Starting phenix.real_space_refine on Thu Feb 13 12:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7op1_13011/02_2025/7op1_13011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7op1_13011/02_2025/7op1_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_13011/02_2025/7op1_13011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7op1_13011/02_2025/7op1_13011.map" model { file = "/net/cci-nas-00/data/ceres_data/7op1_13011/02_2025/7op1_13011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7op1_13011/02_2025/7op1_13011.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.80, per 1000 atoms: 0.66 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 3.23 Time building geometry restraints manager: 2.83 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: 2.080 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.770 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- 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= 0.264 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP A 270 HIS 0.004 0.001 HIS A 620 PHE 0.025 0.001 PHE A1180 TYR 0.024 0.002 TYR A 412 ARG 0.005 0.000 ARG A 204 *********************** 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 : 0.937 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: 0.1914 time to fit residues: 24.4077 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 : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.156404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121717 restraints weight = 11437.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119865 restraints weight = 14641.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120880 restraints weight = 14908.684| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0928 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= 0.176 Angle : 0.529 6.246 12159 Z= 0.281 Chirality : 0.041 0.152 1387 Planarity : 0.004 0.040 1516 Dihedral : 5.623 59.396 1206 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.63 % Allowed : 5.84 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1082 helix: 1.28 (0.24), residues: 507 sheet: -0.83 (0.46), residues: 137 loop : -1.55 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 270 HIS 0.002 0.001 HIS A1225 PHE 0.015 0.001 PHE A 277 TYR 0.019 0.001 TYR A 412 ARG 0.002 0.000 ARG A 834 *********************** 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 81 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.980 Fit side-chains REVERT: A 611 LEU cc_start: 0.8142 (tp) cc_final: 0.7871 (tp) REVERT: A 780 PHE cc_start: 0.8037 (t80) cc_final: 0.7831 (t80) REVERT: A 1365 MET cc_start: 0.7123 (mmt) cc_final: 0.6873 (mmp) outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 0.2037 time to fit residues: 23.9868 Evaluate side-chains 75 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.0050 chunk 41 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122824 restraints weight = 11698.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119704 restraints weight = 16364.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121000 restraints weight = 15850.834| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1257 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= 0.163 Angle : 0.491 5.714 12159 Z= 0.261 Chirality : 0.040 0.145 1387 Planarity : 0.004 0.038 1516 Dihedral : 5.321 59.751 1206 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.63 % Allowed : 7.92 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.27), residues: 1082 helix: 1.52 (0.24), residues: 509 sheet: -0.56 (0.46), residues: 137 loop : -1.48 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 270 HIS 0.002 0.001 HIS A1052 PHE 0.012 0.001 PHE A1180 TYR 0.018 0.001 TYR A 412 ARG 0.002 0.000 ARG A 204 *********************** 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 82 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.958 Fit side-chains REVERT: A 471 ASP cc_start: 0.7829 (m-30) cc_final: 0.7536 (m-30) REVERT: A 611 LEU cc_start: 0.8097 (tp) cc_final: 0.7817 (tp) REVERT: A 1095 ASP cc_start: 0.8284 (p0) cc_final: 0.8022 (p0) REVERT: A 1098 ASN cc_start: 0.8178 (t0) cc_final: 0.7945 (t0) REVERT: A 1365 MET cc_start: 0.7072 (mmt) cc_final: 0.6806 (mmp) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.1902 time to fit residues: 22.6612 Evaluate side-chains 73 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 569 THR 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 102 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.155878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121738 restraints weight = 11590.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119552 restraints weight = 15620.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120872 restraints weight = 14437.295| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1366 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= 0.205 Angle : 0.511 9.438 12159 Z= 0.266 Chirality : 0.041 0.143 1387 Planarity : 0.004 0.039 1516 Dihedral : 5.245 59.312 1206 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.25 % Allowed : 9.38 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 1082 helix: 1.52 (0.24), residues: 511 sheet: -0.59 (0.45), residues: 148 loop : -1.41 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 270 HIS 0.003 0.001 HIS A1052 PHE 0.013 0.001 PHE A1180 TYR 0.018 0.001 TYR A 412 ARG 0.002 0.000 ARG A 204 *********************** 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 86 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.971 Fit side-chains REVERT: A 471 ASP cc_start: 0.7806 (m-30) cc_final: 0.7425 (m-30) REVERT: A 611 LEU cc_start: 0.8156 (tp) cc_final: 0.7798 (tp) REVERT: A 1095 ASP cc_start: 0.8329 (p0) cc_final: 0.8095 (p0) REVERT: A 1293 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: A 1365 MET cc_start: 0.7012 (mmt) cc_final: 0.6750 (mmp) outliers start: 12 outliers final: 5 residues processed: 83 average time/residue: 0.1903 time to fit residues: 23.3042 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 : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 569 THR 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 40 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 63 optimal weight: 40.0000 chunk 10 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 A1352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.103153 restraints weight = 11877.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.101899 restraints weight = 18309.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103208 restraints weight = 16106.611| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1452 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= 0.231 Angle : 0.524 9.881 12159 Z= 0.273 Chirality : 0.042 0.141 1387 Planarity : 0.004 0.040 1516 Dihedral : 5.230 59.557 1206 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.77 % Allowed : 10.53 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.27), residues: 1082 helix: 1.54 (0.24), residues: 510 sheet: -0.58 (0.45), residues: 150 loop : -1.32 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 270 HIS 0.003 0.001 HIS A1052 PHE 0.013 0.001 PHE A1180 TYR 0.017 0.001 TYR A 412 ARG 0.002 0.000 ARG A 204 *********************** 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 90 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.986 Fit side-chains REVERT: A 365 LYS cc_start: 0.8856 (tmtt) cc_final: 0.8614 (tmtt) REVERT: A 611 LEU cc_start: 0.8135 (tp) cc_final: 0.7774 (tp) REVERT: A 711 ASN cc_start: 0.7309 (m110) cc_final: 0.6755 (p0) REVERT: A 934 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8727 (ttmm) REVERT: A 1071 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8765 (mtt) REVERT: A 1095 ASP cc_start: 0.8305 (p0) cc_final: 0.8092 (p0) REVERT: A 1098 ASN cc_start: 0.8229 (t0) cc_final: 0.7994 (t0) REVERT: A 1293 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: A 1365 MET cc_start: 0.7110 (mmt) cc_final: 0.6854 (mmp) outliers start: 17 outliers final: 8 residues processed: 84 average time/residue: 0.1984 time to fit residues: 24.3903 Evaluate side-chains 83 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 360 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 1071 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 1293 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 30 optimal weight: 0.0040 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.5598 ------------------------------------------------------------------------------- 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 A 482 GLN A1352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.115139 restraints weight = 11672.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112851 restraints weight = 20600.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113696 restraints weight = 19043.038| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 8956 Z= 0.439 Angle : 0.617 6.558 12159 Z= 0.325 Chirality : 0.045 0.143 1387 Planarity : 0.004 0.045 1516 Dihedral : 5.694 59.943 1206 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.56 % Allowed : 11.99 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.27), residues: 1082 helix: 1.20 (0.24), residues: 511 sheet: -0.58 (0.47), residues: 136 loop : -1.34 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 270 HIS 0.004 0.001 HIS A1201 PHE 0.018 0.002 PHE A1180 TYR 0.022 0.002 TYR A 412 ARG 0.003 0.000 ARG A 204 *********************** 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 85 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.758 Fit side-chains REVERT: A 711 ASN cc_start: 0.7386 (m110) cc_final: 0.6869 (p0) REVERT: A 1293 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7242 (mp0) outliers start: 15 outliers final: 11 residues processed: 81 average time/residue: 0.2102 time to fit residues: 25.4037 Evaluate side-chains 79 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 A1352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.152455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112274 restraints weight = 11783.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109904 restraints weight = 17124.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112082 restraints weight = 14453.613| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1571 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= 0.158 Angle : 0.500 6.932 12159 Z= 0.262 Chirality : 0.041 0.140 1387 Planarity : 0.004 0.049 1516 Dihedral : 5.168 56.792 1206 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.15 % Allowed : 12.72 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1082 helix: 1.57 (0.24), residues: 510 sheet: -0.47 (0.44), residues: 150 loop : -1.27 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 270 HIS 0.003 0.001 HIS A1052 PHE 0.014 0.001 PHE A 780 TYR 0.013 0.001 TYR A 412 ARG 0.002 0.000 ARG A 292 *********************** 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: 11 poor density : 76 time to evaluate : 0.931 Fit side-chains REVERT: A 339 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8749 (m-10) REVERT: A 365 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8595 (tmtt) REVERT: A 711 ASN cc_start: 0.7320 (m110) cc_final: 0.6799 (p0) REVERT: A 934 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8732 (ttmm) REVERT: A 1095 ASP cc_start: 0.8261 (p0) cc_final: 0.8039 (p0) REVERT: A 1293 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: A 1365 MET cc_start: 0.7261 (mmp) cc_final: 0.6959 (mmt) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.1956 time to fit residues: 23.8115 Evaluate side-chains 82 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 458 PHE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 569 THR 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 108 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 103 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.164872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123910 restraints weight = 11821.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122803 restraints weight = 12865.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124108 restraints weight = 11593.071| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8956 Z= 0.169 Angle : 0.490 6.120 12159 Z= 0.256 Chirality : 0.040 0.138 1387 Planarity : 0.004 0.047 1516 Dihedral : 4.898 58.409 1206 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.36 % Allowed : 12.83 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 1082 helix: 1.66 (0.24), residues: 512 sheet: -0.28 (0.45), residues: 150 loop : -1.24 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 270 HIS 0.002 0.001 HIS A1052 PHE 0.013 0.001 PHE A1361 TYR 0.013 0.001 TYR A 412 ARG 0.002 0.000 ARG A 438 *********************** 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 90 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.830 Fit side-chains REVERT: A 339 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8685 (m-10) REVERT: A 365 LYS cc_start: 0.8798 (tmtt) cc_final: 0.8571 (tmtt) REVERT: A 711 ASN cc_start: 0.7290 (m110) cc_final: 0.6822 (p0) REVERT: A 934 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8743 (ttmm) REVERT: A 1095 ASP cc_start: 0.8225 (p0) cc_final: 0.7995 (p0) REVERT: A 1293 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: A 1365 MET cc_start: 0.7259 (mmp) cc_final: 0.6925 (mmt) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.2068 time to fit residues: 25.4640 Evaluate side-chains 83 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 511 THR 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 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 4 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.0270 chunk 71 optimal weight: 0.0010 chunk 25 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 GLN A1352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125938 restraints weight = 11747.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126155 restraints weight = 13238.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128119 restraints weight = 10925.686| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1828 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= 0.151 Angle : 0.487 6.729 12159 Z= 0.252 Chirality : 0.040 0.141 1387 Planarity : 0.004 0.046 1516 Dihedral : 4.764 59.739 1206 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.46 % Allowed : 12.72 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1082 helix: 1.74 (0.24), residues: 513 sheet: -0.21 (0.45), residues: 151 loop : -1.20 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 270 HIS 0.002 0.000 HIS A1052 PHE 0.013 0.001 PHE A1361 TYR 0.011 0.001 TYR A 412 ARG 0.003 0.000 ARG A 292 *********************** 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 89 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.001 Fit side-chains REVERT: A 365 LYS cc_start: 0.8752 (tmtt) cc_final: 0.8517 (tmtt) REVERT: A 711 ASN cc_start: 0.7309 (m110) cc_final: 0.6955 (p0) REVERT: A 757 MET cc_start: 0.7620 (ttp) cc_final: 0.7385 (mtp) REVERT: A 934 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8728 (ttmm) REVERT: A 1095 ASP cc_start: 0.8197 (p0) cc_final: 0.7966 (p0) REVERT: A 1293 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7071 (mp0) outliers start: 14 outliers final: 8 residues processed: 87 average time/residue: 0.1941 time to fit residues: 24.7196 Evaluate side-chains 80 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 511 THR 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 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 26 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125476 restraints weight = 11722.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124571 restraints weight = 13546.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126745 restraints weight = 11959.281| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1886 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= 0.163 Angle : 0.500 7.755 12159 Z= 0.258 Chirality : 0.040 0.140 1387 Planarity : 0.004 0.046 1516 Dihedral : 4.686 59.962 1206 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.04 % Allowed : 13.66 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.27), residues: 1082 helix: 1.80 (0.24), residues: 512 sheet: -0.06 (0.46), residues: 141 loop : -1.24 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 270 HIS 0.003 0.000 HIS A1052 PHE 0.014 0.001 PHE A1361 TYR 0.011 0.001 TYR A 412 ARG 0.002 0.000 ARG A1288 ********************** 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 83 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.943 Fit side-chains REVERT: A 365 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8392 (tmtt) REVERT: A 711 ASN cc_start: 0.7342 (m110) cc_final: 0.6958 (p0) REVERT: A 757 MET cc_start: 0.7688 (ttp) cc_final: 0.7465 (mtp) REVERT: A 934 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8730 (ttmm) REVERT: A 1095 ASP cc_start: 0.8250 (p0) cc_final: 0.8027 (p0) REVERT: A 1293 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: A 1365 MET cc_start: 0.7170 (mmp) cc_final: 0.6894 (mmt) outliers start: 10 outliers final: 8 residues processed: 81 average time/residue: 0.2028 time to fit residues: 24.0099 Evaluate side-chains 81 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 511 THR 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 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 50 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 54 optimal weight: 0.0470 chunk 83 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 58 optimal weight: 0.0370 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124703 restraints weight = 11730.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124593 restraints weight = 12775.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126821 restraints weight = 10262.453| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1947 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= 0.168 Angle : 0.496 7.424 12159 Z= 0.256 Chirality : 0.040 0.146 1387 Planarity : 0.004 0.044 1516 Dihedral : 4.598 58.579 1206 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.04 % Allowed : 13.76 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1082 helix: 1.82 (0.24), residues: 511 sheet: 0.01 (0.46), residues: 141 loop : -1.17 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 270 HIS 0.003 0.000 HIS A1052 PHE 0.015 0.001 PHE A1361 TYR 0.011 0.001 TYR A 412 ARG 0.003 0.000 ARG A 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2612.41 seconds wall clock time: 47 minutes 43.22 seconds (2863.22 seconds total)