Starting phenix.real_space_refine on Mon Jun 9 16:17:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qfq_13947/06_2025/7qfq_13947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qfq_13947/06_2025/7qfq_13947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qfq_13947/06_2025/7qfq_13947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qfq_13947/06_2025/7qfq_13947.map" model { file = "/net/cci-nas-00/data/ceres_data/7qfq_13947/06_2025/7qfq_13947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qfq_13947/06_2025/7qfq_13947.cif" } resolution = 3.6 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= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 6878 2.51 5 N 1714 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10659 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1291, 10659 Classifications: {'peptide': 1291} Link IDs: {'PTRANS': 40, 'TRANS': 1250} Time building chain proxies: 6.28, per 1000 atoms: 0.59 Number of scatterers: 10659 At special positions: 0 Unit cell: (79.57, 128.62, 164.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 2032 8.00 N 1714 7.00 C 6878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 446 " distance=2.04 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: 2.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 18 sheets defined 32.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 81 through 102 removed outlier: 4.414A pdb=" N LYS A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.776A pdb=" N HIS A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.898A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.700A pdb=" N ILE A 280 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 306 Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 409 through 412 removed outlier: 3.619A pdb=" N GLN A 412 " --> pdb=" O TYR A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 412' Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.719A pdb=" N ASN A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 418' Processing helix chain 'A' and resid 459 through 463 removed outlier: 3.743A pdb=" N PHE A 463 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.875A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 589 through 606 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 638 through 647 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 677 through 741 removed outlier: 4.640A pdb=" N ASN A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR A 741 " --> pdb=" O ARG A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 removed outlier: 3.947A pdb=" N LYS A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 787 removed outlier: 4.363A pdb=" N ILE A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 813 removed outlier: 3.904A pdb=" N ALA A 791 " --> pdb=" O MET A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 821 through 831 Processing helix chain 'A' and resid 839 through 844 removed outlier: 4.236A pdb=" N TYR A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 859 removed outlier: 3.702A pdb=" N ILE A 850 " --> pdb=" O ASP A 846 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 947 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1263 through 1270 removed outlier: 4.455A pdb=" N VAL A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 22 removed outlier: 7.013A pdb=" N ILE A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP A 44 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 141 removed outlier: 3.631A pdb=" N THR A 508 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 221 removed outlier: 6.665A pdb=" N VAL A 200 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 202 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 331 through 332 removed outlier: 3.590A pdb=" N VAL A 331 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 446 through 450 removed outlier: 7.219A pdb=" N LYS A 433 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE A 530 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN A 435 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 472 removed outlier: 7.008A pdb=" N GLU A 471 " --> pdb=" O LEU A 667 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 556 removed outlier: 3.758A pdb=" N VAL A 569 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 868 through 870 removed outlier: 4.079A pdb=" N ARG A 869 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 876 " --> pdb=" O ARG A 869 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 884 through 886 Processing sheet with id=AB2, first strand: chain 'A' and resid 899 through 901 removed outlier: 3.735A pdb=" N ALA A1014 " --> pdb=" O THR A1026 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A1026 " --> pdb=" O ALA A1014 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE A1016 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER A1024 " --> pdb=" O ILE A1016 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 899 through 901 Processing sheet with id=AB4, first strand: chain 'A' and resid 982 through 987 removed outlier: 3.617A pdb=" N LYS A 983 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 970 " --> pdb=" O ARG A 967 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 953 " --> pdb=" O ILE A 964 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 966 " --> pdb=" O THR A 951 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR A 951 " --> pdb=" O ILE A 966 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN A 954 " --> pdb=" O ILE A1041 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A1041 " --> pdb=" O ASN A 954 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 3.804A pdb=" N TYR A1109 " --> pdb=" O LEU A1122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1122 " --> pdb=" O TYR A1109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1172 through 1173 Processing sheet with id=AB7, first strand: chain 'A' and resid 1179 through 1181 Processing sheet with id=AB8, first strand: chain 'A' and resid 1208 through 1211 Processing sheet with id=AB9, first strand: chain 'A' and resid 1238 through 1245 removed outlier: 3.677A pdb=" N GLU A1252 " --> pdb=" O GLU A1245 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 993 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: 3.70 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3395 1.35 - 1.47: 2693 1.47 - 1.60: 4745 1.60 - 1.72: 0 1.72 - 1.85: 60 Bond restraints: 10893 Sorted by residual: bond pdb=" N ASN A 873 " pdb=" CA ASN A 873 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.41e+00 bond pdb=" CB CYS A 446 " pdb=" SG CYS A 446 " ideal model delta sigma weight residual 1.808 1.845 -0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" C ILE A 310 " pdb=" O ILE A 310 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.73e-01 bond pdb=" CG PRO A 313 " pdb=" CD PRO A 313 " ideal model delta sigma weight residual 1.503 1.534 -0.031 3.40e-02 8.65e+02 8.47e-01 bond pdb=" CG LEU A 232 " pdb=" CD1 LEU A 232 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.34e-01 ... (remaining 10888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 14451 1.68 - 3.36: 224 3.36 - 5.04: 33 5.04 - 6.72: 6 6.72 - 8.40: 2 Bond angle restraints: 14716 Sorted by residual: angle pdb=" N ILE A1018 " pdb=" CA ILE A1018 " pdb=" C ILE A1018 " ideal model delta sigma weight residual 113.53 108.95 4.58 9.80e-01 1.04e+00 2.19e+01 angle pdb=" N LYS A 418 " pdb=" CA LYS A 418 " pdb=" CB LYS A 418 " ideal model delta sigma weight residual 113.65 108.77 4.88 1.47e+00 4.63e-01 1.10e+01 angle pdb=" C LYS A 675 " pdb=" N ASN A 676 " pdb=" CA ASN A 676 " ideal model delta sigma weight residual 122.46 127.08 -4.62 1.41e+00 5.03e-01 1.07e+01 angle pdb=" CA MET A 956 " pdb=" CB MET A 956 " pdb=" CG MET A 956 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.43e+00 angle pdb=" C MET A1056 " pdb=" N LYS A1057 " pdb=" CA LYS A1057 " ideal model delta sigma weight residual 122.17 117.84 4.33 1.54e+00 4.22e-01 7.90e+00 ... (remaining 14711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5959 17.82 - 35.63: 521 35.63 - 53.45: 75 53.45 - 71.27: 7 71.27 - 89.09: 5 Dihedral angle restraints: 6567 sinusoidal: 2728 harmonic: 3839 Sorted by residual: dihedral pdb=" CA ASN A 417 " pdb=" C ASN A 417 " pdb=" N LYS A 418 " pdb=" CA LYS A 418 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ILE A 932 " pdb=" C ILE A 932 " pdb=" N ARG A 933 " pdb=" CA ARG A 933 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA THR A 707 " pdb=" C THR A 707 " pdb=" N VAL A 708 " pdb=" CA VAL A 708 " ideal model delta harmonic sigma weight residual 180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1214 0.047 - 0.095: 263 0.095 - 0.142: 104 0.142 - 0.189: 3 0.189 - 0.236: 1 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CB ILE A 46 " pdb=" CA ILE A 46 " pdb=" CG1 ILE A 46 " pdb=" CG2 ILE A 46 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CG LEU A1237 " pdb=" CB LEU A1237 " pdb=" CD1 LEU A1237 " pdb=" CD2 LEU A1237 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ASN A 873 " pdb=" N ASN A 873 " pdb=" C ASN A 873 " pdb=" CB ASN A 873 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1582 not shown) Planarity restraints: 1893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 312 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO A 313 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 934 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 935 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 935 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 935 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 223 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.50e+00 pdb=" N PRO A 224 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 224 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 224 " -0.022 5.00e-02 4.00e+02 ... (remaining 1890 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 363 2.72 - 3.27: 10482 3.27 - 3.81: 15569 3.81 - 4.36: 18190 4.36 - 4.90: 31984 Nonbonded interactions: 76588 Sorted by model distance: nonbonded pdb=" OG1 THR A 951 " pdb=" O ILE A 964 " model vdw 2.177 3.040 nonbonded pdb=" OE2 GLU A 253 " pdb=" OG SER A 260 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR A1080 " pdb=" OE2 GLU A1082 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP A 346 " pdb=" NZ LYS A 350 " model vdw 2.262 3.120 nonbonded pdb=" NH2 ARG A 933 " pdb=" OD1 ASN A1000 " model vdw 2.269 3.120 ... (remaining 76583 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.480 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 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 : 0.002 0.037 10894 Z= 0.120 Angle : 0.544 8.396 14718 Z= 0.303 Chirality : 0.044 0.236 1585 Planarity : 0.004 0.078 1893 Dihedral : 12.927 89.086 4098 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.70 (0.24), residues: 1289 helix: 2.15 (0.29), residues: 364 sheet: -0.93 (0.43), residues: 157 loop : -1.79 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 693 HIS 0.001 0.001 HIS A 428 PHE 0.018 0.001 PHE A 923 TYR 0.018 0.001 TYR A 540 ARG 0.005 0.000 ARG A 933 Details of bonding type rmsd hydrogen bonds : bond 0.11396 ( 350) hydrogen bonds : angle 4.88619 ( 993) SS BOND : bond 0.00558 ( 1) SS BOND : angle 3.87442 ( 2) covalent geometry : bond 0.00240 (10893) covalent geometry : angle 0.54250 (14716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.112 Fit side-chains REVERT: A 388 ASP cc_start: 0.7813 (t70) cc_final: 0.7437 (t0) REVERT: A 931 TRP cc_start: 0.8006 (m100) cc_final: 0.7451 (m-10) REVERT: A 1075 TYR cc_start: 0.8003 (t80) cc_final: 0.7542 (t80) REVERT: A 1100 MET cc_start: 0.5734 (tpt) cc_final: 0.5344 (tpt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2232 time to fit residues: 40.1308 Evaluate side-chains 103 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 52 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 766 GLN A1052 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.245461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.197479 restraints weight = 12193.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.194055 restraints weight = 19666.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.196099 restraints weight = 17947.117| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10894 Z= 0.113 Angle : 0.486 5.836 14718 Z= 0.264 Chirality : 0.044 0.189 1585 Planarity : 0.004 0.050 1893 Dihedral : 4.152 21.137 1411 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.01 % Allowed : 6.05 % Favored : 92.94 % 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: -0.70 (0.24), residues: 1289 helix: 2.15 (0.29), residues: 366 sheet: -1.06 (0.42), residues: 167 loop : -1.77 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 693 HIS 0.006 0.001 HIS A 428 PHE 0.011 0.001 PHE A 221 TYR 0.027 0.001 TYR A 741 ARG 0.005 0.000 ARG A 933 Details of bonding type rmsd hydrogen bonds : bond 0.05167 ( 350) hydrogen bonds : angle 4.37710 ( 993) SS BOND : bond 0.00216 ( 1) SS BOND : angle 2.85189 ( 2) covalent geometry : bond 0.00253 (10893) covalent geometry : angle 0.48515 (14716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.120 Fit side-chains REVERT: A 122 ARG cc_start: 0.6388 (ptt-90) cc_final: 0.5800 (ptt180) REVERT: A 388 ASP cc_start: 0.7268 (t70) cc_final: 0.6960 (t0) REVERT: A 852 MET cc_start: 0.2903 (tpt) cc_final: 0.1022 (ptt) REVERT: A 873 ASN cc_start: 0.6933 (m-40) cc_final: 0.6530 (p0) REVERT: A 1075 TYR cc_start: 0.8062 (t80) cc_final: 0.7529 (t80) REVERT: A 1099 TYR cc_start: 0.7140 (m-80) cc_final: 0.6840 (m-10) REVERT: A 1100 MET cc_start: 0.5957 (tpt) cc_final: 0.5359 (tpt) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 0.2272 time to fit residues: 38.0828 Evaluate side-chains 109 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.0570 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN A 507 ASN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.244493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.196186 restraints weight = 12231.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.191627 restraints weight = 19550.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.194619 restraints weight = 16275.069| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10894 Z= 0.110 Angle : 0.464 5.130 14718 Z= 0.253 Chirality : 0.043 0.166 1585 Planarity : 0.003 0.038 1893 Dihedral : 4.091 21.628 1411 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.43 % Allowed : 8.74 % Favored : 89.83 % 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: -0.65 (0.24), residues: 1289 helix: 2.23 (0.29), residues: 362 sheet: -1.12 (0.42), residues: 168 loop : -1.71 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 693 HIS 0.003 0.001 HIS A 428 PHE 0.013 0.001 PHE A 221 TYR 0.011 0.001 TYR A 540 ARG 0.003 0.000 ARG A 933 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 350) hydrogen bonds : angle 4.23195 ( 993) SS BOND : bond 0.00193 ( 1) SS BOND : angle 2.32341 ( 2) covalent geometry : bond 0.00251 (10893) covalent geometry : angle 0.46359 (14716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.209 Fit side-chains REVERT: A 172 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 350 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7572 (mtmm) REVERT: A 388 ASP cc_start: 0.7265 (t70) cc_final: 0.6963 (t0) REVERT: A 852 MET cc_start: 0.2650 (tpt) cc_final: 0.1228 (ptt) REVERT: A 873 ASN cc_start: 0.6957 (m-40) cc_final: 0.6548 (p0) REVERT: A 1075 TYR cc_start: 0.8012 (t80) cc_final: 0.7539 (t80) REVERT: A 1100 MET cc_start: 0.6119 (tpt) cc_final: 0.5392 (tpt) outliers start: 17 outliers final: 12 residues processed: 115 average time/residue: 0.2297 time to fit residues: 38.6338 Evaluate side-chains 109 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 766 GLN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.242916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.194505 restraints weight = 12148.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.191648 restraints weight = 18366.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.194201 restraints weight = 15961.309| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10894 Z= 0.124 Angle : 0.474 5.487 14718 Z= 0.258 Chirality : 0.044 0.153 1585 Planarity : 0.004 0.082 1893 Dihedral : 4.114 21.304 1411 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.51 % Allowed : 11.09 % Favored : 87.39 % 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: -0.73 (0.24), residues: 1289 helix: 2.18 (0.29), residues: 362 sheet: -1.34 (0.40), residues: 180 loop : -1.72 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 693 HIS 0.009 0.001 HIS A 428 PHE 0.018 0.001 PHE A1004 TYR 0.015 0.001 TYR A 421 ARG 0.009 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.05408 ( 350) hydrogen bonds : angle 4.21776 ( 993) SS BOND : bond 0.00161 ( 1) SS BOND : angle 1.87956 ( 2) covalent geometry : bond 0.00290 (10893) covalent geometry : angle 0.47351 (14716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 2.859 Fit side-chains REVERT: A 172 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 218 ARG cc_start: 0.7796 (ptt180) cc_final: 0.7548 (ptt-90) REVERT: A 350 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7551 (mtmm) REVERT: A 852 MET cc_start: 0.2926 (tpt) cc_final: 0.1410 (ptt) REVERT: A 873 ASN cc_start: 0.6897 (m-40) cc_final: 0.6510 (p0) REVERT: A 1075 TYR cc_start: 0.7997 (t80) cc_final: 0.7558 (t80) REVERT: A 1100 MET cc_start: 0.6222 (tpt) cc_final: 0.5400 (tpt) outliers start: 18 outliers final: 11 residues processed: 109 average time/residue: 0.2780 time to fit residues: 47.7986 Evaluate side-chains 106 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.240831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.193211 restraints weight = 12135.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.190740 restraints weight = 20856.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.192573 restraints weight = 17406.347| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10894 Z= 0.146 Angle : 0.507 7.113 14718 Z= 0.274 Chirality : 0.044 0.158 1585 Planarity : 0.004 0.072 1893 Dihedral : 4.198 22.659 1411 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.02 % Allowed : 12.44 % Favored : 85.55 % 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: -0.82 (0.24), residues: 1289 helix: 2.08 (0.29), residues: 362 sheet: -1.25 (0.40), residues: 175 loop : -1.80 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1002 HIS 0.003 0.001 HIS A 428 PHE 0.018 0.001 PHE A1004 TYR 0.023 0.001 TYR A 421 ARG 0.004 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.05833 ( 350) hydrogen bonds : angle 4.30853 ( 993) SS BOND : bond 0.00135 ( 1) SS BOND : angle 2.12642 ( 2) covalent geometry : bond 0.00351 (10893) covalent geometry : angle 0.50690 (14716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.206 Fit side-chains REVERT: A 172 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8114 (p) REVERT: A 218 ARG cc_start: 0.7799 (ptt180) cc_final: 0.7531 (ptt-90) REVERT: A 852 MET cc_start: 0.3054 (tpt) cc_final: 0.1438 (ptt) REVERT: A 873 ASN cc_start: 0.6793 (m-40) cc_final: 0.6284 (p0) REVERT: A 1075 TYR cc_start: 0.7997 (t80) cc_final: 0.7602 (t80) outliers start: 24 outliers final: 16 residues processed: 113 average time/residue: 0.2186 time to fit residues: 36.5305 Evaluate side-chains 104 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.0040 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 766 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.242291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.194166 restraints weight = 12220.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.190608 restraints weight = 20347.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.193222 restraints weight = 17079.639| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10894 Z= 0.118 Angle : 0.472 6.198 14718 Z= 0.255 Chirality : 0.043 0.146 1585 Planarity : 0.004 0.054 1893 Dihedral : 4.095 22.089 1411 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.85 % Allowed : 12.86 % Favored : 85.29 % 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: -0.73 (0.24), residues: 1289 helix: 2.16 (0.29), residues: 362 sheet: -1.14 (0.42), residues: 163 loop : -1.76 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 693 HIS 0.003 0.001 HIS A 428 PHE 0.014 0.001 PHE A1004 TYR 0.020 0.001 TYR A 421 ARG 0.004 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.05482 ( 350) hydrogen bonds : angle 4.22518 ( 993) SS BOND : bond 0.00155 ( 1) SS BOND : angle 1.72744 ( 2) covalent geometry : bond 0.00277 (10893) covalent geometry : angle 0.47188 (14716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.097 Fit side-chains REVERT: A 218 ARG cc_start: 0.7750 (ptt180) cc_final: 0.7500 (ptt-90) REVERT: A 852 MET cc_start: 0.2969 (tpt) cc_final: 0.1421 (ptt) REVERT: A 873 ASN cc_start: 0.6796 (m-40) cc_final: 0.6270 (p0) REVERT: A 1075 TYR cc_start: 0.8004 (t80) cc_final: 0.7643 (t80) REVERT: A 1099 TYR cc_start: 0.7427 (m-80) cc_final: 0.7060 (m-10) outliers start: 22 outliers final: 18 residues processed: 106 average time/residue: 0.2180 time to fit residues: 33.8432 Evaluate side-chains 104 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.236099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.188982 restraints weight = 12220.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.185677 restraints weight = 20651.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.187924 restraints weight = 18028.485| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10894 Z= 0.157 Angle : 0.503 6.536 14718 Z= 0.272 Chirality : 0.044 0.147 1585 Planarity : 0.004 0.049 1893 Dihedral : 4.202 22.643 1411 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.76 % Allowed : 14.54 % Favored : 83.70 % 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: -0.88 (0.24), residues: 1289 helix: 1.99 (0.29), residues: 362 sheet: -1.23 (0.42), residues: 163 loop : -1.83 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1002 HIS 0.003 0.001 HIS A 428 PHE 0.017 0.001 PHE A 221 TYR 0.025 0.001 TYR A 421 ARG 0.004 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.05988 ( 350) hydrogen bonds : angle 4.33637 ( 993) SS BOND : bond 0.00153 ( 1) SS BOND : angle 1.66870 ( 2) covalent geometry : bond 0.00382 (10893) covalent geometry : angle 0.50304 (14716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.596 Fit side-chains REVERT: A 218 ARG cc_start: 0.7769 (ptt180) cc_final: 0.7471 (ptt-90) REVERT: A 852 MET cc_start: 0.3093 (tpt) cc_final: 0.1451 (ptt) REVERT: A 873 ASN cc_start: 0.6757 (m-40) cc_final: 0.6252 (p0) REVERT: A 1075 TYR cc_start: 0.8040 (t80) cc_final: 0.7647 (t80) REVERT: A 1099 TYR cc_start: 0.7450 (m-80) cc_final: 0.7214 (m-10) outliers start: 21 outliers final: 18 residues processed: 109 average time/residue: 0.2860 time to fit residues: 48.1585 Evaluate side-chains 109 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 120 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.232991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.182386 restraints weight = 12099.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.176836 restraints weight = 16854.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.180247 restraints weight = 15385.877| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 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 : 0.005 0.048 10894 Z= 0.202 Angle : 0.563 6.781 14718 Z= 0.307 Chirality : 0.046 0.166 1585 Planarity : 0.004 0.045 1893 Dihedral : 4.431 23.511 1411 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.27 % Allowed : 14.45 % Favored : 83.28 % 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: -1.10 (0.23), residues: 1289 helix: 1.69 (0.28), residues: 364 sheet: -1.39 (0.40), residues: 173 loop : -1.91 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1002 HIS 0.004 0.001 HIS A 428 PHE 0.023 0.002 PHE A1004 TYR 0.028 0.001 TYR A 421 ARG 0.004 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.06744 ( 350) hydrogen bonds : angle 4.53234 ( 993) SS BOND : bond 0.00306 ( 1) SS BOND : angle 2.63119 ( 2) covalent geometry : bond 0.00496 (10893) covalent geometry : angle 0.56232 (14716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 1.252 Fit side-chains REVERT: A 218 ARG cc_start: 0.7657 (ptt180) cc_final: 0.7360 (ptt-90) REVERT: A 852 MET cc_start: 0.3223 (tpt) cc_final: 0.1373 (ptt) REVERT: A 873 ASN cc_start: 0.6956 (m-40) cc_final: 0.6319 (p0) REVERT: A 1058 TYR cc_start: 0.6904 (m-10) cc_final: 0.6636 (m-10) REVERT: A 1075 TYR cc_start: 0.8144 (t80) cc_final: 0.7720 (t80) REVERT: A 1099 TYR cc_start: 0.7489 (m-80) cc_final: 0.7263 (m-10) REVERT: A 1100 MET cc_start: 0.6794 (tpt) cc_final: 0.6142 (tpp) outliers start: 27 outliers final: 19 residues processed: 112 average time/residue: 0.2241 time to fit residues: 37.3215 Evaluate side-chains 108 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 94 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 103 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 86 optimal weight: 0.0040 chunk 110 optimal weight: 0.0980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.238823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.187685 restraints weight = 12185.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.181896 restraints weight = 15037.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.183985 restraints weight = 13126.355| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10894 Z= 0.110 Angle : 0.486 8.854 14718 Z= 0.263 Chirality : 0.043 0.141 1585 Planarity : 0.003 0.046 1893 Dihedral : 4.087 23.897 1411 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.09 % Allowed : 15.71 % Favored : 83.19 % 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: -0.81 (0.24), residues: 1289 helix: 2.08 (0.29), residues: 362 sheet: -1.33 (0.40), residues: 173 loop : -1.76 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 693 HIS 0.002 0.000 HIS A 428 PHE 0.020 0.001 PHE A1004 TYR 0.019 0.001 TYR A 421 ARG 0.005 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 350) hydrogen bonds : angle 4.16121 ( 993) SS BOND : bond 0.00190 ( 1) SS BOND : angle 2.27719 ( 2) covalent geometry : bond 0.00248 (10893) covalent geometry : angle 0.48580 (14716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.079 Fit side-chains REVERT: A 218 ARG cc_start: 0.7800 (ptt180) cc_final: 0.7581 (ptt-90) REVERT: A 478 GLN cc_start: 0.7221 (tp-100) cc_final: 0.6266 (pm20) REVERT: A 852 MET cc_start: 0.2882 (tpt) cc_final: 0.1284 (ptt) REVERT: A 873 ASN cc_start: 0.7212 (m-40) cc_final: 0.6413 (p0) REVERT: A 1058 TYR cc_start: 0.6561 (m-10) cc_final: 0.6344 (m-10) REVERT: A 1075 TYR cc_start: 0.8099 (t80) cc_final: 0.7673 (t80) REVERT: A 1099 TYR cc_start: 0.7278 (m-80) cc_final: 0.7021 (m-10) REVERT: A 1100 MET cc_start: 0.6784 (tpt) cc_final: 0.6199 (tpp) outliers start: 13 outliers final: 12 residues processed: 107 average time/residue: 0.2270 time to fit residues: 35.5975 Evaluate side-chains 106 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1019 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 = 0.4759 r_free = 0.4759 target = 0.241813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.193666 restraints weight = 12302.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.189161 restraints weight = 20523.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.192047 restraints weight = 16244.911| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10894 Z= 0.118 Angle : 0.487 7.414 14718 Z= 0.265 Chirality : 0.043 0.139 1585 Planarity : 0.003 0.047 1893 Dihedral : 4.070 23.566 1411 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.01 % Allowed : 16.05 % Favored : 82.94 % 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: -0.78 (0.24), residues: 1289 helix: 2.11 (0.29), residues: 362 sheet: -1.33 (0.40), residues: 173 loop : -1.74 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 931 HIS 0.002 0.001 HIS A 428 PHE 0.020 0.001 PHE A1004 TYR 0.015 0.001 TYR A 421 ARG 0.005 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.05321 ( 350) hydrogen bonds : angle 4.14662 ( 993) SS BOND : bond 0.00235 ( 1) SS BOND : angle 2.64454 ( 2) covalent geometry : bond 0.00271 (10893) covalent geometry : angle 0.48636 (14716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.308 Fit side-chains REVERT: A 218 ARG cc_start: 0.7815 (ptt180) cc_final: 0.7598 (ptt-90) REVERT: A 478 GLN cc_start: 0.7238 (tp-100) cc_final: 0.6325 (pm20) REVERT: A 852 MET cc_start: 0.2934 (tpt) cc_final: 0.1284 (ptt) REVERT: A 873 ASN cc_start: 0.6924 (m-40) cc_final: 0.6314 (p0) REVERT: A 1058 TYR cc_start: 0.6604 (m-10) cc_final: 0.6350 (m-10) REVERT: A 1075 TYR cc_start: 0.8025 (t80) cc_final: 0.7630 (t80) REVERT: A 1100 MET cc_start: 0.6747 (tpt) cc_final: 0.6147 (tpp) outliers start: 12 outliers final: 12 residues processed: 104 average time/residue: 0.2319 time to fit residues: 35.5201 Evaluate side-chains 106 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.240506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.193103 restraints weight = 12264.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.188808 restraints weight = 21022.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.190970 restraints weight = 17622.621| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10894 Z= 0.141 Angle : 0.516 8.345 14718 Z= 0.279 Chirality : 0.044 0.141 1585 Planarity : 0.004 0.050 1893 Dihedral : 4.131 23.633 1411 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.09 % Allowed : 16.55 % Favored : 82.35 % 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: -0.85 (0.24), residues: 1289 helix: 1.96 (0.29), residues: 368 sheet: -1.32 (0.40), residues: 173 loop : -1.78 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1002 HIS 0.003 0.001 HIS A 428 PHE 0.020 0.001 PHE A1004 TYR 0.020 0.001 TYR A 421 ARG 0.005 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.05618 ( 350) hydrogen bonds : angle 4.19929 ( 993) SS BOND : bond 0.00231 ( 1) SS BOND : angle 2.78001 ( 2) covalent geometry : bond 0.00336 (10893) covalent geometry : angle 0.51478 (14716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.12 seconds wall clock time: 65 minutes 13.66 seconds (3913.66 seconds total)