Starting phenix.real_space_refine on Thu Sep 26 17:38:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/09_2024/7si3_25137.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/09_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_25137/09_2024/7si3_25137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/09_2024/7si3_25137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/09_2024/7si3_25137.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si3_25137/09_2024/7si3_25137.cif" } 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. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13500 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 13494 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 34, 'TRANS': 838} 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 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.33, per 1000 atoms: 0.47 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.0 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... Secondary structure from input PDB file: 37 helices and 6 sheets defined 56.6% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 535 through 546 Processing helix chain 'A' and resid 574 through 575 No H-bonds generated for 'chain 'A' and resid 574 through 575' Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 611 through 623 Processing helix chain 'A' and resid 641 through 671 Proline residue: A 660 - end of helix Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 690 through 707 Processing helix chain 'A' and resid 707 through 721 removed outlier: 4.469A pdb=" N PHE A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 752 Processing helix chain 'A' and resid 762 through 783 removed outlier: 3.531A pdb=" N PHE A 770 " --> pdb=" O MET A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 796 removed outlier: 3.920A pdb=" N GLN A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 891 through 906 Processing helix chain 'A' and resid 912 through 943 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 944 through 951 removed outlier: 3.935A pdb=" N ILE A 948 " --> pdb=" O PHE A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 956 Processing helix chain 'A' and resid 959 through 980 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 1010 through 1018 removed outlier: 4.534A pdb=" N ALA A1015 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N HIS A1016 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1062 Processing helix chain 'A' and resid 1066 through 1080 Processing helix chain 'A' and resid 1105 through 1112 removed outlier: 3.760A pdb=" N VAL A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1163 Processing helix chain 'A' and resid 1168 through 1181 removed outlier: 3.655A pdb=" N LYS A1181 " --> pdb=" O SER A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1218 removed outlier: 4.110A pdb=" N ALA A1209 " --> pdb=" O LYS A1205 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A1210 " --> pdb=" O GLN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1250 through 1264 removed outlier: 3.637A pdb=" N ASP A1264 " --> pdb=" O ALA A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1284 Processing helix chain 'A' and resid 1294 through 1301 Processing helix chain 'A' and resid 1310 through 1347 removed outlier: 4.150A pdb=" N VAL A1314 " --> pdb=" O LEU A1310 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR A1337 " --> pdb=" O PHE A1333 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASN A1338 " --> pdb=" O ALA A1334 " (cutoff:3.500A) Proline residue: A1343 - end of helix Processing helix chain 'A' and resid 1349 through 1353 Processing helix chain 'A' and resid 1359 through 1378 Processing helix chain 'A' and resid 1379 through 1382 Processing helix chain 'A' and resid 1386 through 1394 removed outlier: 3.533A pdb=" N TYR A1390 " --> pdb=" O ASP A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1406 Processing sheet with id=AA1, first strand: chain 'A' and resid 513 through 518 Processing sheet with id=AA2, first strand: chain 'A' and resid 589 through 594 Processing sheet with id=AA3, first strand: chain 'A' and resid 814 through 818 removed outlier: 4.171A pdb=" N ALA A 801 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A 827 " --> pdb=" O VAL A 803 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 881 " --> pdb=" O ILE A 843 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP A 839 " --> pdb=" O THR A 885 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 840 " --> pdb=" O VAL A 869 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 861 through 863 Processing sheet with id=AA5, first strand: chain 'A' and resid 1004 through 1006 removed outlier: 6.267A pdb=" N GLY A1287 " --> pdb=" O ILE A1303 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU A1305 " --> pdb=" O GLY A1287 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ALA A1289 " --> pdb=" O LEU A1305 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A1268 " --> pdb=" O VAL A1286 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A1288 " --> pdb=" O VAL A1268 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET A1270 " --> pdb=" O ILE A1288 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE A1290 " --> pdb=" O MET A1270 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLY A1272 " --> pdb=" O ILE A1290 " (cutoff:3.500A) 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: 7.242A pdb=" N VAL A1222 " --> pdb=" O LYS A1244 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N PHE A1246 " --> pdb=" O VAL A1222 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A1224 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL A1245 " --> pdb=" O HIS A1409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1035 through 1041 removed outlier: 4.866A pdb=" N VAL A1036 " --> pdb=" O ALA A1201 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ALA A1201 " --> pdb=" O VAL A1036 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU A1194 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE A1190 " --> pdb=" O LEU A1194 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1152 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: 4.86 Time building geometry restraints manager: 4.07 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: 0.00 - 14.23: 24770 14.23 - 28.46: 4 28.46 - 42.69: 0 42.69 - 56.92: 0 56.92 - 71.15: 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: 5732 16.52 - 33.03: 412 33.03 - 49.55: 117 49.55 - 66.06: 45 66.06 - 82.58: 8 Dihedral angle restraints: 6314 sinusoidal: 3520 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 6311 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: 649 2.20 - 2.80: 28200 2.80 - 3.40: 36228 3.40 - 4.00: 45939 4.00 - 4.60: 72285 Nonbonded interactions: 183301 Sorted by model distance: nonbonded pdb=" OD1 ASP A1228 " pdb=" H ASN A1229 " model vdw 1.600 2.450 nonbonded pdb=" OD1 ASP A 839 " pdb=" H ALA A 871 " model vdw 1.611 2.450 nonbonded pdb="HH12 ARG A1326 " pdb=" OE1 GLN A1378 " model vdw 1.641 2.450 nonbonded pdb=" O LEU A1012 " pdb=" HG SER A1320 " model vdw 1.660 2.450 nonbonded pdb=" O VAL A1275 " pdb=" HG SER A1278 " model vdw 1.672 2.450 ... (remaining 183296 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: 0.100 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: 0.220 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.000 Find NCS groups from input model: 0.080 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- 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= 0.189 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 : 1.028 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: 0.3661 time to fit residues: 58.1166 Evaluate side-chains 105 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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: 0.6980 chunk 65 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7635 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6696 Z= 0.158 Angle : 0.835 30.456 9068 Z= 0.337 Chirality : 0.043 0.144 1115 Planarity : 0.003 0.033 1128 Dihedral : 2.963 12.347 911 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.15 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: 3.45 (0.29), residues: 858 helix: 3.23 (0.24), residues: 459 sheet: 2.12 (0.44), residues: 134 loop : 0.65 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 936 HIS 0.003 0.001 HIS A1213 PHE 0.008 0.001 PHE A1023 TYR 0.014 0.001 TYR A 716 ARG 0.002 0.000 ARG A 775 *********************** 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 110 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 HIS cc_start: 0.7069 (t-90) cc_final: 0.6667 (t-90) REVERT: A 759 THR cc_start: 0.7290 (p) cc_final: 0.7025 (p) REVERT: A 1406 ILE cc_start: 0.8001 (mt) cc_final: 0.7744 (mt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3447 time to fit residues: 52.8067 Evaluate side-chains 106 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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: 0.7761 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6696 Z= 0.249 Angle : 0.858 31.489 9068 Z= 0.354 Chirality : 0.044 0.140 1115 Planarity : 0.004 0.037 1128 Dihedral : 3.434 18.137 911 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.24 % Allowed : 5.12 % Favored : 93.64 % 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: 2.84 (0.29), residues: 858 helix: 2.68 (0.24), residues: 462 sheet: 1.69 (0.44), residues: 134 loop : 0.56 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 936 HIS 0.004 0.001 HIS A 779 PHE 0.013 0.002 PHE A 760 TYR 0.014 0.001 TYR A 716 ARG 0.003 0.000 ARG A 775 *********************** 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 118 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 844 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6937 (tm-30) REVERT: A 1299 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7925 (mm-30) outliers start: 9 outliers final: 6 residues processed: 111 average time/residue: 0.3997 time to fit residues: 59.5253 Evaluate side-chains 114 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 918 SER 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: 50.0000 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 50.0000 chunk 37 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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: 0.7728 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6696 Z= 0.150 Angle : 0.833 30.844 9068 Z= 0.334 Chirality : 0.043 0.138 1115 Planarity : 0.003 0.036 1128 Dihedral : 3.329 16.984 911 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.28 % Allowed : 7.19 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.29), residues: 858 helix: 2.74 (0.24), residues: 461 sheet: 1.63 (0.45), residues: 134 loop : 0.53 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 PHE 0.007 0.001 PHE A1023 TYR 0.023 0.001 TYR A 716 ARG 0.002 0.000 ARG A 775 *********************** 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 119 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 117 average time/residue: 0.3937 time to fit residues: 62.0897 Evaluate side-chains 108 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 817 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 62 optimal weight: 40.0000 chunk 34 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN A 693 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6696 Z= 0.204 Angle : 0.846 31.936 9068 Z= 0.343 Chirality : 0.043 0.136 1115 Planarity : 0.003 0.035 1128 Dihedral : 3.456 18.494 911 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.69 % Allowed : 7.88 % Favored : 91.42 % 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: 2.63 (0.29), residues: 858 helix: 2.48 (0.24), residues: 468 sheet: 1.55 (0.44), residues: 136 loop : 0.49 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 PHE 0.008 0.001 PHE A 760 TYR 0.025 0.001 TYR A 954 ARG 0.002 0.000 ARG A 775 *********************** REFINEMENT MACRO_CYCLE 5 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 112 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 ILE cc_start: 0.8401 (tp) cc_final: 0.8177 (tt) REVERT: A 844 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7001 (tm-30) outliers start: 5 outliers final: 3 residues processed: 109 average time/residue: 0.4510 time to fit residues: 66.7041 Evaluate side-chains 110 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1292 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.7752 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6696 Z= 0.151 Angle : 0.833 31.205 9068 Z= 0.334 Chirality : 0.042 0.136 1115 Planarity : 0.003 0.035 1128 Dihedral : 3.384 18.212 911 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.41 % Allowed : 8.16 % Favored : 91.42 % 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: 2.70 (0.29), residues: 858 helix: 2.57 (0.24), residues: 468 sheet: 1.49 (0.44), residues: 137 loop : 0.52 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 PHE 0.006 0.001 PHE A1023 TYR 0.017 0.001 TYR A 716 ARG 0.001 0.000 ARG A 775 *********************** REFINEMENT MACRO_CYCLE 6 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: 3 poor density : 110 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 ILE cc_start: 0.8402 (tp) cc_final: 0.8182 (tt) REVERT: A 844 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6977 (tm-30) outliers start: 3 outliers final: 2 residues processed: 113 average time/residue: 0.4012 time to fit residues: 60.9449 Evaluate side-chains 109 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 1222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 50.0000 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6696 Z= 0.159 Angle : 0.835 31.428 9068 Z= 0.335 Chirality : 0.042 0.134 1115 Planarity : 0.003 0.035 1128 Dihedral : 3.397 18.251 911 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.69 % Allowed : 8.02 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.29), residues: 858 helix: 2.58 (0.24), residues: 468 sheet: 1.49 (0.44), residues: 137 loop : 0.58 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 PHE 0.006 0.001 PHE A1023 TYR 0.015 0.001 TYR A 716 ARG 0.001 0.000 ARG A 775 *********************** REFINEMENT MACRO_CYCLE 7 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 : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 ILE cc_start: 0.8418 (tp) cc_final: 0.8209 (tt) REVERT: A 844 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6971 (tm-30) outliers start: 5 outliers final: 4 residues processed: 109 average time/residue: 0.4057 time to fit residues: 60.1568 Evaluate side-chains 110 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 41 optimal weight: 0.0070 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- 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: 0.7736 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6696 Z= 0.139 Angle : 0.830 30.665 9068 Z= 0.331 Chirality : 0.042 0.134 1115 Planarity : 0.003 0.034 1128 Dihedral : 3.330 17.701 911 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.28 % Allowed : 8.85 % Favored : 90.87 % 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: 2.83 (0.29), residues: 858 helix: 2.67 (0.24), residues: 468 sheet: 1.49 (0.44), residues: 137 loop : 0.61 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 936 HIS 0.002 0.000 HIS A 779 PHE 0.005 0.001 PHE A1023 TYR 0.013 0.001 TYR A 716 ARG 0.001 0.000 ARG A1157 *********************** REFINEMENT MACRO_CYCLE 8 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 112 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 ILE cc_start: 0.8412 (tp) cc_final: 0.8209 (tt) REVERT: A 844 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6975 (tm-30) REVERT: A 1406 ILE cc_start: 0.8137 (mt) cc_final: 0.7841 (mt) outliers start: 2 outliers final: 2 residues processed: 112 average time/residue: 0.4003 time to fit residues: 60.3333 Evaluate side-chains 111 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 1222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7739 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6696 Z= 0.143 Angle : 0.830 30.940 9068 Z= 0.331 Chirality : 0.042 0.133 1115 Planarity : 0.003 0.035 1128 Dihedral : 3.317 17.291 911 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.55 % Allowed : 8.44 % Favored : 91.01 % 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: 2.86 (0.29), residues: 858 helix: 2.71 (0.24), residues: 468 sheet: 1.45 (0.44), residues: 137 loop : 0.64 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 936 HIS 0.002 0.000 HIS A 779 PHE 0.005 0.001 PHE A1023 TYR 0.012 0.001 TYR A 716 ARG 0.002 0.000 ARG A1267 *********************** REFINEMENT MACRO_CYCLE 9 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: 4 poor density : 109 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 ILE cc_start: 0.8428 (tp) cc_final: 0.8217 (tt) REVERT: A 844 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6990 (tm-30) REVERT: A 1406 ILE cc_start: 0.8131 (mt) cc_final: 0.7839 (mt) outliers start: 4 outliers final: 4 residues processed: 111 average time/residue: 0.3912 time to fit residues: 58.6341 Evaluate side-chains 111 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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: 0.7773 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6696 Z= 0.185 Angle : 0.839 32.202 9068 Z= 0.337 Chirality : 0.043 0.134 1115 Planarity : 0.003 0.034 1128 Dihedral : 3.406 18.480 911 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.69 % Allowed : 8.30 % Favored : 91.01 % 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: 2.73 (0.29), residues: 858 helix: 2.59 (0.24), residues: 468 sheet: 1.45 (0.44), residues: 137 loop : 0.56 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 936 HIS 0.004 0.001 HIS A1213 PHE 0.008 0.001 PHE A1023 TYR 0.013 0.001 TYR A 716 ARG 0.002 0.000 ARG A 585 ********************** REFINEMENT MACRO_CYCLE 10 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 116 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 ILE cc_start: 0.8441 (tp) cc_final: 0.8232 (tt) outliers start: 5 outliers final: 5 residues processed: 113 average time/residue: 0.3907 time to fit residues: 59.8550 Evaluate side-chains 116 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 864 LYS Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 50.0000 chunk 12 optimal weight: 30.0000 chunk 60 optimal weight: 40.0000 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.214199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.140392 restraints weight = 21812.669| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.48 r_work: 0.3260 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6696 Z= 0.161 Angle : 0.837 31.459 9068 Z= 0.335 Chirality : 0.042 0.135 1115 Planarity : 0.003 0.034 1128 Dihedral : 3.387 18.314 911 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.55 % Allowed : 8.44 % Favored : 91.01 % 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: 2.72 (0.29), residues: 858 helix: 2.52 (0.24), residues: 474 sheet: 1.46 (0.43), residues: 136 loop : 0.66 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 936 HIS 0.002 0.000 HIS A 779 PHE 0.006 0.001 PHE A1023 TYR 0.013 0.001 TYR A 716 ARG 0.001 0.000 ARG A1267 =============================================================================== Job complete usr+sys time: 3504.37 seconds wall clock time: 61 minutes 27.05 seconds (3687.05 seconds total)