Starting phenix.real_space_refine on Tue Mar 3 22:16:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7op1_13011/03_2026/7op1_13011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7op1_13011/03_2026/7op1_13011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7op1_13011/03_2026/7op1_13011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7op1_13011/03_2026/7op1_13011.map" model { file = "/net/cci-nas-00/data/ceres_data/7op1_13011/03_2026/7op1_13011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7op1_13011/03_2026/7op1_13011.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 53 5.16 5 C 5683 2.51 5 N 1452 2.21 5 O 1550 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8744 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8724 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1043} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' MG': 1, 'ALF': 1, 'SPM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.38, per 1000 atoms: 0.27 Number of scatterers: 8744 At special positions: 0 Unit cell: (86.17, 101.681, 143.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 53 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1550 8.00 N 1452 7.00 C 5683 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: 0.53 Conformation dependent library (CDL) restraints added in 207.6 milliseconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 48.8% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 228 through 241 Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.544A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.895A pdb=" N TYR A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.513A pdb=" N SER A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 373 removed outlier: 4.072A pdb=" N ALA A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 371 " --> pdb=" O HIS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.573A pdb=" N ALA A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 442 removed outlier: 4.151A pdb=" N ALA A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 4.304A pdb=" N LYS A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 569 through 578 Processing helix chain 'A' and resid 588 through 617 removed outlier: 3.787A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 617 " --> pdb=" O ASN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 636 removed outlier: 3.980A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.059A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 654 " --> pdb=" O PHE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 4.374A pdb=" N VAL A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 712 through 717 Processing helix chain 'A' and resid 748 through 760 Processing helix chain 'A' and resid 773 through 784 removed outlier: 3.736A pdb=" N LYS A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 909 through 914 Processing helix chain 'A' and resid 915 through 921 removed outlier: 3.601A pdb=" N VAL A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 921 " --> pdb=" O ASP A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 949 removed outlier: 4.073A pdb=" N VAL A 942 " --> pdb=" O THR A 938 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 944 " --> pdb=" O THR A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 1044 through 1053 removed outlier: 3.810A pdb=" N TRP A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1065 Processing helix chain 'A' and resid 1072 through 1085 Processing helix chain 'A' and resid 1096 through 1098 No H-bonds generated for 'chain 'A' and resid 1096 through 1098' Processing helix chain 'A' and resid 1099 through 1106 Processing helix chain 'A' and resid 1131 through 1169 removed outlier: 4.147A pdb=" N GLU A1135 " --> pdb=" O ARG A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'A' and resid 1178 through 1187 removed outlier: 3.806A pdb=" N LEU A1187 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1195 removed outlier: 3.704A pdb=" N ILE A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1241 removed outlier: 3.540A pdb=" N LEU A1219 " --> pdb=" O SER A1215 " (cutoff:3.500A) Proline residue: A1221 - end of helix removed outlier: 3.642A pdb=" N SER A1224 " --> pdb=" O VAL A1220 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS A1225 " --> pdb=" O PRO A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1281 removed outlier: 3.788A pdb=" N LEU A1266 " --> pdb=" O GLU A1262 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A1275 " --> pdb=" O CYS A1271 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A1276 " --> pdb=" O PHE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1293 Processing helix chain 'A' and resid 1294 through 1314 removed outlier: 4.188A pdb=" N LEU A1298 " --> pdb=" O THR A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1321 Processing helix chain 'A' and resid 1329 through 1353 removed outlier: 3.596A pdb=" N LYS A1333 " --> pdb=" O SER A1329 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A1334 " --> pdb=" O TRP A1330 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A1335 " --> pdb=" O THR A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1371 removed outlier: 3.783A pdb=" N TRP A1357 " --> pdb=" O TYR A1353 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A1371 " --> pdb=" O GLN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1393 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 210 Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.947A pdb=" N TRP A 270 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 293 removed outlier: 4.134A pdb=" N ARG A 292 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 453 Processing sheet with id=AA6, first strand: chain 'A' and resid 472 through 474 removed outlier: 7.241A pdb=" N ASP A 486 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 7.029A pdb=" N ASN A 497 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A 543 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 661 through 662 removed outlier: 3.639A pdb=" N PHE A1123 " --> pdb=" O GLY A1109 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A1108 " --> pdb=" O CYS A1090 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 676 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N CYS A1093 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 691 through 697 removed outlier: 7.211A pdb=" N ILE A 930 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 695 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE A 928 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 697 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N VAL A 926 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N PHE A 925 " --> pdb=" O THR A 900 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 900 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 927 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 894 " --> pdb=" O PHE A 931 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER A 846 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ALA A 835 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 848 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL A 830 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 793 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 764 through 766 Processing sheet with id=AB2, first strand: chain 'A' and resid 955 through 956 removed outlier: 6.649A pdb=" N MET A 955 " --> pdb=" O TYR A1068 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 981 through 985 410 hydrogen bonds defined for protein. 1194 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: 1.33 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2717 1.34 - 1.46: 1444 1.46 - 1.57: 4714 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 8956 Sorted by residual: bond pdb=" F1 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.684 1.783 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" F3 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" F2 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" F4 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" CG GLN A 653 " pdb=" CD GLN A 653 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.12e+00 ... (remaining 8951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.21: 12153 14.21 - 28.41: 4 28.41 - 42.62: 0 42.62 - 56.83: 0 56.83 - 71.04: 2 Bond angle restraints: 12159 Sorted by residual: angle pdb=" F1 ALF A1402 " pdb="AL ALF A1402 " pdb=" F2 ALF A1402 " ideal model delta sigma weight residual 108.68 179.72 -71.04 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF A1402 " pdb="AL ALF A1402 " pdb=" F4 ALF A1402 " ideal model delta sigma weight residual 109.63 179.59 -69.96 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F2 ALF A1402 " pdb="AL ALF A1402 " pdb=" F3 ALF A1402 " ideal model delta sigma weight residual 109.59 89.03 20.56 3.00e+00 1.11e-01 4.70e+01 angle pdb=" F1 ALF A1402 " pdb="AL ALF A1402 " pdb=" F4 ALF A1402 " ideal model delta sigma weight residual 109.02 89.10 19.92 3.00e+00 1.11e-01 4.41e+01 angle pdb=" F2 ALF A1402 " pdb="AL ALF A1402 " pdb=" F4 ALF A1402 " ideal model delta sigma weight residual 110.21 90.77 19.44 3.00e+00 1.11e-01 4.20e+01 ... (remaining 12154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 4766 17.45 - 34.89: 463 34.89 - 52.34: 68 52.34 - 69.78: 10 69.78 - 87.23: 6 Dihedral angle restraints: 5313 sinusoidal: 2103 harmonic: 3210 Sorted by residual: dihedral pdb=" CA TYR A 327 " pdb=" C TYR A 327 " pdb=" N TYR A 328 " pdb=" CA TYR A 328 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TYR A 413 " pdb=" C TYR A 413 " pdb=" N TYR A 414 " pdb=" CA TYR A 414 " ideal model delta harmonic sigma weight residual -180.00 -162.26 -17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP A 347 " pdb=" C ASP A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 768 0.029 - 0.059: 403 0.059 - 0.088: 120 0.088 - 0.117: 76 0.117 - 0.147: 20 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA PRO A 348 " pdb=" N PRO A 348 " pdb=" C PRO A 348 " pdb=" CB PRO A 348 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA VAL A 580 " pdb=" N VAL A 580 " pdb=" C VAL A 580 " pdb=" CB VAL A 580 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 495 " pdb=" N ILE A 495 " pdb=" C ILE A 495 " pdb=" CB ILE A 495 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1384 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 347 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" CG ASP A 347 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP A 347 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 347 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 982 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 983 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 983 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 983 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 877 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 878 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 878 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 878 " 0.026 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 34 2.46 - 3.07: 5754 3.07 - 3.68: 12276 3.68 - 4.29: 17574 4.29 - 4.90: 30019 Nonbonded interactions: 65657 Sorted by model distance: nonbonded pdb="MG MG A1401 " pdb=" F3 ALF A1402 " model vdw 1.848 2.120 nonbonded pdb="MG MG A1401 " pdb=" F2 ALF A1402 " model vdw 1.971 2.120 nonbonded pdb=" OD2 ASP A 680 " pdb=" F2 ALF A1402 " model vdw 2.069 2.990 nonbonded pdb=" OD2 ASP A 680 " pdb="MG MG A1401 " model vdw 2.081 2.170 nonbonded pdb=" OG SER A1290 " pdb=" OE1 GLU A1293 " model vdw 2.135 3.040 ... (remaining 65652 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.990 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 0.099 8956 Z= 0.196 Angle : 1.157 71.036 12159 Z= 0.482 Chirality : 0.043 0.147 1387 Planarity : 0.004 0.048 1516 Dihedral : 13.672 87.230 3235 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.26), residues: 1082 helix: 0.90 (0.24), residues: 485 sheet: -1.18 (0.51), residues: 114 loop : -1.71 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 204 TYR 0.024 0.002 TYR A 412 PHE 0.025 0.001 PHE A1180 TRP 0.018 0.002 TRP A 270 HIS 0.004 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8956) covalent geometry : angle 1.15748 (12159) hydrogen bonds : bond 0.15222 ( 406) hydrogen bonds : angle 6.30243 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.322 Fit side-chains REVERT: A 1365 MET cc_start: 0.7292 (mmt) cc_final: 0.7041 (mmp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0796 time to fit residues: 10.1873 Evaluate side-chains 69 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.155383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.120677 restraints weight = 11540.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118181 restraints weight = 15181.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119073 restraints weight = 16341.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119255 restraints weight = 12008.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118925 restraints weight = 12529.807| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8956 Z= 0.135 Angle : 0.541 6.292 12159 Z= 0.288 Chirality : 0.042 0.154 1387 Planarity : 0.004 0.040 1516 Dihedral : 5.697 59.615 1206 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.63 % Allowed : 6.36 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.26), residues: 1082 helix: 1.22 (0.24), residues: 507 sheet: -0.79 (0.49), residues: 123 loop : -1.57 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.021 0.001 TYR A 412 PHE 0.017 0.001 PHE A1180 TRP 0.013 0.001 TRP A 270 HIS 0.002 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8956) covalent geometry : angle 0.54080 (12159) hydrogen bonds : bond 0.05041 ( 406) hydrogen bonds : angle 4.48751 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.249 Fit side-chains REVERT: A 251 TYR cc_start: 0.8204 (m-80) cc_final: 0.7874 (m-10) REVERT: A 611 LEU cc_start: 0.8141 (tp) cc_final: 0.7799 (tp) REVERT: A 780 PHE cc_start: 0.8095 (t80) cc_final: 0.7885 (t80) REVERT: A 1095 ASP cc_start: 0.8349 (p0) cc_final: 0.8060 (p0) REVERT: A 1365 MET cc_start: 0.7118 (mmt) cc_final: 0.6864 (mmp) outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.0813 time to fit residues: 9.7090 Evaluate side-chains 74 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 1170 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 72 optimal weight: 0.0470 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117731 restraints weight = 11519.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.115711 restraints weight = 19020.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116477 restraints weight = 17684.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115560 restraints weight = 14300.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116028 restraints weight = 12575.375| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8956 Z= 0.167 Angle : 0.544 5.949 12159 Z= 0.289 Chirality : 0.042 0.147 1387 Planarity : 0.004 0.039 1516 Dihedral : 5.635 58.485 1206 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.83 % Allowed : 9.18 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.26), residues: 1082 helix: 1.24 (0.24), residues: 511 sheet: -0.62 (0.49), residues: 124 loop : -1.51 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 204 TYR 0.022 0.001 TYR A 412 PHE 0.017 0.001 PHE A1180 TRP 0.013 0.001 TRP A 270 HIS 0.003 0.001 HIS A1201 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8956) covalent geometry : angle 0.54406 (12159) hydrogen bonds : bond 0.05361 ( 406) hydrogen bonds : angle 4.31769 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.323 Fit side-chains REVERT: A 611 LEU cc_start: 0.8252 (tp) cc_final: 0.7849 (tp) REVERT: A 1095 ASP cc_start: 0.8370 (p0) cc_final: 0.8131 (p0) REVERT: A 1365 MET cc_start: 0.7104 (mmt) cc_final: 0.6832 (mmp) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.0878 time to fit residues: 10.1870 Evaluate side-chains 73 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1170 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.0370 chunk 87 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121166 restraints weight = 11730.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118028 restraints weight = 17302.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119399 restraints weight = 16806.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.119073 restraints weight = 13242.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119260 restraints weight = 12071.490| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8956 Z= 0.126 Angle : 0.507 5.953 12159 Z= 0.267 Chirality : 0.041 0.152 1387 Planarity : 0.004 0.040 1516 Dihedral : 5.405 59.191 1206 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.46 % Allowed : 10.22 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.27), residues: 1082 helix: 1.45 (0.24), residues: 510 sheet: -0.63 (0.47), residues: 135 loop : -1.38 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.017 0.001 TYR A 412 PHE 0.011 0.001 PHE A1180 TRP 0.012 0.001 TRP A 270 HIS 0.003 0.001 HIS A1052 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8956) covalent geometry : angle 0.50668 (12159) hydrogen bonds : bond 0.04703 ( 406) hydrogen bonds : angle 4.16835 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.310 Fit side-chains REVERT: A 611 LEU cc_start: 0.8192 (tp) cc_final: 0.7868 (tp) REVERT: A 934 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8683 (ttmm) REVERT: A 1095 ASP cc_start: 0.8327 (p0) cc_final: 0.8094 (p0) REVERT: A 1098 ASN cc_start: 0.8224 (t0) cc_final: 0.7962 (t0) REVERT: A 1293 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: A 1365 MET cc_start: 0.7031 (mmt) cc_final: 0.6783 (mmp) outliers start: 14 outliers final: 6 residues processed: 87 average time/residue: 0.0822 time to fit residues: 10.4533 Evaluate side-chains 76 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1293 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117543 restraints weight = 11794.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117551 restraints weight = 14116.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118901 restraints weight = 11515.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118997 restraints weight = 8469.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119310 restraints weight = 7564.429| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8956 Z= 0.248 Angle : 0.615 6.678 12159 Z= 0.325 Chirality : 0.045 0.158 1387 Planarity : 0.004 0.042 1516 Dihedral : 5.792 59.222 1206 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.88 % Allowed : 12.20 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.26), residues: 1082 helix: 1.12 (0.24), residues: 511 sheet: -0.64 (0.47), residues: 136 loop : -1.38 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 204 TYR 0.023 0.002 TYR A 412 PHE 0.017 0.002 PHE A1180 TRP 0.013 0.001 TRP A 270 HIS 0.004 0.001 HIS A1201 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 8956) covalent geometry : angle 0.61516 (12159) hydrogen bonds : bond 0.06338 ( 406) hydrogen bonds : angle 4.45594 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.341 Fit side-chains REVERT: A 360 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8326 (pp) REVERT: A 711 ASN cc_start: 0.7523 (m110) cc_final: 0.6864 (p0) REVERT: A 934 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8757 (ttmm) REVERT: A 1293 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: A 1365 MET cc_start: 0.7123 (mmt) cc_final: 0.6826 (mmp) outliers start: 18 outliers final: 13 residues processed: 86 average time/residue: 0.0782 time to fit residues: 9.7461 Evaluate side-chains 85 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1310 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS A 386 GLN A 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121737 restraints weight = 11627.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119246 restraints weight = 16010.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120607 restraints weight = 15292.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120425 restraints weight = 11900.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120296 restraints weight = 12944.364| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8956 Z= 0.107 Angle : 0.501 10.677 12159 Z= 0.261 Chirality : 0.040 0.140 1387 Planarity : 0.004 0.045 1516 Dihedral : 5.208 57.474 1206 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.04 % Allowed : 13.97 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.27), residues: 1082 helix: 1.52 (0.24), residues: 511 sheet: -0.53 (0.44), residues: 150 loop : -1.30 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 204 TYR 0.012 0.001 TYR A 412 PHE 0.011 0.001 PHE A 396 TRP 0.013 0.001 TRP A 407 HIS 0.002 0.001 HIS A1052 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8956) covalent geometry : angle 0.50069 (12159) hydrogen bonds : bond 0.04303 ( 406) hydrogen bonds : angle 4.02624 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.331 Fit side-chains REVERT: A 711 ASN cc_start: 0.7184 (m110) cc_final: 0.6829 (p0) REVERT: A 757 MET cc_start: 0.7661 (ttp) cc_final: 0.7441 (mtp) REVERT: A 1293 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: A 1365 MET cc_start: 0.7087 (mmt) cc_final: 0.6872 (mmp) outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 0.0842 time to fit residues: 10.1172 Evaluate side-chains 77 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1293 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 0.0010 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS A 386 GLN A1352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.165716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124531 restraints weight = 11803.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124803 restraints weight = 10914.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126395 restraints weight = 8474.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126378 restraints weight = 5922.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126360 restraints weight = 6026.806| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8956 Z= 0.101 Angle : 0.479 5.633 12159 Z= 0.251 Chirality : 0.040 0.139 1387 Planarity : 0.004 0.045 1516 Dihedral : 4.892 59.873 1206 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.25 % Allowed : 13.97 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.27), residues: 1082 helix: 1.69 (0.24), residues: 512 sheet: -0.40 (0.44), residues: 150 loop : -1.24 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 438 TYR 0.012 0.001 TYR A 412 PHE 0.012 0.001 PHE A1361 TRP 0.012 0.001 TRP A 270 HIS 0.002 0.000 HIS A1052 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8956) covalent geometry : angle 0.47911 (12159) hydrogen bonds : bond 0.03995 ( 406) hydrogen bonds : angle 3.85964 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.342 Fit side-chains REVERT: A 365 LYS cc_start: 0.8771 (tmtt) cc_final: 0.8553 (tmtt) REVERT: A 471 ASP cc_start: 0.7879 (m-30) cc_final: 0.7575 (m-30) REVERT: A 711 ASN cc_start: 0.7331 (m110) cc_final: 0.6822 (p0) REVERT: A 934 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8731 (ttmm) REVERT: A 1293 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: A 1365 MET cc_start: 0.7056 (mmt) cc_final: 0.6830 (mmp) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.0913 time to fit residues: 10.7497 Evaluate side-chains 82 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1293 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS A 386 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.166146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.125595 restraints weight = 11655.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124942 restraints weight = 14457.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128119 restraints weight = 11584.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127715 restraints weight = 8134.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128278 restraints weight = 7481.504| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8956 Z= 0.103 Angle : 0.477 5.647 12159 Z= 0.250 Chirality : 0.040 0.137 1387 Planarity : 0.003 0.044 1516 Dihedral : 4.744 58.770 1206 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.25 % Allowed : 13.97 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.27), residues: 1082 helix: 1.73 (0.24), residues: 513 sheet: -0.24 (0.43), residues: 156 loop : -1.23 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.011 0.001 TYR A 412 PHE 0.011 0.001 PHE A1361 TRP 0.014 0.001 TRP A 270 HIS 0.002 0.000 HIS A1052 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8956) covalent geometry : angle 0.47747 (12159) hydrogen bonds : bond 0.03958 ( 406) hydrogen bonds : angle 3.82937 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.324 Fit side-chains REVERT: A 365 LYS cc_start: 0.8739 (tmtt) cc_final: 0.8493 (tmtt) REVERT: A 711 ASN cc_start: 0.7267 (m110) cc_final: 0.6863 (p0) REVERT: A 934 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8729 (ttmm) REVERT: A 1293 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: A 1365 MET cc_start: 0.7008 (mmt) cc_final: 0.6784 (mmp) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 0.0823 time to fit residues: 10.0418 Evaluate side-chains 78 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1393 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 95 optimal weight: 0.0970 chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A1098 ASN A1352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122390 restraints weight = 11664.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121671 restraints weight = 11777.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124211 restraints weight = 9602.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124219 restraints weight = 7194.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124119 restraints weight = 6607.524| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8956 Z= 0.142 Angle : 0.522 7.457 12159 Z= 0.271 Chirality : 0.041 0.137 1387 Planarity : 0.004 0.045 1516 Dihedral : 4.899 58.179 1206 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.67 % Allowed : 13.76 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.27), residues: 1082 helix: 1.65 (0.24), residues: 512 sheet: -0.24 (0.45), residues: 140 loop : -1.32 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.014 0.001 TYR A1379 PHE 0.014 0.001 PHE A1361 TRP 0.013 0.001 TRP A 270 HIS 0.003 0.001 HIS A1052 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8956) covalent geometry : angle 0.52161 (12159) hydrogen bonds : bond 0.04702 ( 406) hydrogen bonds : angle 3.91583 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.329 Fit side-chains REVERT: A 339 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8764 (m-10) REVERT: A 365 LYS cc_start: 0.8766 (tmtt) cc_final: 0.8516 (tmtt) REVERT: A 711 ASN cc_start: 0.7564 (m110) cc_final: 0.6970 (p0) REVERT: A 1293 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: A 1365 MET cc_start: 0.7041 (mmt) cc_final: 0.6790 (mmp) outliers start: 16 outliers final: 14 residues processed: 84 average time/residue: 0.0794 time to fit residues: 9.8598 Evaluate side-chains 85 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 TYR Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1393 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 96 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125604 restraints weight = 11674.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124693 restraints weight = 14558.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127949 restraints weight = 11937.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127391 restraints weight = 8571.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127443 restraints weight = 7371.235| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8956 Z= 0.104 Angle : 0.494 8.976 12159 Z= 0.256 Chirality : 0.040 0.138 1387 Planarity : 0.003 0.044 1516 Dihedral : 4.758 59.388 1206 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.36 % Allowed : 14.18 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 1082 helix: 1.77 (0.24), residues: 512 sheet: -0.16 (0.46), residues: 141 loop : -1.25 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 438 TYR 0.011 0.001 TYR A 412 PHE 0.016 0.001 PHE A1361 TRP 0.014 0.001 TRP A 270 HIS 0.003 0.000 HIS A1052 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8956) covalent geometry : angle 0.49421 (12159) hydrogen bonds : bond 0.04124 ( 406) hydrogen bonds : angle 3.78893 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.305 Fit side-chains REVERT: A 386 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7119 (pt0) REVERT: A 711 ASN cc_start: 0.7350 (m110) cc_final: 0.6960 (p0) REVERT: A 934 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8730 (ttmm) REVERT: A 1293 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: A 1365 MET cc_start: 0.6996 (mmt) cc_final: 0.6774 (mmp) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.0910 time to fit residues: 10.6501 Evaluate side-chains 80 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1393 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.0030 chunk 62 optimal weight: 0.0470 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.6094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS A 386 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.161812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120492 restraints weight = 11567.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120003 restraints weight = 14393.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121683 restraints weight = 11866.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121903 restraints weight = 8587.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122073 restraints weight = 8521.319| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8956 Z= 0.179 Angle : 0.550 7.633 12159 Z= 0.287 Chirality : 0.042 0.139 1387 Planarity : 0.004 0.044 1516 Dihedral : 4.999 55.240 1206 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.67 % Allowed : 14.08 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.27), residues: 1082 helix: 1.54 (0.24), residues: 513 sheet: -0.03 (0.45), residues: 145 loop : -1.31 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.016 0.001 TYR A1379 PHE 0.017 0.001 PHE A1361 TRP 0.013 0.001 TRP A 270 HIS 0.003 0.001 HIS A1201 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8956) covalent geometry : angle 0.54961 (12159) hydrogen bonds : bond 0.05223 ( 406) hydrogen bonds : angle 3.99255 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1367.13 seconds wall clock time: 24 minutes 17.75 seconds (1457.75 seconds total)