Starting phenix.real_space_refine on Sat Jan 20 02:44:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/01_2024/7si3_25137_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/01_2024/7si3_25137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/01_2024/7si3_25137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/01_2024/7si3_25137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/01_2024/7si3_25137_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/01_2024/7si3_25137_updated.pdb" } resolution = 3.19 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 ------------------------------------------------------------------------------- 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= 1.000 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 49 5.16 5 C 4234 2.51 5 N 1109 2.21 5 O 1201 1.98 5 F 4 1.80 5 H 6901 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13500 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 13500 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'peptide': 873, 'undetermined': 2} Link IDs: {'PTRANS': 34, 'TRANS': 838, None: 2} Not linked: pdbres="ARG A1417 " pdbres=" MG A1501 " Not linked: pdbres=" MG A1501 " pdbres="ALF A1502 " Unresolved chain links: 1 Chain breaks: 6 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 6.46, per 1000 atoms: 0.48 Number of scatterers: 13500 At special positions: 0 Unit cell: (90.95, 92.65, 140.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 49 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1201 8.00 N 1109 7.00 C 4234 6.00 H 6901 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 499 " distance=2.03 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: 10.66 Conformation dependent library (CDL) restraints added in 1.4 seconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... running ksdssp... Bad HELIX record, was skipped: HELIX 3 3 SER A 574 ARG A 585 12 Secondary structure from input PDB file: 35 helices and 7 sheets defined 48.5% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 641 through 670 Proline residue: A 660 - end of helix Processing helix chain 'A' and resid 691 through 706 Processing helix chain 'A' and resid 709 through 721 Processing helix chain 'A' and resid 726 through 751 Processing helix chain 'A' and resid 761 through 782 Proline residue: A 765 - end of helix removed outlier: 3.531A pdb=" N PHE A 770 " --> pdb=" O MET A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 892 through 905 Processing helix chain 'A' and resid 913 through 942 removed outlier: 3.565A pdb=" N TYR A 920 " --> pdb=" O LYS A 916 " (cutoff:3.500A) Proline residue: A 923 - end of helix Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 952 through 955 Processing helix chain 'A' and resid 960 through 979 Processing helix chain 'A' and resid 986 through 1002 removed outlier: 3.859A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1013 No H-bonds generated for 'chain 'A' and resid 1011 through 1013' Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1050 through 1060 Processing helix chain 'A' and resid 1067 through 1079 Processing helix chain 'A' and resid 1106 through 1111 Processing helix chain 'A' and resid 1157 through 1162 Processing helix chain 'A' and resid 1169 through 1181 removed outlier: 3.655A pdb=" N LYS A1181 " --> pdb=" O SER A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1218 removed outlier: 4.407A pdb=" N LEU A1210 " --> pdb=" O GLN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1240 Processing helix chain 'A' and resid 1251 through 1264 removed outlier: 3.637A pdb=" N ASP A1264 " --> pdb=" O ALA A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1310 through 1333 removed outlier: 3.500A pdb=" N VAL A1324 " --> pdb=" O LYS A1321 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A1325 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A1328 " --> pdb=" O ARG A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1346 Proline residue: A1343 - end of helix Processing helix chain 'A' and resid 1350 through 1352 No H-bonds generated for 'chain 'A' and resid 1350 through 1352' Processing helix chain 'A' and resid 1358 through 1381 removed outlier: 3.860A pdb=" N GLY A1361 " --> pdb=" O PRO A1358 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A1369 " --> pdb=" O ALA A1366 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A1370 " --> pdb=" O ALA A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1393 Processing helix chain 'A' and resid 1403 through 1405 No H-bonds generated for 'chain 'A' and resid 1403 through 1405' Processing sheet with id= A, first strand: chain 'A' and resid 549 through 552 Processing sheet with id= B, first strand: chain 'A' and resid 626 through 628 Processing sheet with id= C, first strand: chain 'A' and resid 799 through 803 Processing sheet with id= D, first strand: chain 'A' and resid 827 through 830 removed outlier: 7.197A pdb=" N ASP A 839 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 861 through 863 Processing sheet with id= F, first strand: chain 'A' and resid 1004 through 1006 removed outlier: 6.812A pdb=" N ALA A1020 " --> pdb=" O ALA A1269 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL A1271 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET A1022 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP A1221 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE A1023 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A1223 " --> pdb=" O PHE A1023 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A1244 " --> pdb=" O LEU A1224 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER A1407 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ALA A1247 " --> pdb=" O SER A1407 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS A1409 " --> pdb=" O ALA A1247 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1090 through 1094 removed outlier: 5.832A pdb=" N ILE A1190 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU A1194 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ALA A1201 " --> pdb=" O VAL A1036 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL A1036 " --> pdb=" O ALA A1201 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 888 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: 5.02 Time building geometry restraints manager: 11.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6886 1.04 - 1.23: 132 1.23 - 1.43: 2447 1.43 - 1.63: 4045 1.63 - 1.82: 87 Bond restraints: 13597 Sorted by residual: bond pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" F4 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.686 1.785 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CB PRO A 909 " pdb=" CG PRO A 909 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.58e-01 ... (remaining 13592 not shown) Histogram of bond angle deviations from ideal: 89.97 - 107.97: 1988 107.97 - 125.97: 22679 125.97 - 143.96: 107 143.96 - 161.96: 0 161.96 - 179.96: 2 Bond angle restraints: 24776 Sorted by residual: angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F2 ALF A1502 " ideal model delta sigma weight residual 108.68 179.83 -71.15 3.00e+00 1.11e-01 5.62e+02 angle pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.63 179.96 -70.33 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 110.21 90.01 20.20 3.00e+00 1.11e-01 4.53e+01 angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F3 ALF A1502 " ideal model delta sigma weight residual 109.69 90.02 19.67 3.00e+00 1.11e-01 4.30e+01 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F3 ALF A1502 " ideal model delta sigma weight residual 109.59 89.97 19.62 3.00e+00 1.11e-01 4.28e+01 ... (remaining 24771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 5704 16.52 - 33.03: 378 33.03 - 49.55: 83 49.55 - 66.06: 18 66.06 - 82.58: 8 Dihedral angle restraints: 6191 sinusoidal: 3397 harmonic: 2794 Sorted by residual: dihedral pdb=" CG ARG A1157 " pdb=" CD ARG A1157 " pdb=" NE ARG A1157 " pdb=" CZ ARG A1157 " ideal model delta sinusoidal sigma weight residual -90.00 -133.95 43.95 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA ASP A 682 " pdb=" CB ASP A 682 " pdb=" CG ASP A 682 " pdb=" OD1 ASP A 682 " ideal model delta sinusoidal sigma weight residual -30.00 -84.33 54.33 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CB LYS A 835 " pdb=" CG LYS A 835 " pdb=" CD LYS A 835 " pdb=" CE LYS A 835 " ideal model delta sinusoidal sigma weight residual -60.00 -118.80 58.80 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 740 0.027 - 0.054: 184 0.054 - 0.081: 102 0.081 - 0.108: 50 0.108 - 0.135: 39 Chirality restraints: 1115 Sorted by residual: chirality pdb=" CA ILE A1154 " pdb=" N ILE A1154 " pdb=" C ILE A1154 " pdb=" CB ILE A1154 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL A1094 " pdb=" N VAL A1094 " pdb=" C VAL A1094 " pdb=" CB VAL A1094 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE A 566 " pdb=" N ILE A 566 " pdb=" C ILE A 566 " pdb=" CB ILE A 566 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1112 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 908 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO A 909 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 909 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 909 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 831 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.72e+00 pdb=" N PRO A 832 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 832 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 832 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 864 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 865 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 865 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 865 " 0.020 5.00e-02 4.00e+02 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 689 2.20 - 2.80: 28249 2.80 - 3.40: 36264 3.40 - 4.00: 46018 4.00 - 4.60: 72376 Nonbonded interactions: 183596 Sorted by model distance: nonbonded pdb=" OD1 ASP A1228 " pdb=" H ASN A1229 " model vdw 1.600 1.850 nonbonded pdb=" OD1 ASP A 839 " pdb=" H ALA A 871 " model vdw 1.611 1.850 nonbonded pdb="HH12 ARG A1326 " pdb=" OE1 GLN A1378 " model vdw 1.641 1.850 nonbonded pdb=" O LEU A1012 " pdb=" HG SER A1320 " model vdw 1.660 1.850 nonbonded pdb=" O VAL A1275 " pdb=" HG SER A1278 " model vdw 1.672 1.850 ... (remaining 183591 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 individual isotropic 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: 0.150 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: 0.200 Extract box with map and model: 1.350 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 46.310 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.003 0.101 6696 Z= 0.186 Angle : 1.193 71.147 9068 Z= 0.425 Chirality : 0.041 0.135 1115 Planarity : 0.003 0.043 1128 Dihedral : 12.999 82.577 2456 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 3.72 (0.30), residues: 858 helix: 3.49 (0.24), residues: 455 sheet: 1.97 (0.44), residues: 145 loop : 0.85 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 936 HIS 0.001 0.000 HIS A1031 PHE 0.009 0.001 PHE A 944 TYR 0.005 0.000 TYR A 950 ARG 0.001 0.000 ARG A1326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 HIS cc_start: 0.7090 (t-90) cc_final: 0.6744 (t-90) REVERT: A 759 THR cc_start: 0.7065 (p) cc_final: 0.6779 (p) REVERT: A 864 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7626 (mtmt) REVERT: A 929 SER cc_start: 0.8395 (t) cc_final: 0.8176 (m) REVERT: A 1299 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7119 (mm-30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3674 time to fit residues: 58.0744 Evaluate side-chains 105 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6696 Z= 0.133 Angle : 0.820 29.814 9068 Z= 0.327 Chirality : 0.042 0.141 1115 Planarity : 0.004 0.032 1128 Dihedral : 2.871 11.694 911 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: 3.07 (0.29), residues: 858 helix: 2.83 (0.24), residues: 454 sheet: 2.12 (0.45), residues: 134 loop : 0.63 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 936 HIS 0.003 0.000 HIS A1213 PHE 0.005 0.001 PHE A1023 TYR 0.016 0.001 TYR A 716 ARG 0.001 0.000 ARG A1267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 HIS cc_start: 0.7093 (t-90) cc_final: 0.6753 (t-90) REVERT: A 759 THR cc_start: 0.7345 (p) cc_final: 0.7076 (p) REVERT: A 1299 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7167 (mm-30) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3708 time to fit residues: 56.0286 Evaluate side-chains 106 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN A 684 ASN A 693 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6696 Z= 0.254 Angle : 0.849 31.801 9068 Z= 0.348 Chirality : 0.044 0.149 1115 Planarity : 0.004 0.039 1128 Dihedral : 3.445 18.559 911 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.97 % Allowed : 5.67 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.29), residues: 858 helix: 2.13 (0.25), residues: 455 sheet: 1.58 (0.46), residues: 126 loop : 0.63 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 936 HIS 0.004 0.001 HIS A1213 PHE 0.016 0.002 PHE A 760 TYR 0.015 0.001 TYR A 716 ARG 0.002 0.000 ARG A 862 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 HIS cc_start: 0.7010 (t-90) cc_final: 0.6719 (t-90) REVERT: A 1406 ILE cc_start: 0.8160 (mt) cc_final: 0.7897 (mt) outliers start: 7 outliers final: 5 residues processed: 107 average time/residue: 0.3783 time to fit residues: 55.4554 Evaluate side-chains 109 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1292 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 50.0000 chunk 37 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6696 Z= 0.203 Angle : 0.836 31.576 9068 Z= 0.336 Chirality : 0.043 0.136 1115 Planarity : 0.003 0.037 1128 Dihedral : 3.444 18.395 911 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.69 % Allowed : 7.47 % Favored : 91.84 % 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: 2.17 (0.29), residues: 858 helix: 1.95 (0.25), residues: 461 sheet: 1.51 (0.46), residues: 125 loop : 0.63 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 936 HIS 0.003 0.001 HIS A1213 PHE 0.010 0.001 PHE A1023 TYR 0.024 0.001 TYR A 716 ARG 0.001 0.000 ARG A 862 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 844 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7023 (tm-30) outliers start: 5 outliers final: 4 residues processed: 106 average time/residue: 0.3757 time to fit residues: 54.4090 Evaluate side-chains 108 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1302 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 40.0000 chunk 34 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1865 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: