Starting phenix.real_space_refine on Sat Dec 9 09:43:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/12_2023/7qfq_13947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/12_2023/7qfq_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_13947/12_2023/7qfq_13947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/12_2023/7qfq_13947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/12_2023/7qfq_13947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfq_13947/12_2023/7qfq_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-1.21rc1-5172/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: 5.90, 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: 3.88 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: 1.38 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: 3.76 Time building geometry restraints manager: 4.21 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: 1.470 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: 6.320 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.630 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- 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 : 1.327 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2308 time to fit residues: 41.7680 Evaluate side-chains 102 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6100 ------------------------------------------------------------------------------- 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: 2.9990 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 766 GLN A1052 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10893 Z= 0.269 Angle : 0.538 5.958 14716 Z= 0.292 Chirality : 0.046 0.231 1585 Planarity : 0.004 0.052 1893 Dihedral : 4.409 23.461 1411 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.26 % Allowed : 7.90 % 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: -0.87 (0.23), residues: 1289 helix: 1.94 (0.29), residues: 361 sheet: -0.75 (0.44), residues: 152 loop : -1.91 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1002 HIS 0.003 0.001 HIS A 237 PHE 0.020 0.002 PHE A 221 TYR 0.025 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 116 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.249 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.2265 time to fit residues: 36.3878 Evaluate side-chains 106 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1052 time to fit residues: 3.5127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 126 optimal weight: 0.0980 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 40 optimal weight: 0.0060 chunk 94 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 A1052 GLN A1070 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10893 Z= 0.143 Angle : 0.460 6.698 14716 Z= 0.250 Chirality : 0.043 0.149 1585 Planarity : 0.003 0.040 1893 Dihedral : 4.123 23.750 1411 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.59 % Allowed : 10.67 % Favored : 88.74 % 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: 2.25 (0.29), residues: 361 sheet: -0.90 (0.43), residues: 158 loop : -1.77 (0.21), residues: 770 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 0.013 0.001 TYR A 421 ARG 0.005 0.000 ARG A 122 *********************** 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 112 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.574 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 108 average time/residue: 0.2665 time to fit residues: 43.7274 Evaluate side-chains 99 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1313 time to fit residues: 2.0946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 0.0870 chunk 124 optimal weight: 10.0000 chunk 61 optimal weight: 0.2980 chunk 111 optimal weight: 0.0050 chunk 33 optimal weight: 0.0970 overall best weight: 0.1970 ------------------------------------------------------------------------------- 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 A1070 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10893 Z= 0.113 Angle : 0.432 6.004 14716 Z= 0.234 Chirality : 0.043 0.144 1585 Planarity : 0.003 0.038 1893 Dihedral : 3.871 20.925 1411 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.34 % Allowed : 12.02 % Favored : 86.64 % 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: -0.44 (0.24), residues: 1289 helix: 2.50 (0.29), residues: 355 sheet: -0.69 (0.43), residues: 153 loop : -1.66 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 693 HIS 0.001 0.000 HIS A 428 PHE 0.011 0.001 PHE A1004 TYR 0.014 0.001 TYR A 540 ARG 0.003 0.000 ARG A 122 *********************** 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 115 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.217 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 106 average time/residue: 0.2214 time to fit residues: 35.5243 Evaluate side-chains 97 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1090 time to fit residues: 3.2114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.0030 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A1070 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10893 Z= 0.202 Angle : 0.478 6.929 14716 Z= 0.258 Chirality : 0.044 0.145 1585 Planarity : 0.003 0.042 1893 Dihedral : 3.985 21.627 1411 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.92 % Allowed : 13.19 % Favored : 85.88 % 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: 2.28 (0.29), residues: 361 sheet: -0.75 (0.44), residues: 153 loop : -1.77 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 693 HIS 0.003 0.001 HIS A 428 PHE 0.017 0.001 PHE A 221 TYR 0.025 0.001 TYR A1099 ARG 0.006 0.000 ARG A 122 *********************** 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 109 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.108 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 107 average time/residue: 0.2250 time to fit residues: 35.9253 Evaluate side-chains 96 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1036 time to fit residues: 2.7397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- 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 A1070 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10893 Z= 0.256 Angle : 0.509 6.058 14716 Z= 0.276 Chirality : 0.045 0.220 1585 Planarity : 0.004 0.043 1893 Dihedral : 4.197 22.662 1411 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.34 % Allowed : 14.29 % Favored : 84.37 % 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: -0.80 (0.24), residues: 1289 helix: 2.06 (0.29), residues: 361 sheet: -0.91 (0.43), residues: 153 loop : -1.85 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1002 HIS 0.003 0.001 HIS A 428 PHE 0.018 0.002 PHE A 221 TYR 0.030 0.001 TYR A 421 ARG 0.003 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 112 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.202 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.2454 time to fit residues: 37.8185 Evaluate side-chains 102 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1285 time to fit residues: 4.5248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A1070 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10893 Z= 0.177 Angle : 0.473 6.705 14716 Z= 0.256 Chirality : 0.043 0.186 1585 Planarity : 0.003 0.044 1893 Dihedral : 4.064 23.357 1411 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.25 % Allowed : 15.80 % Favored : 83.95 % 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: 2.18 (0.29), residues: 361 sheet: -1.12 (0.42), residues: 158 loop : -1.77 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 693 HIS 0.002 0.000 HIS A 428 PHE 0.013 0.001 PHE A1004 TYR 0.023 0.001 TYR A 421 ARG 0.002 0.000 ARG A 933 *********************** 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 99 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 1.180 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 0.2370 time to fit residues: 34.5766 Evaluate side-chains 93 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0938 time to fit residues: 1.7847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.8328 > 50: distance: 23 - 119: 32.459 distance: 26 - 116: 26.890 distance: 41 - 100: 36.072 distance: 44 - 97: 35.556 distance: 59 - 63: 34.245 distance: 63 - 64: 40.565 distance: 64 - 65: 48.404 distance: 64 - 67: 70.734 distance: 65 - 66: 29.342 distance: 65 - 72: 64.518 distance: 67 - 68: 55.598 distance: 68 - 69: 39.749 distance: 69 - 70: 15.901 distance: 69 - 71: 34.016 distance: 72 - 73: 27.647 distance: 73 - 74: 42.268 distance: 73 - 76: 49.456 distance: 74 - 80: 60.164 distance: 76 - 77: 56.488 distance: 77 - 78: 44.902 distance: 78 - 79: 43.867 distance: 80 - 81: 17.413 distance: 81 - 82: 33.989 distance: 81 - 84: 33.020 distance: 82 - 89: 39.059 distance: 84 - 85: 33.280 distance: 85 - 86: 48.478 distance: 86 - 87: 35.237 distance: 87 - 88: 19.823 distance: 89 - 90: 40.431 distance: 90 - 91: 34.051 distance: 91 - 92: 39.457 distance: 91 - 97: 32.900 distance: 93 - 94: 39.450 distance: 94 - 95: 40.961 distance: 94 - 96: 40.678 distance: 97 - 98: 34.778 distance: 98 - 99: 20.812 distance: 98 - 101: 51.495 distance: 99 - 100: 21.881 distance: 99 - 108: 48.034 distance: 101 - 102: 48.604 distance: 102 - 103: 32.437 distance: 102 - 104: 25.330 distance: 103 - 105: 43.672 distance: 104 - 106: 40.396 distance: 105 - 107: 35.568 distance: 106 - 107: 7.820 distance: 108 - 109: 32.482 distance: 109 - 110: 43.641 distance: 109 - 112: 47.799 distance: 110 - 111: 31.969 distance: 110 - 116: 42.487 distance: 112 - 113: 3.885 distance: 113 - 114: 27.323 distance: 113 - 115: 37.492 distance: 116 - 117: 41.044 distance: 117 - 118: 39.978 distance: 118 - 119: 55.214 distance: 118 - 121: 63.097 distance: 121 - 122: 58.141 distance: 121 - 127: 41.416 distance: 122 - 123: 28.575 distance: 122 - 125: 21.977 distance: 123 - 124: 40.872 distance: 123 - 128: 14.916 distance: 125 - 126: 59.768 distance: 126 - 127: 41.265 distance: 128 - 129: 17.566 distance: 129 - 130: 33.702 distance: 129 - 132: 53.986 distance: 130 - 136: 39.409 distance: 132 - 133: 38.811 distance: 132 - 134: 37.717 distance: 133 - 135: 39.977 distance: 136 - 137: 38.814 distance: 137 - 138: 27.200 distance: 137 - 140: 14.947 distance: 138 - 148: 34.624 distance: 140 - 141: 28.321 distance: 141 - 142: 41.336 distance: 141 - 143: 14.388 distance: 142 - 144: 41.662 distance: 143 - 145: 43.745 distance: 144 - 146: 22.362 distance: 145 - 146: 29.863 distance: 146 - 147: 25.309