP 0.010 0.002 TRP A 175 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.24 ( 8075) covalent geometry : angle 0.57574 / 0.28 (10993) hydrogen bonds : bond 0.03675 / 2.53 ( 412) hydrogen bonds : angle 4.36708 / 3.05 ( 1182) Misc. bond : bond 0.00109 / 0.06 ( 1) link_NAG-ASN : bond 0.00245 / 0.13 ( 1) link_NAG-ASN : angle 3.42808 / 1.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 44 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 102 LEU cc_start: 0.9059 (mm) cc_final: 0.8785 (tm) REVERT: A 676 MET cc_start: 0.8854 (tpp) cc_final: 0.8142 (tpp) REVERT: A 899 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8065 (tp30) REVERT: A 910 MET cc_start: 0.8409 (pp-130) cc_final: 0.7788 (ppp) outliers start: 4 outliers final: 1 residues processed: 44 average time/residue: 0.6873 time to fit residues: 33.5358 Evaluate side-chains 41 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.066240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.056690 restraints weight = 99847.572| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.99 r_work: 0.3070 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8077 Z= 0.110 Angle : 0.509 7.012 10996 Z= 0.245 Chirality : 0.040 0.195 1349 Planarity : 0.004 0.031 1317 Dihedral : 9.265 159.467 1788 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.25 % Allowed : 8.93 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.28), residues: 976 helix: 2.14 (0.24), residues: 468 sheet: -0.76 (0.41), residues: 160 loop : -0.75 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 980 TYR 0.014 0.001 TYR A 936 PHE 0.009 0.001 PHE A 934 TRP 0.006 0.001 TRP A 258 HIS 0.002 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8075) covalent geometry : angle 0.50583 / 0.24 (10993) hydrogen bonds : bond 0.03295 / 2.25 ( 412) hydrogen bonds : angle 4.12930 / 2.87 ( 1182) Misc. bond : bond 0.00021 / 0.01 ( 1) link_NAG-ASN : bond 0.00377 / 0.20 ( 1) link_NAG-ASN : angle 3.46451 / 1.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.413 Fit side-chains REVERT: A 102 LEU cc_start: 0.9038 (mm) cc_final: 0.8763 (tm) REVERT: A 637 MET cc_start: 0.6799 (tmm) cc_final: 0.6471 (ttt) REVERT: A 676 MET cc_start: 0.8814 (tpp) cc_final: 0.8466 (tpp) REVERT: A 910 MET cc_start: 0.8352 (pp-130) cc_final: 0.7763 (ppp) outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 0.7219 time to fit residues: 33.5833 Evaluate side-chains 40 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 626 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 = 0.3437 r_free = 0.3437 target = 0.065534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056032 restraints weight = 99445.886| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.95 r_work: 0.3051 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8077 Z= 0.177 Angle : 0.537 7.072 10996 Z= 0.261 Chirality : 0.041 0.164 1349 Planarity : 0.004 0.028 1317 Dihedral : 9.188 161.778 1788 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.13 % Allowed : 9.06 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.28), residues: 976 helix: 2.12 (0.24), residues: 473 sheet: -0.82 (0.40), residues: 162 loop : -0.70 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 853 TYR 0.015 0.001 TYR A 936 PHE 0.008 0.001 PHE A 934 TRP 0.007 0.001 TRP A 258 HIS 0.002 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 8075) covalent geometry : angle 0.53257 / 0.26 (10993) hydrogen bonds : bond 0.03404 / 2.33 ( 412) hydrogen bonds : angle 4.18278 / 2.90 ( 1182) Misc. bond : bond 0.00074 / 0.04 ( 1) link_NAG-ASN : bond 0.00260 / 0.14 ( 1) link_NAG-ASN : angle 4.06309 / 2.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.292 Fit side-chains REVERT: A 637 MET cc_start: 0.6792 (tmm) cc_final: 0.6449 (ttt) REVERT: A 676 MET cc_start: 0.8824 (tpp) cc_final: 0.8138 (tpp) REVERT: A 910 MET cc_start: 0.8340 (pp-130) cc_final: 0.7706 (ppp) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.6933 time to fit residues: 30.7108 Evaluate side-chains 40 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.066481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.056939 restraints weight = 99910.516| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.99 r_work: 0.3076 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8077 Z= 0.092 Angle : 0.507 7.006 10996 Z= 0.240 Chirality : 0.039 0.137 1349 Planarity : 0.004 0.033 1317 Dihedral : 8.770 162.826 1788 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.13 % Allowed : 9.06 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.07 (0.28), residues: 976 helix: 2.25 (0.24), residues: 468 sheet: -0.78 (0.40), residues: 163 loop : -0.67 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 991 TYR 0.013 0.001 TYR A 936 PHE 0.007 0.001 PHE A1159 TRP 0.005 0.001 TRP A 258 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 8075) covalent geometry : angle 0.50186 / 0.24 (10993) hydrogen bonds : bond 0.03103 / 2.11 ( 412) hydrogen bonds : angle 3.96044 / 2.74 ( 1182) Misc. bond : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : bond 0.00352 / 0.19 ( 1) link_NAG-ASN : angle 4.33005 / 2.39 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.394 Fit side-chains REVERT: A 102 LEU cc_start: 0.9050 (mm) cc_final: 0.8764 (tm) REVERT: A 637 MET cc_start: 0.6718 (tmm) cc_final: 0.6407 (ttt) REVERT: A 676 MET cc_start: 0.8789 (tpp) cc_final: 0.8121 (tpp) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.7076 time to fit residues: 32.9149 Evaluate side-chains 40 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 626 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 = 0.3439 r_free = 0.3439 target = 0.065587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055970 restraints weight = 100060.976| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.97 r_work: 0.3048 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8077 Z= 0.189 Angle : 0.542 8.100 10996 Z= 0.262 Chirality : 0.041 0.135 1349 Planarity : 0.004 0.030 1317 Dihedral : 8.767 164.922 1788 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.25 % Allowed : 9.06 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.04 (0.28), residues: 976 helix: 2.21 (0.24), residues: 473 sheet: -0.85 (0.40), residues: 162 loop : -0.66 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1073 TYR 0.015 0.001 TYR A 936 PHE 0.007 0.001 PHE A 963 TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 ( 8075) covalent geometry : angle 0.53669 / 0.26 (10993) hydrogen bonds : bond 0.03354 / 2.29 ( 412) hydrogen bonds : angle 4.12646 / 2.86 ( 1182) Misc. bond : bond 0.00083 / 0.04 ( 1) link_NAG-ASN : bond 0.00232 / 0.12 ( 1) link_NAG-ASN : angle 4.64220 / 2.55 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3423.11 seconds wall clock time: 58 minutes 52.63 seconds (3532.63 seconds total)