Starting phenix.real_space_refine on Fri Mar 15 05:07:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/03_2024/7qfq_13947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/03_2024/7qfq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/03_2024/7qfq_13947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/03_2024/7qfq_13947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/03_2024/7qfq_13947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/03_2024/7qfq_13947.pdb" } 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 Residue "A GLU 23": "OE1" <-> "OE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 552": "OD1" <-> "OD2" Residue "A TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1086": "OD1" <-> "OD2" Residue "A TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.81, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 3.49 Conformation dependent library (CDL) restraints added in 1.8 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: 1.42 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: 3.55 Time building geometry restraints manager: 3.91 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: 99.73 - 106.60: 207 106.60 - 113.46: 5726 113.46 - 120.33: 4036 120.33 - 127.20: 4681 127.20 - 134.07: 66 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 2.440 nonbonded pdb=" OE2 GLU A 253 " pdb=" OG SER A 260 " model vdw 2.261 2.440 nonbonded pdb=" OH TYR A1080 " pdb=" OE2 GLU A1082 " model vdw 2.261 2.440 nonbonded pdb=" OD1 ASP A 346 " pdb=" NZ LYS A 350 " model vdw 2.262 2.520 nonbonded pdb=" NH2 ARG A 933 " pdb=" OD1 ASN A1000 " model vdw 2.269 2.520 ... (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: 1.820 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: 6.060 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.820 Find NCS groups from input model: 0.260 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- 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 10893 Z= 0.153 Angle : 0.542 8.396 14716 Z= 0.302 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.191 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: 0.2253 time to fit residues: 40.5816 Evaluate side-chains 103 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 117 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 709 ASN A 766 GLN A1052 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10893 Z= 0.270 Angle : 0.539 5.812 14716 Z= 0.292 Chirality : 0.046 0.226 1585 Planarity : 0.004 0.051 1893 Dihedral : 4.411 23.168 1411 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.18 % Allowed : 7.98 % Favored : 90.84 % 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 (0.23), residues: 1289 helix: 1.93 (0.29), residues: 361 sheet: -0.76 (0.44), residues: 152 loop : -1.91 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 693 HIS 0.013 0.003 HIS A 180 PHE 0.019 0.002 PHE A 221 TYR 0.026 0.001 TYR A 741 ARG 0.004 0.000 ARG A 933 *********************** 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 119 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.212 Fit side-chains REVERT: A 122 ARG cc_start: 0.6419 (ptt-90) cc_final: 0.5827 (ptt180) REVERT: A 388 ASP cc_start: 0.7683 (t70) cc_final: 0.7473 (t0) REVERT: A 507 ASN cc_start: 0.6871 (OUTLIER) cc_final: 0.6654 (p0) REVERT: A 873 ASN cc_start: 0.7277 (m-40) cc_final: 0.6819 (p0) REVERT: A 931 TRP cc_start: 0.7793 (m100) cc_final: 0.7321 (m-10) REVERT: A 1075 TYR cc_start: 0.8146 (t80) cc_final: 0.7484 (t80) REVERT: A 1100 MET cc_start: 0.6105 (tpt) cc_final: 0.5432 (tpt) outliers start: 14 outliers final: 9 residues processed: 111 average time/residue: 0.2179 time to fit residues: 35.7593 Evaluate side-chains 107 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 300 VAL 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 708 VAL 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 65 optimal weight: 0.0770 chunk 36 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 A1052 GLN A1070 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10893 Z= 0.167 Angle : 0.473 6.564 14716 Z= 0.257 Chirality : 0.043 0.154 1585 Planarity : 0.004 0.046 1893 Dihedral : 4.225 24.180 1411 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.26 % Allowed : 10.42 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.24), residues: 1289 helix: 2.13 (0.29), residues: 361 sheet: -0.75 (0.45), residues: 153 loop : -1.83 (0.21), residues: 775 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 0.014 0.001 TYR A 421 ARG 0.002 0.000 ARG A 933 *********************** 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 119 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.213 Fit side-chains REVERT: A 172 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8088 (p) REVERT: A 388 ASP cc_start: 0.7539 (t70) cc_final: 0.7312 (t0) REVERT: A 852 MET cc_start: 0.2959 (tpt) cc_final: 0.1670 (ptt) REVERT: A 873 ASN cc_start: 0.7251 (m-40) cc_final: 0.6784 (p0) REVERT: A 1075 TYR cc_start: 0.8142 (t80) cc_final: 0.7521 (t80) REVERT: A 1100 MET cc_start: 0.6110 (tpt) cc_final: 0.5387 (tpt) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.2180 time to fit residues: 36.3121 Evaluate side-chains 110 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 174 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 402 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10893 Z= 0.160 Angle : 0.455 5.424 14716 Z= 0.247 Chirality : 0.043 0.165 1585 Planarity : 0.003 0.039 1893 Dihedral : 4.109 22.746 1411 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.76 % Allowed : 12.10 % 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: -0.67 (0.24), residues: 1289 helix: 2.21 (0.29), residues: 361 sheet: -0.81 (0.44), residues: 153 loop : -1.80 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 693 HIS 0.002 0.001 HIS A 428 PHE 0.013 0.001 PHE A 559 TYR 0.014 0.001 TYR A 421 ARG 0.002 0.000 ARG A 933 *********************** 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 123 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.235 Fit side-chains REVERT: A 172 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8071 (p) REVERT: A 350 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7611 (mttt) REVERT: A 388 ASP cc_start: 0.7515 (t70) cc_final: 0.7273 (t0) REVERT: A 852 MET cc_start: 0.2798 (tpt) cc_final: 0.1622 (ptt) REVERT: A 873 ASN cc_start: 0.7304 (m-40) cc_final: 0.6699 (p0) REVERT: A 1075 TYR cc_start: 0.8093 (t80) cc_final: 0.7542 (t80) REVERT: A 1100 MET cc_start: 0.6246 (tpt) cc_final: 0.5465 (tpt) outliers start: 21 outliers final: 14 residues processed: 113 average time/residue: 0.2526 time to fit residues: 42.2011 Evaluate side-chains 112 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 67 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 300 VAL 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 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1083 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** A1052 GLN A1070 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10893 Z= 0.364 Angle : 0.589 5.946 14716 Z= 0.319 Chirality : 0.047 0.165 1585 Planarity : 0.004 0.045 1893 Dihedral : 4.595 25.101 1411 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.18 % Allowed : 13.78 % Favored : 84.03 % 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: -1.13 (0.23), residues: 1289 helix: 1.63 (0.28), residues: 364 sheet: -1.20 (0.42), residues: 165 loop : -1.97 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1002 HIS 0.005 0.001 HIS A 428 PHE 0.024 0.002 PHE A 221 TYR 0.034 0.002 TYR A 421 ARG 0.003 0.000 ARG A 689 *********************** 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 127 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 1.265 Fit side-chains REVERT: A 172 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8156 (p) REVERT: A 852 MET cc_start: 0.2883 (tpt) cc_final: 0.1555 (ptt) REVERT: A 873 ASN cc_start: 0.7314 (m-40) cc_final: 0.6742 (p0) REVERT: A 1075 TYR cc_start: 0.8243 (t80) cc_final: 0.7663 (t80) REVERT: A 1100 MET cc_start: 0.6698 (tpt) cc_final: 0.6108 (tpp) outliers start: 26 outliers final: 21 residues processed: 118 average time/residue: 0.1881 time to fit residues: 34.6102 Evaluate side-chains 116 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 67 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL 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 473 ILE 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 707 THR Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1083 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10893 Z= 0.189 Angle : 0.486 6.218 14716 Z= 0.265 Chirality : 0.044 0.152 1585 Planarity : 0.003 0.043 1893 Dihedral : 4.334 24.458 1411 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.27 % Allowed : 14.87 % Favored : 82.86 % 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: 2.00 (0.29), residues: 361 sheet: -0.99 (0.44), residues: 153 loop : -1.89 (0.21), residues: 775 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 0.015 0.001 PHE A1004 TYR 0.024 0.001 TYR A 421 ARG 0.002 0.000 ARG A 933 *********************** 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 127 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.102 Fit side-chains REVERT: A 350 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7735 (mtmt) REVERT: A 852 MET cc_start: 0.2777 (tpt) cc_final: 0.1482 (ptt) REVERT: A 873 ASN cc_start: 0.7276 (m-40) cc_final: 0.6710 (p0) REVERT: A 1075 TYR cc_start: 0.8202 (t80) cc_final: 0.7661 (t80) REVERT: A 1099 TYR cc_start: 0.7363 (m-80) cc_final: 0.7083 (m-10) REVERT: A 1100 MET cc_start: 0.6756 (tpt) cc_final: 0.6159 (tpp) outliers start: 27 outliers final: 21 residues processed: 120 average time/residue: 0.1977 time to fit residues: 35.9875 Evaluate side-chains 115 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 67 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 300 VAL 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 436 MET 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 1061 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1083 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10893 Z= 0.170 Angle : 0.472 8.271 14716 Z= 0.255 Chirality : 0.043 0.157 1585 Planarity : 0.003 0.043 1893 Dihedral : 4.141 23.981 1411 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.93 % Allowed : 15.97 % Favored : 82.10 % 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: -0.75 (0.24), residues: 1289 helix: 2.16 (0.29), residues: 361 sheet: -1.05 (0.42), residues: 163 loop : -1.82 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 693 HIS 0.002 0.000 HIS A 428 PHE 0.012 0.001 PHE A1004 TYR 0.021 0.001 TYR A 421 ARG 0.002 0.000 ARG A1074 *********************** 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 119 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.230 Fit side-chains REVERT: A 350 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7720 (mtmt) REVERT: A 852 MET cc_start: 0.2778 (tpt) cc_final: 0.1699 (ptt) REVERT: A 873 ASN cc_start: 0.7331 (m-40) cc_final: 0.6694 (p0) REVERT: A 956 MET cc_start: 0.4601 (mmt) cc_final: 0.4398 (mmp) REVERT: A 1075 TYR cc_start: 0.8162 (t80) cc_final: 0.7635 (t80) REVERT: A 1100 MET cc_start: 0.6779 (tpt) cc_final: 0.6124 (tpp) outliers start: 23 outliers final: 21 residues processed: 111 average time/residue: 0.2014 time to fit residues: 34.0173 Evaluate side-chains 113 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 67 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 300 VAL 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 436 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 620 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 1061 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1083 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.0010 chunk 11 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10893 Z= 0.164 Angle : 0.465 6.848 14716 Z= 0.250 Chirality : 0.043 0.139 1585 Planarity : 0.003 0.046 1893 Dihedral : 4.035 23.227 1411 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.10 % Allowed : 15.88 % Favored : 82.02 % 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: -0.68 (0.24), residues: 1289 helix: 2.25 (0.29), residues: 361 sheet: -1.03 (0.42), residues: 163 loop : -1.77 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 693 HIS 0.002 0.000 HIS A 428 PHE 0.012 0.001 PHE A 221 TYR 0.020 0.001 TYR A 421 ARG 0.001 0.000 ARG A1074 *********************** 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 120 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 1.109 Fit side-chains REVERT: A 92 MET cc_start: 0.8325 (mmt) cc_final: 0.7864 (mmt) REVERT: A 172 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.7996 (p) REVERT: A 350 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7681 (mtmt) REVERT: A 852 MET cc_start: 0.2603 (tpt) cc_final: 0.1663 (ptt) REVERT: A 873 ASN cc_start: 0.7342 (m-40) cc_final: 0.6722 (p0) REVERT: A 1075 TYR cc_start: 0.8151 (t80) cc_final: 0.7622 (t80) REVERT: A 1100 MET cc_start: 0.6687 (tpt) cc_final: 0.5976 (tpp) outliers start: 25 outliers final: 23 residues processed: 112 average time/residue: 0.2005 time to fit residues: 33.9557 Evaluate side-chains 116 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 67 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 300 VAL 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 436 MET 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 1061 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1083 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 10.0000 chunk 115 optimal weight: 0.0000 chunk 119 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 0.0370 chunk 90 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.9066 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10893 Z= 0.204 Angle : 0.496 8.077 14716 Z= 0.264 Chirality : 0.043 0.139 1585 Planarity : 0.003 0.047 1893 Dihedral : 4.096 23.286 1411 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.27 % Allowed : 15.88 % Favored : 81.85 % 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: -0.74 (0.24), residues: 1289 helix: 2.17 (0.29), residues: 361 sheet: -1.10 (0.41), residues: 163 loop : -1.78 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1002 HIS 0.003 0.001 HIS A 428 PHE 0.021 0.001 PHE A1004 TYR 0.022 0.001 TYR A 421 ARG 0.002 0.000 ARG A1032 *********************** 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 119 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 1.262 Fit side-chains REVERT: A 172 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8039 (p) REVERT: A 350 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7686 (mtmt) REVERT: A 852 MET cc_start: 0.2762 (tpt) cc_final: 0.1801 (ptt) REVERT: A 873 ASN cc_start: 0.7367 (m-40) cc_final: 0.6731 (p0) REVERT: A 1075 TYR cc_start: 0.8164 (t80) cc_final: 0.7659 (t80) outliers start: 27 outliers final: 26 residues processed: 111 average time/residue: 0.2098 time to fit residues: 35.0298 Evaluate side-chains 117 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 67 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 342 VAL 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 436 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 620 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 Chi-restraints excluded: chain A residue 1083 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 chunk 62 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 0.3980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10893 Z= 0.141 Angle : 0.461 8.018 14716 Z= 0.245 Chirality : 0.042 0.140 1585 Planarity : 0.003 0.046 1893 Dihedral : 3.919 22.944 1411 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.93 % Allowed : 16.39 % Favored : 81.68 % 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: -0.61 (0.24), residues: 1289 helix: 2.22 (0.29), residues: 368 sheet: -0.99 (0.42), residues: 163 loop : -1.72 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 693 HIS 0.002 0.000 HIS A 428 PHE 0.019 0.001 PHE A1004 TYR 0.018 0.001 TYR A 421 ARG 0.001 0.000 ARG A 933 ********************** 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 114 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.329 Fit side-chains REVERT: A 172 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7951 (p) REVERT: A 680 LYS cc_start: 0.7543 (mmtp) cc_final: 0.7307 (mmmm) REVERT: A 852 MET cc_start: 0.2638 (tpt) cc_final: 0.1739 (ptt) REVERT: A 873 ASN cc_start: 0.7334 (m-40) cc_final: 0.6716 (p0) REVERT: A 1075 TYR cc_start: 0.8132 (t80) cc_final: 0.7634 (t80) outliers start: 23 outliers final: 21 residues processed: 106 average time/residue: 0.2190 time to fit residues: 35.0569 Evaluate side-chains 111 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 67 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 400 ILE 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 620 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 Chi-restraints excluded: chain A residue 1083 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 102 optimal weight: 0.0980 chunk 42 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.0270 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 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 = 0.4735 r_free = 0.4735 target = 0.237277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.188201 restraints weight = 12018.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.183133 restraints weight = 18009.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.186533 restraints weight = 15248.800| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10893 Z= 0.131 Angle : 0.453 7.864 14716 Z= 0.239 Chirality : 0.042 0.143 1585 Planarity : 0.003 0.047 1893 Dihedral : 3.802 22.826 1411 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.02 % Allowed : 16.81 % Favored : 81.18 % 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: -0.54 (0.24), residues: 1289 helix: 2.27 (0.29), residues: 369 sheet: -0.96 (0.42), residues: 163 loop : -1.68 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 693 HIS 0.002 0.000 HIS A 428 PHE 0.018 0.001 PHE A1004 TYR 0.017 0.001 TYR A 421 ARG 0.001 0.000 ARG A 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.82 seconds wall clock time: 38 minutes 3.00 seconds (2283.00 seconds total)