Starting phenix.real_space_refine on Wed Feb 4 02:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gn0_51459/02_2026/9gn0_51459.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gn0_51459/02_2026/9gn0_51459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gn0_51459/02_2026/9gn0_51459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gn0_51459/02_2026/9gn0_51459.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gn0_51459/02_2026/9gn0_51459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gn0_51459/02_2026/9gn0_51459.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 4 5.16 5 C 5281 2.51 5 N 1394 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8331 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8331 Classifications: {'peptide': 1042} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 1018} Chain breaks: 8 Time building chain proxies: 2.01, per 1000 atoms: 0.24 Number of scatterers: 8331 At special positions: 0 Unit cell: (78.2, 107.64, 134.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 4 16.00 O 1652 8.00 N 1394 7.00 C 5281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 274.2 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1978 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 55.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.572A pdb=" N VAL A 10 " --> pdb=" O THR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 38 removed outlier: 3.993A pdb=" N GLN A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 61 removed outlier: 3.906A pdb=" N MET A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.696A pdb=" N THR A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 93 removed outlier: 4.018A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.754A pdb=" N HIS A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 111 through 133 removed outlier: 3.595A pdb=" N LYS A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 182 through 201 Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.843A pdb=" N TYR A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.552A pdb=" N SER A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 301 through 316 removed outlier: 3.638A pdb=" N GLN A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 485 through 502 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 554 through 563 Processing helix chain 'A' and resid 564 through 600 removed outlier: 5.723A pdb=" N GLU A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 removed outlier: 4.001A pdb=" N GLU A 606 " --> pdb=" O PHE A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 631 through 646 removed outlier: 3.904A pdb=" N TYR A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 641 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 693 removed outlier: 3.781A pdb=" N LYS A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A 680 " --> pdb=" O ASP A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 733 removed outlier: 3.986A pdb=" N THR A 732 " --> pdb=" O ASN A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 748 removed outlier: 3.698A pdb=" N GLN A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP A 748 " --> pdb=" O TYR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 Processing helix chain 'A' and resid 780 through 797 removed outlier: 3.591A pdb=" N ILE A 785 " --> pdb=" O ASP A 781 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A 786 " --> pdb=" O ASN A 782 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 831 removed outlier: 3.608A pdb=" N ASP A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 855 removed outlier: 3.690A pdb=" N TYR A 845 " --> pdb=" O ASP A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 871 removed outlier: 3.791A pdb=" N GLN A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1019 removed outlier: 3.916A pdb=" N SER A1019 " --> pdb=" O SER A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1032 Processing helix chain 'A' and resid 1074 through 1078 removed outlier: 4.292A pdb=" N TYR A1077 " --> pdb=" O ASN A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 removed outlier: 4.241A pdb=" N LEU A1090 " --> pdb=" O SER A1086 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A1091 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1112 Processing helix chain 'A' and resid 1126 through 1142 removed outlier: 3.522A pdb=" N LYS A1131 " --> pdb=" O LEU A1127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A1134 " --> pdb=" O GLN A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1202 removed outlier: 3.784A pdb=" N SER A1201 " --> pdb=" O ASN A1198 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A1202 " --> pdb=" O TYR A1199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1198 through 1202' Processing helix chain 'A' and resid 1220 through 1225 Processing helix chain 'A' and resid 1228 through 1233 removed outlier: 4.233A pdb=" N LEU A1232 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A1233 " --> pdb=" O ASP A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1242 removed outlier: 4.519A pdb=" N ASP A1240 " --> pdb=" O SER A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1259 Processing helix chain 'A' and resid 1260 through 1274 Processing helix chain 'A' and resid 1284 through 1289 Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 291 removed outlier: 3.669A pdb=" N GLY A 287 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 204 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 323 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS A 449 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS A 325 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269 Processing sheet with id=AA4, first strand: chain 'A' and resid 479 through 480 Processing sheet with id=AA5, first strand: chain 'A' and resid 1010 through 1014 removed outlier: 5.387A pdb=" N PHE A1010 " --> pdb=" O SER A 882 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER A 882 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY A1012 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 880 " --> pdb=" O GLY A1012 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 877 " --> pdb=" O VAL A1219 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A1214 " --> pdb=" O ILE A1189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1010 through 1014 removed outlier: 5.387A pdb=" N PHE A1010 " --> pdb=" O SER A 882 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER A 882 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY A1012 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 880 " --> pdb=" O GLY A1012 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 877 " --> pdb=" O VAL A1219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1280 through 1282 400 hydrogen bonds defined for protein. 1137 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: 1.69 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1460 1.30 - 1.42: 2146 1.42 - 1.55: 4860 1.55 - 1.67: 1 1.67 - 1.80: 8 Bond restraints: 8475 Sorted by residual: bond pdb=" C SER A 305 " pdb=" O SER A 305 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.17e-02 7.31e+03 2.72e+01 bond pdb=" C SER A 305 " pdb=" N ALA A 306 " ideal model delta sigma weight residual 1.335 1.280 0.055 1.36e-02 5.41e+03 1.63e+01 bond pdb=" CA SER A 305 " pdb=" C SER A 305 " ideal model delta sigma weight residual 1.523 1.478 0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" CA ARG A 484 " pdb=" C ARG A 484 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.24e-02 6.50e+03 1.23e+01 bond pdb=" CA SER A 305 " pdb=" CB SER A 305 " ideal model delta sigma weight residual 1.528 1.475 0.054 1.56e-02 4.11e+03 1.18e+01 ... (remaining 8470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 11106 1.40 - 2.79: 254 2.79 - 4.19: 46 4.19 - 5.59: 17 5.59 - 6.99: 5 Bond angle restraints: 11428 Sorted by residual: angle pdb=" N SER A 305 " pdb=" CA SER A 305 " pdb=" CB SER A 305 " ideal model delta sigma weight residual 110.12 104.70 5.42 1.47e+00 4.63e-01 1.36e+01 angle pdb=" C THR A 710 " pdb=" CA THR A 710 " pdb=" CB THR A 710 " ideal model delta sigma weight residual 111.17 104.66 6.51 1.96e+00 2.60e-01 1.10e+01 angle pdb=" O GLY A 503 " pdb=" C GLY A 503 " pdb=" N LEU A 504 " ideal model delta sigma weight residual 122.57 125.42 -2.85 9.10e-01 1.21e+00 9.84e+00 angle pdb=" N SER A1231 " pdb=" CA SER A1231 " pdb=" C SER A1231 " ideal model delta sigma weight residual 112.89 116.70 -3.81 1.24e+00 6.50e-01 9.45e+00 angle pdb=" C PHE A 304 " pdb=" N SER A 305 " pdb=" CA SER A 305 " ideal model delta sigma weight residual 120.28 124.23 -3.95 1.34e+00 5.57e-01 8.70e+00 ... (remaining 11423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4207 17.34 - 34.68: 669 34.68 - 52.02: 189 52.02 - 69.36: 31 69.36 - 86.71: 14 Dihedral angle restraints: 5110 sinusoidal: 2059 harmonic: 3051 Sorted by residual: dihedral pdb=" CA ASP A 756 " pdb=" C ASP A 756 " pdb=" N ILE A 757 " pdb=" CA ILE A 757 " ideal model delta harmonic sigma weight residual -180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG A1007 " pdb=" C ARG A1007 " pdb=" N TYR A1008 " pdb=" CA TYR A1008 " ideal model delta harmonic sigma weight residual -180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA HIS A 468 " pdb=" C HIS A 468 " pdb=" N LEU A 469 " pdb=" CA LEU A 469 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 731 0.029 - 0.058: 362 0.058 - 0.087: 131 0.087 - 0.116: 43 0.116 - 0.145: 4 Chirality restraints: 1271 Sorted by residual: chirality pdb=" CA ILE A 459 " pdb=" N ILE A 459 " pdb=" C ILE A 459 " pdb=" CB ILE A 459 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE A 697 " pdb=" N ILE A 697 " pdb=" C ILE A 697 " pdb=" CB ILE A 697 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA TYR A 744 " pdb=" N TYR A 744 " pdb=" C TYR A 744 " pdb=" CB TYR A 744 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 1268 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 301 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 302 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 313 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C LEU A 313 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU A 313 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 314 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1260 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A1261 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A1261 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1261 " -0.019 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 855 2.74 - 3.28: 8798 3.28 - 3.82: 14686 3.82 - 4.36: 18424 4.36 - 4.90: 30307 Nonbonded interactions: 73070 Sorted by model distance: nonbonded pdb=" OG SER A1086 " pdb=" OD1 ASN A1089 " model vdw 2.202 3.040 nonbonded pdb=" ND2 ASN A 200 " pdb=" OH TYR A 522 " model vdw 2.213 3.120 nonbonded pdb=" O PHE A1034 " pdb=" NZ LYS A1193 " model vdw 2.227 3.120 nonbonded pdb=" O ILE A 104 " pdb=" OG1 THR A 108 " model vdw 2.228 3.040 nonbonded pdb=" O VAL A 98 " pdb=" OG1 THR A 102 " model vdw 2.228 3.040 ... (remaining 73065 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: 10.850 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.170 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8475 Z= 0.199 Angle : 0.568 6.986 11428 Z= 0.317 Chirality : 0.039 0.145 1271 Planarity : 0.003 0.048 1488 Dihedral : 18.425 86.706 3132 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.73 % Allowed : 29.65 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -1.02 (0.26), residues: 1024 helix: -0.58 (0.23), residues: 502 sheet: 0.08 (0.69), residues: 53 loop : -0.71 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.017 0.002 TYR A 312 PHE 0.018 0.002 PHE A 57 TRP 0.019 0.002 TRP A 854 HIS 0.004 0.001 HIS A 688 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8475) covalent geometry : angle 0.56752 (11428) hydrogen bonds : bond 0.17093 ( 389) hydrogen bonds : angle 7.96473 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: A 69 ARG cc_start: 0.6803 (mmp80) cc_final: 0.6598 (mmp80) REVERT: A 153 LYS cc_start: 0.7208 (mttp) cc_final: 0.6516 (tmtt) REVERT: A 331 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6070 (mm) REVERT: A 607 ARG cc_start: 0.6041 (OUTLIER) cc_final: 0.5404 (ttp-170) REVERT: A 753 LYS cc_start: 0.7310 (mttt) cc_final: 0.6557 (tppt) REVERT: A 835 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: A 836 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5497 (ttp80) REVERT: A 871 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5514 (mp) REVERT: A 938 VAL cc_start: 0.6919 (OUTLIER) cc_final: 0.6687 (t) REVERT: A 1011 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6124 (mmt180) REVERT: A 1077 TYR cc_start: 0.6336 (m-80) cc_final: 0.5947 (m-80) REVERT: A 1122 ASP cc_start: 0.4138 (OUTLIER) cc_final: 0.3632 (p0) REVERT: A 1239 LYS cc_start: 0.6758 (ptpp) cc_final: 0.6449 (pttm) outliers start: 44 outliers final: 30 residues processed: 124 average time/residue: 0.0991 time to fit residues: 17.0250 Evaluate side-chains 125 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 665 ASN Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1122 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1198 ASN Chi-restraints excluded: chain A residue 1268 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 630 HIS A 724 ASN A 738 ASN ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.181374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.152996 restraints weight = 9226.289| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.82 r_work: 0.4038 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8475 Z= 0.181 Angle : 0.578 10.532 11428 Z= 0.309 Chirality : 0.041 0.148 1271 Planarity : 0.004 0.044 1488 Dihedral : 8.212 59.191 1176 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.26 % Allowed : 27.39 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.89 (0.26), residues: 1024 helix: -0.44 (0.22), residues: 513 sheet: 0.20 (0.69), residues: 53 loop : -0.71 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 496 TYR 0.021 0.002 TYR A 312 PHE 0.018 0.002 PHE A 197 TRP 0.017 0.002 TRP A 854 HIS 0.005 0.001 HIS A1109 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8475) covalent geometry : angle 0.57812 (11428) hydrogen bonds : bond 0.04636 ( 389) hydrogen bonds : angle 5.97805 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: A 153 LYS cc_start: 0.6942 (mttp) cc_final: 0.6358 (tmtt) REVERT: A 208 ARG cc_start: 0.3948 (OUTLIER) cc_final: 0.3666 (ppt170) REVERT: A 313 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7302 (mt) REVERT: A 537 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6576 (t0) REVERT: A 607 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5511 (ttp-170) REVERT: A 753 LYS cc_start: 0.7346 (mttt) cc_final: 0.6570 (tppt) REVERT: A 830 SER cc_start: 0.7585 (OUTLIER) cc_final: 0.7351 (p) REVERT: A 1077 TYR cc_start: 0.6289 (m-80) cc_final: 0.5895 (m-80) REVERT: A 1239 LYS cc_start: 0.6913 (ptpp) cc_final: 0.6604 (pttm) REVERT: A 1294 GLN cc_start: 0.7318 (tt0) cc_final: 0.7110 (tt0) outliers start: 49 outliers final: 26 residues processed: 136 average time/residue: 0.0979 time to fit residues: 18.6163 Evaluate side-chains 120 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1198 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.182981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.154488 restraints weight = 9061.016| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.84 r_work: 0.4018 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8475 Z= 0.160 Angle : 0.554 10.461 11428 Z= 0.294 Chirality : 0.040 0.154 1271 Planarity : 0.004 0.046 1488 Dihedral : 7.038 57.402 1133 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.73 % Allowed : 27.28 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.68 (0.26), residues: 1024 helix: -0.26 (0.23), residues: 496 sheet: 0.12 (0.68), residues: 53 loop : -0.59 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.019 0.002 TYR A 312 PHE 0.018 0.002 PHE A 197 TRP 0.017 0.002 TRP A 854 HIS 0.004 0.001 HIS A1109 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8475) covalent geometry : angle 0.55436 (11428) hydrogen bonds : bond 0.04306 ( 389) hydrogen bonds : angle 5.67434 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 96 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: A 153 LYS cc_start: 0.7021 (mttp) cc_final: 0.6471 (tttm) REVERT: A 208 ARG cc_start: 0.4268 (OUTLIER) cc_final: 0.3892 (ppt170) REVERT: A 607 ARG cc_start: 0.6037 (OUTLIER) cc_final: 0.5608 (ttp-170) REVERT: A 674 LEU cc_start: 0.6633 (mt) cc_final: 0.6409 (mt) REVERT: A 678 LYS cc_start: 0.5475 (OUTLIER) cc_final: 0.5169 (tptt) REVERT: A 753 LYS cc_start: 0.7458 (mttt) cc_final: 0.6601 (tppt) REVERT: A 830 SER cc_start: 0.7533 (OUTLIER) cc_final: 0.7280 (p) REVERT: A 1019 SER cc_start: 0.6300 (OUTLIER) cc_final: 0.5940 (p) REVERT: A 1077 TYR cc_start: 0.6284 (m-80) cc_final: 0.5935 (m-80) REVERT: A 1239 LYS cc_start: 0.6925 (ptpp) cc_final: 0.6580 (pttm) outliers start: 44 outliers final: 25 residues processed: 130 average time/residue: 0.1015 time to fit residues: 18.1367 Evaluate side-chains 126 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1198 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 98 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.182350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.154363 restraints weight = 9270.296| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.80 r_work: 0.4039 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8475 Z= 0.171 Angle : 0.563 10.848 11428 Z= 0.298 Chirality : 0.040 0.151 1271 Planarity : 0.004 0.045 1488 Dihedral : 7.075 59.909 1129 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.12 % Allowed : 26.10 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.81 (0.26), residues: 1024 helix: -0.37 (0.22), residues: 502 sheet: 0.07 (0.67), residues: 53 loop : -0.66 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A1007 TYR 0.020 0.002 TYR A 312 PHE 0.017 0.002 PHE A 197 TRP 0.017 0.002 TRP A 854 HIS 0.004 0.001 HIS A1109 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8475) covalent geometry : angle 0.56349 (11428) hydrogen bonds : bond 0.04193 ( 389) hydrogen bonds : angle 5.59531 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 99 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7070 (mttp) cc_final: 0.6558 (tttm) REVERT: A 537 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6648 (t0) REVERT: A 557 PHE cc_start: 0.6720 (t80) cc_final: 0.6509 (t80) REVERT: A 607 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5667 (ttp-170) REVERT: A 674 LEU cc_start: 0.6676 (mt) cc_final: 0.6475 (mt) REVERT: A 678 LYS cc_start: 0.5515 (OUTLIER) cc_final: 0.5226 (tptt) REVERT: A 753 LYS cc_start: 0.7482 (mttt) cc_final: 0.6663 (tppt) REVERT: A 830 SER cc_start: 0.7541 (OUTLIER) cc_final: 0.7299 (p) REVERT: A 938 VAL cc_start: 0.6966 (OUTLIER) cc_final: 0.6749 (t) REVERT: A 1019 SER cc_start: 0.6264 (OUTLIER) cc_final: 0.5944 (p) REVERT: A 1077 TYR cc_start: 0.6351 (m-80) cc_final: 0.6032 (m-80) REVERT: A 1239 LYS cc_start: 0.6964 (ptpp) cc_final: 0.6676 (pttm) REVERT: A 1294 GLN cc_start: 0.7230 (tt0) cc_final: 0.7011 (tt0) outliers start: 57 outliers final: 32 residues processed: 145 average time/residue: 0.0979 time to fit residues: 19.8311 Evaluate side-chains 133 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1198 ASN Chi-restraints excluded: chain A residue 1265 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 73 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS A 704 GLN ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.181715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.153927 restraints weight = 9204.657| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.79 r_work: 0.4036 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8475 Z= 0.176 Angle : 0.571 11.170 11428 Z= 0.302 Chirality : 0.041 0.187 1271 Planarity : 0.004 0.048 1488 Dihedral : 6.541 59.715 1124 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.80 % Allowed : 27.07 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.79 (0.26), residues: 1024 helix: -0.34 (0.22), residues: 498 sheet: -0.04 (0.67), residues: 53 loop : -0.62 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 39 TYR 0.021 0.002 TYR A 312 PHE 0.017 0.002 PHE A 197 TRP 0.017 0.002 TRP A 854 HIS 0.004 0.001 HIS A1109 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8475) covalent geometry : angle 0.57072 (11428) hydrogen bonds : bond 0.04126 ( 389) hydrogen bonds : angle 5.51443 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 104 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7119 (mp0) cc_final: 0.6820 (mp0) REVERT: A 153 LYS cc_start: 0.7046 (mttp) cc_final: 0.6585 (tttm) REVERT: A 537 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6748 (t0) REVERT: A 557 PHE cc_start: 0.6835 (t80) cc_final: 0.6548 (t80) REVERT: A 607 ARG cc_start: 0.6022 (OUTLIER) cc_final: 0.5661 (ttp-170) REVERT: A 678 LYS cc_start: 0.5535 (OUTLIER) cc_final: 0.5269 (tptt) REVERT: A 753 LYS cc_start: 0.7510 (mttt) cc_final: 0.6682 (tppt) REVERT: A 830 SER cc_start: 0.7552 (OUTLIER) cc_final: 0.7307 (p) REVERT: A 938 VAL cc_start: 0.7080 (OUTLIER) cc_final: 0.6858 (t) REVERT: A 1077 TYR cc_start: 0.6344 (m-80) cc_final: 0.6053 (m-80) REVERT: A 1239 LYS cc_start: 0.6978 (ptpp) cc_final: 0.6693 (pttm) REVERT: A 1298 ARG cc_start: 0.7399 (ptm160) cc_final: 0.7140 (ttp-170) outliers start: 54 outliers final: 37 residues processed: 146 average time/residue: 0.0965 time to fit residues: 19.5788 Evaluate side-chains 138 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1198 ASN Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1271 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 52 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.182615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.155042 restraints weight = 9070.999| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.78 r_work: 0.4036 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8475 Z= 0.164 Angle : 0.569 11.317 11428 Z= 0.300 Chirality : 0.040 0.170 1271 Planarity : 0.004 0.074 1488 Dihedral : 6.339 59.746 1122 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.37 % Allowed : 27.60 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.26), residues: 1024 helix: -0.31 (0.22), residues: 498 sheet: -0.06 (0.67), residues: 53 loop : -0.63 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 39 TYR 0.019 0.002 TYR A 312 PHE 0.028 0.002 PHE A 42 TRP 0.018 0.002 TRP A 854 HIS 0.004 0.001 HIS A1109 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8475) covalent geometry : angle 0.56895 (11428) hydrogen bonds : bond 0.04055 ( 389) hydrogen bonds : angle 5.42323 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.6965 (mttp) cc_final: 0.6574 (tttm) REVERT: A 537 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6744 (t0) REVERT: A 678 LYS cc_start: 0.5368 (OUTLIER) cc_final: 0.5125 (tptt) REVERT: A 753 LYS cc_start: 0.7472 (mttt) cc_final: 0.6665 (tppt) REVERT: A 830 SER cc_start: 0.7674 (OUTLIER) cc_final: 0.7347 (p) REVERT: A 938 VAL cc_start: 0.7067 (OUTLIER) cc_final: 0.6856 (t) REVERT: A 1019 SER cc_start: 0.6160 (OUTLIER) cc_final: 0.5891 (p) REVERT: A 1077 TYR cc_start: 0.6331 (m-80) cc_final: 0.6091 (m-80) REVERT: A 1203 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.6799 (mt0) REVERT: A 1239 LYS cc_start: 0.6984 (ptpp) cc_final: 0.6705 (pttm) REVERT: A 1298 ARG cc_start: 0.7394 (ptm160) cc_final: 0.7123 (ttp-170) outliers start: 50 outliers final: 34 residues processed: 138 average time/residue: 0.0878 time to fit residues: 17.1057 Evaluate side-chains 132 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1198 ASN Chi-restraints excluded: chain A residue 1203 GLN Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1271 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1263 ASN A1294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.182192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.154668 restraints weight = 9184.837| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.76 r_work: 0.4017 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8475 Z= 0.170 Angle : 0.575 11.417 11428 Z= 0.303 Chirality : 0.040 0.169 1271 Planarity : 0.004 0.066 1488 Dihedral : 6.025 58.305 1117 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.80 % Allowed : 27.28 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.80 (0.26), residues: 1024 helix: -0.32 (0.22), residues: 498 sheet: -0.12 (0.66), residues: 53 loop : -0.67 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 39 TYR 0.020 0.002 TYR A 312 PHE 0.048 0.002 PHE A 42 TRP 0.018 0.002 TRP A 854 HIS 0.004 0.001 HIS A1109 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8475) covalent geometry : angle 0.57523 (11428) hydrogen bonds : bond 0.04050 ( 389) hydrogen bonds : angle 5.39171 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 91 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.6998 (mttp) cc_final: 0.6593 (tttm) REVERT: A 315 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6856 (mt) REVERT: A 478 TYR cc_start: 0.6980 (p90) cc_final: 0.5771 (p90) REVERT: A 537 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6780 (t0) REVERT: A 678 LYS cc_start: 0.5387 (OUTLIER) cc_final: 0.5164 (tptt) REVERT: A 753 LYS cc_start: 0.7517 (mttt) cc_final: 0.7117 (mmmt) REVERT: A 830 SER cc_start: 0.7684 (OUTLIER) cc_final: 0.7361 (p) REVERT: A 1019 SER cc_start: 0.6135 (OUTLIER) cc_final: 0.5877 (p) REVERT: A 1077 TYR cc_start: 0.6309 (m-80) cc_final: 0.6086 (m-80) REVERT: A 1239 LYS cc_start: 0.7104 (ptpp) cc_final: 0.6691 (pttm) REVERT: A 1294 GLN cc_start: 0.7214 (tt0) cc_final: 0.6978 (tt0) REVERT: A 1298 ARG cc_start: 0.7414 (ptm160) cc_final: 0.7133 (ttp-170) outliers start: 54 outliers final: 38 residues processed: 135 average time/residue: 0.0891 time to fit residues: 17.1674 Evaluate side-chains 130 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1198 ASN Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1271 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 0.0070 chunk 99 optimal weight: 0.5980 chunk 101 optimal weight: 0.1980 chunk 87 optimal weight: 0.0770 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.187838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.160473 restraints weight = 8999.236| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 1.78 r_work: 0.4108 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3974 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8475 Z= 0.110 Angle : 0.519 11.673 11428 Z= 0.274 Chirality : 0.038 0.154 1271 Planarity : 0.004 0.055 1488 Dihedral : 5.781 59.420 1117 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.62 % Allowed : 27.93 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.26), residues: 1024 helix: 0.06 (0.23), residues: 493 sheet: -0.09 (0.68), residues: 53 loop : -0.52 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1007 TYR 0.021 0.001 TYR A 850 PHE 0.037 0.002 PHE A 42 TRP 0.023 0.003 TRP A 854 HIS 0.003 0.001 HIS A1109 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8475) covalent geometry : angle 0.51948 (11428) hydrogen bonds : bond 0.03623 ( 389) hydrogen bonds : angle 5.09613 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6628 (tttm) REVERT: A 478 TYR cc_start: 0.6848 (p90) cc_final: 0.5705 (p90) REVERT: A 537 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6535 (t0) REVERT: A 607 ARG cc_start: 0.5982 (OUTLIER) cc_final: 0.5504 (ttp-170) REVERT: A 678 LYS cc_start: 0.5418 (OUTLIER) cc_final: 0.5100 (tptt) REVERT: A 753 LYS cc_start: 0.7399 (mttt) cc_final: 0.7024 (mmmt) REVERT: A 830 SER cc_start: 0.7420 (OUTLIER) cc_final: 0.7090 (p) REVERT: A 1019 SER cc_start: 0.6098 (OUTLIER) cc_final: 0.5821 (p) REVERT: A 1077 TYR cc_start: 0.6280 (m-80) cc_final: 0.5912 (m-80) REVERT: A 1203 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6660 (mt0) REVERT: A 1232 LEU cc_start: 0.7554 (mp) cc_final: 0.7292 (mp) REVERT: A 1239 LYS cc_start: 0.7049 (ptpp) cc_final: 0.6654 (pttm) outliers start: 43 outliers final: 24 residues processed: 125 average time/residue: 0.0969 time to fit residues: 16.9814 Evaluate side-chains 115 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1198 ASN Chi-restraints excluded: chain A residue 1203 GLN Chi-restraints excluded: chain A residue 1271 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 92 optimal weight: 0.0870 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 78 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1141 ASN A1294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.185098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.157082 restraints weight = 9014.706| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 1.84 r_work: 0.4054 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8475 Z= 0.144 Angle : 0.548 9.103 11428 Z= 0.290 Chirality : 0.039 0.162 1271 Planarity : 0.004 0.050 1488 Dihedral : 5.801 59.474 1117 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.44 % Allowed : 29.00 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.44 (0.26), residues: 1024 helix: 0.01 (0.23), residues: 493 sheet: 0.02 (0.69), residues: 53 loop : -0.51 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 39 TYR 0.017 0.002 TYR A 312 PHE 0.033 0.002 PHE A 42 TRP 0.018 0.003 TRP A 854 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8475) covalent geometry : angle 0.54821 (11428) hydrogen bonds : bond 0.03829 ( 389) hydrogen bonds : angle 5.15228 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7027 (mttp) cc_final: 0.6604 (tttm) REVERT: A 537 ASP cc_start: 0.6844 (OUTLIER) cc_final: 0.6577 (t0) REVERT: A 607 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.5588 (ttp-170) REVERT: A 678 LYS cc_start: 0.5548 (OUTLIER) cc_final: 0.5321 (tptt) REVERT: A 753 LYS cc_start: 0.7433 (mttt) cc_final: 0.7046 (mmmt) REVERT: A 830 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.7296 (p) REVERT: A 1019 SER cc_start: 0.6057 (OUTLIER) cc_final: 0.5835 (p) REVERT: A 1077 TYR cc_start: 0.6335 (m-80) cc_final: 0.5901 (m-80) REVERT: A 1239 LYS cc_start: 0.7054 (ptpp) cc_final: 0.6641 (pttm) outliers start: 32 outliers final: 25 residues processed: 110 average time/residue: 0.0947 time to fit residues: 14.5794 Evaluate side-chains 110 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1198 ASN Chi-restraints excluded: chain A residue 1271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 29 optimal weight: 0.0270 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 65 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN A1141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.184902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.157691 restraints weight = 9015.860| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 1.74 r_work: 0.4062 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8475 Z= 0.144 Angle : 0.552 12.100 11428 Z= 0.290 Chirality : 0.039 0.160 1271 Planarity : 0.004 0.048 1488 Dihedral : 5.770 59.557 1117 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.97 % Allowed : 28.36 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.26), residues: 1024 helix: -0.03 (0.23), residues: 493 sheet: -0.01 (0.68), residues: 53 loop : -0.49 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 39 TYR 0.019 0.002 TYR A 312 PHE 0.029 0.002 PHE A 42 TRP 0.019 0.003 TRP A 881 HIS 0.003 0.001 HIS A1109 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8475) covalent geometry : angle 0.55204 (11428) hydrogen bonds : bond 0.03774 ( 389) hydrogen bonds : angle 5.14668 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6701 (tttm) REVERT: A 478 TYR cc_start: 0.6922 (p90) cc_final: 0.5639 (p90) REVERT: A 537 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6584 (t0) REVERT: A 607 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5590 (ttp-170) REVERT: A 830 SER cc_start: 0.7556 (OUTLIER) cc_final: 0.7298 (p) REVERT: A 1019 SER cc_start: 0.6117 (OUTLIER) cc_final: 0.5873 (p) REVERT: A 1077 TYR cc_start: 0.6344 (m-80) cc_final: 0.5959 (m-80) REVERT: A 1239 LYS cc_start: 0.7090 (ptpp) cc_final: 0.6706 (pttm) outliers start: 37 outliers final: 25 residues processed: 116 average time/residue: 0.0935 time to fit residues: 15.2102 Evaluate side-chains 114 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1198 ASN Chi-restraints excluded: chain A residue 1271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.0370 chunk 31 optimal weight: 0.0010 chunk 95 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.184226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.157021 restraints weight = 9004.148| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 1.74 r_work: 0.4069 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8475 Z= 0.151 Angle : 0.557 8.884 11428 Z= 0.296 Chirality : 0.039 0.162 1271 Planarity : 0.004 0.045 1488 Dihedral : 5.776 58.918 1117 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.54 % Allowed : 28.68 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.48 (0.26), residues: 1024 helix: -0.07 (0.23), residues: 493 sheet: -0.03 (0.68), residues: 53 loop : -0.48 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 39 TYR 0.019 0.002 TYR A 312 PHE 0.029 0.002 PHE A 42 TRP 0.018 0.003 TRP A 881 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8475) covalent geometry : angle 0.55744 (11428) hydrogen bonds : bond 0.03837 ( 389) hydrogen bonds : angle 5.19155 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3092.60 seconds wall clock time: 53 minutes 50.31 seconds (3230.31 seconds total)