Starting phenix.real_space_refine on Tue Jul 29 13:10:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eal_47835/07_2025/9eal_47835.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eal_47835/07_2025/9eal_47835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eal_47835/07_2025/9eal_47835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eal_47835/07_2025/9eal_47835.map" model { file = "/net/cci-nas-00/data/ceres_data/9eal_47835/07_2025/9eal_47835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eal_47835/07_2025/9eal_47835.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 16 5.16 5 C 6763 2.51 5 N 2039 2.21 5 O 2477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11438 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2038 Classifications: {'RNA': 95} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 83} Chain: "C" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 648 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 8420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 8420 Classifications: {'peptide': 1156} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PTRANS': 31, 'TRANS': 1124} Chain breaks: 3 Unresolved non-hydrogen bonds: 1025 Unresolved non-hydrogen angles: 1261 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 22, 'ASP:plan': 37, 'PHE:plan': 13, 'GLU:plan': 46, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 580 Time building chain proxies: 14.69, per 1000 atoms: 1.28 Number of scatterers: 11438 At special positions: 0 Unit cell: (85.8196, 135.812, 122.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 143 15.00 O 2477 8.00 N 2039 7.00 C 6763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.38 Conformation dependent library (CDL) restraints added in 1.7 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 54.8% alpha, 7.3% beta 52 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 5.20 Creating SS restraints... Processing helix chain 'A' and resid 59 through 86 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.618A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.781A pdb=" N GLU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.754A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 195 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 286 through 306 removed outlier: 4.531A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.997A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.884A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.790A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 527 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.606A pdb=" N GLU A 573 " --> pdb=" O PHE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.857A pdb=" N TYR A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 643 removed outlier: 3.578A pdb=" N PHE A 643 " --> pdb=" O ALA A 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.519A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 701 through 714 removed outlier: 3.876A pdb=" N LYS A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.509A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.529A pdb=" N SER A 964 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.422A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR A 995 " --> pdb=" O ALA A 991 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1046 removed outlier: 4.183A pdb=" N PHE A1045 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.486A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.658A pdb=" N LEU A1194 " --> pdb=" O LYS A1191 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1191 through 1195' Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 removed outlier: 3.545A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 3.651A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.502A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1344 Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.114A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 1050 through 1051 Processing sheet with id=AA4, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 3.780A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.586A pdb=" N PHE A1134 " --> pdb=" O ILE A1120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.533A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1219 through 1222 removed outlier: 3.720A pdb=" N GLU A1219 " --> pdb=" O SER A1216 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN A1221 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU A1214 " --> pdb=" O GLN A1221 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1325 437 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 9.75 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2441 1.33 - 1.45: 3308 1.45 - 1.57: 5890 1.57 - 1.69: 283 1.69 - 1.81: 30 Bond restraints: 11952 Sorted by residual: bond pdb=" N ARG A 395 " pdb=" CA ARG A 395 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.32e-02 5.74e+03 7.47e+00 bond pdb=" N ASP A 969 " pdb=" CA ASP A 969 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.19e-02 7.06e+03 7.15e+00 bond pdb=" N LYS A 959 " pdb=" CA LYS A 959 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.34e-02 5.57e+03 7.13e+00 bond pdb=" N ASP A 965 " pdb=" CA ASP A 965 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.17e-02 7.31e+03 6.80e+00 bond pdb=" N PHE A 970 " pdb=" CA PHE A 970 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.32e-02 5.74e+03 6.54e+00 ... (remaining 11947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 16572 2.84 - 5.68: 267 5.68 - 8.51: 39 8.51 - 11.35: 3 11.35 - 14.19: 1 Bond angle restraints: 16882 Sorted by residual: angle pdb=" CB MET A 648 " pdb=" CG MET A 648 " pdb=" SD MET A 648 " ideal model delta sigma weight residual 112.70 126.89 -14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" C ASP A 628 " pdb=" N ARG A 629 " pdb=" CA ARG A 629 " ideal model delta sigma weight residual 121.54 130.55 -9.01 1.91e+00 2.74e-01 2.23e+01 angle pdb=" C GLN A 712 " pdb=" N VAL A 713 " pdb=" CA VAL A 713 " ideal model delta sigma weight residual 120.56 125.56 -5.00 1.26e+00 6.30e-01 1.58e+01 angle pdb=" CA PHE A 966 " pdb=" CB PHE A 966 " pdb=" CG PHE A 966 " ideal model delta sigma weight residual 113.80 117.67 -3.87 1.00e+00 1.00e+00 1.50e+01 angle pdb=" O3' U B 59 " pdb=" P C B 60 " pdb=" O5' C B 60 " ideal model delta sigma weight residual 104.00 98.30 5.70 1.50e+00 4.44e-01 1.44e+01 ... (remaining 16877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 6640 35.30 - 70.60: 431 70.60 - 105.90: 24 105.90 - 141.20: 1 141.20 - 176.50: 4 Dihedral angle restraints: 7100 sinusoidal: 3708 harmonic: 3392 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 31.47 168.53 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" CA VAL A1092 " pdb=" C VAL A1092 " pdb=" N ASN A1093 " pdb=" CA ASN A1093 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" O4' G B 5 " pdb=" C1' G B 5 " pdb=" N9 G B 5 " pdb=" C4 G B 5 " ideal model delta sinusoidal sigma weight residual 70.00 -3.39 73.39 1 2.00e+01 2.50e-03 1.71e+01 ... (remaining 7097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1901 0.107 - 0.213: 107 0.213 - 0.320: 4 0.320 - 0.427: 3 0.427 - 0.533: 14 Chirality restraints: 2029 Sorted by residual: chirality pdb=" P A B 69 " pdb=" OP1 A B 69 " pdb=" OP2 A B 69 " pdb=" O5' A B 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" P A B 68 " pdb=" OP1 A B 68 " pdb=" OP2 A B 68 " pdb=" O5' A B 68 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" P A B 17 " pdb=" OP1 A B 17 " pdb=" OP2 A B 17 " pdb=" O5' A B 17 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.58e+00 ... (remaining 2026 not shown) Planarity restraints: 1639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 976 " 0.547 9.50e-02 1.11e+02 2.45e-01 3.69e+01 pdb=" NE ARG A 976 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 976 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 976 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 976 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 967 " 0.412 9.50e-02 1.11e+02 1.84e-01 2.09e+01 pdb=" NE ARG A 967 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 967 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 967 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 967 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 518 " 0.014 2.00e-02 2.50e+03 2.20e-02 8.44e+00 pdb=" CG PHE A 518 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 518 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 518 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 518 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 518 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 518 " -0.001 2.00e-02 2.50e+03 ... (remaining 1636 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1465 2.76 - 3.29: 10575 3.29 - 3.83: 21144 3.83 - 4.36: 24714 4.36 - 4.90: 37834 Nonbonded interactions: 95732 Sorted by model distance: nonbonded pdb=" O2' A B 47 " pdb=" O LEU A 101 " model vdw 2.220 3.040 nonbonded pdb=" O ILE A1273 " pdb=" OG SER A1277 " model vdw 2.267 3.040 nonbonded pdb=" O LEU A 380 " pdb=" OG1 THR A 386 " model vdw 2.293 3.040 nonbonded pdb=" O TYR A 521 " pdb=" OG1 THR A 525 " model vdw 2.306 3.040 nonbonded pdb=" OE1 GLN A1305 " pdb=" OH TYR A1326 " model vdw 2.343 3.040 ... (remaining 95727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 737.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 49.650 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:28.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 816.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.005 0.060 11952 Z= 0.264 Angle : 0.897 14.190 16882 Z= 0.492 Chirality : 0.066 0.533 2029 Planarity : 0.010 0.245 1639 Dihedral : 19.858 176.496 4902 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.81 % Allowed : 22.10 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.23), residues: 1148 helix: -0.70 (0.20), residues: 580 sheet: 0.48 (0.53), residues: 96 loop : -1.32 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1074 HIS 0.008 0.001 HIS A 723 PHE 0.050 0.003 PHE A 518 TYR 0.036 0.002 TYR A 155 ARG 0.018 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.14176 ( 563) hydrogen bonds : angle 6.47676 ( 1525) covalent geometry : bond 0.00493 (11952) covalent geometry : angle 0.89695 (16882) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 314 LYS cc_start: 0.7663 (mmmm) cc_final: 0.6822 (ptmt) REVERT: A 575 PHE cc_start: 0.6076 (p90) cc_final: 0.5764 (p90) REVERT: A 951 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7434 (mtm-85) REVERT: A 1125 ASP cc_start: 0.7609 (p0) cc_final: 0.7402 (p0) REVERT: A 1344 ASP cc_start: 0.6694 (t0) cc_final: 0.6192 (p0) outliers start: 6 outliers final: 2 residues processed: 110 average time/residue: 0.9925 time to fit residues: 121.1476 Evaluate side-chains 90 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 0.0270 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0980 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 0.0070 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS A1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.147169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111825 restraints weight = 20988.624| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.21 r_work: 0.3460 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11952 Z= 0.129 Angle : 0.541 6.074 16882 Z= 0.297 Chirality : 0.037 0.225 2029 Planarity : 0.004 0.040 1639 Dihedral : 20.640 174.287 3193 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.10 % Allowed : 19.41 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1148 helix: 0.70 (0.22), residues: 569 sheet: 0.33 (0.49), residues: 113 loop : -1.04 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1074 HIS 0.004 0.001 HIS A1297 PHE 0.014 0.001 PHE A 972 TYR 0.014 0.001 TYR A 155 ARG 0.006 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 563) hydrogen bonds : angle 4.50909 ( 1525) covalent geometry : bond 0.00270 (11952) covalent geometry : angle 0.54112 (16882) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 314 LYS cc_start: 0.7457 (mmmm) cc_final: 0.6761 (mtpt) REVERT: A 362 TYR cc_start: 0.8354 (t80) cc_final: 0.8125 (t80) REVERT: A 481 VAL cc_start: 0.8800 (t) cc_final: 0.8516 (t) REVERT: A 524 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8603 (tt) REVERT: A 575 PHE cc_start: 0.6011 (p90) cc_final: 0.5739 (p90) REVERT: A 621 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8049 (tm) REVERT: A 942 LYS cc_start: 0.8916 (tppt) cc_final: 0.8520 (mmpt) REVERT: A 951 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6981 (mtm110) REVERT: A 968 LYS cc_start: 0.7816 (tmtt) cc_final: 0.7481 (tppp) REVERT: A 976 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7509 (mtp-110) outliers start: 23 outliers final: 6 residues processed: 121 average time/residue: 1.2027 time to fit residues: 163.1728 Evaluate side-chains 89 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.133892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096840 restraints weight = 21003.057| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.16 r_work: 0.3242 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 11952 Z= 0.304 Angle : 0.666 8.209 16882 Z= 0.358 Chirality : 0.044 0.243 2029 Planarity : 0.005 0.058 1639 Dihedral : 21.082 176.311 3193 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.04 % Allowed : 18.87 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1148 helix: 0.63 (0.21), residues: 581 sheet: -0.18 (0.48), residues: 113 loop : -0.85 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 18 HIS 0.008 0.002 HIS A 167 PHE 0.017 0.003 PHE A1045 TYR 0.028 0.002 TYR A 155 ARG 0.009 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 563) hydrogen bonds : angle 4.64128 ( 1525) covalent geometry : bond 0.00673 (11952) covalent geometry : angle 0.66552 (16882) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 1.094 Fit side-chains REVERT: A 80 CYS cc_start: 0.8565 (t) cc_final: 0.7927 (m) REVERT: A 404 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8220 (p) REVERT: A 942 LYS cc_start: 0.8898 (tppt) cc_final: 0.8650 (mmtm) REVERT: A 951 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7139 (mtm110) REVERT: A 952 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: A 970 PHE cc_start: 0.6442 (m-10) cc_final: 0.6237 (m-80) REVERT: A 976 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8087 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8771 (t0) cc_final: 0.8361 (p0) outliers start: 30 outliers final: 8 residues processed: 103 average time/residue: 1.1697 time to fit residues: 132.3844 Evaluate side-chains 78 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1314 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 6 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 101 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 394 ASN A1317 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.136100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099773 restraints weight = 20823.082| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.09 r_work: 0.3288 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11952 Z= 0.163 Angle : 0.553 7.561 16882 Z= 0.295 Chirality : 0.038 0.237 2029 Planarity : 0.004 0.041 1639 Dihedral : 20.830 178.324 3191 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.91 % Allowed : 19.68 % Favored : 76.42 % 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: 0.37 (0.25), residues: 1148 helix: 1.14 (0.22), residues: 572 sheet: 0.20 (0.52), residues: 86 loop : -0.77 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.004 0.001 HIS A 982 PHE 0.014 0.002 PHE A 518 TYR 0.019 0.001 TYR A 155 ARG 0.009 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 563) hydrogen bonds : angle 4.25474 ( 1525) covalent geometry : bond 0.00356 (11952) covalent geometry : angle 0.55304 (16882) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 1.304 Fit side-chains REVERT: A 80 CYS cc_start: 0.8476 (t) cc_final: 0.7855 (m) REVERT: A 424 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7832 (mmt-90) REVERT: A 942 LYS cc_start: 0.8915 (tppt) cc_final: 0.8632 (mmtm) REVERT: A 951 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7164 (mtm110) REVERT: A 952 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: A 968 LYS cc_start: 0.7894 (tmtt) cc_final: 0.7546 (tppp) REVERT: A 976 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8007 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8627 (t0) cc_final: 0.8235 (p0) outliers start: 29 outliers final: 10 residues processed: 95 average time/residue: 0.9491 time to fit residues: 100.2637 Evaluate side-chains 77 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 40 optimal weight: 0.0030 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 983 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.134276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097527 restraints weight = 20615.916| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.07 r_work: 0.3256 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11952 Z= 0.204 Angle : 0.570 8.130 16882 Z= 0.307 Chirality : 0.039 0.237 2029 Planarity : 0.004 0.053 1639 Dihedral : 20.896 178.800 3191 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.83 % Allowed : 21.83 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1148 helix: 1.08 (0.22), residues: 580 sheet: -0.21 (0.48), residues: 113 loop : -0.66 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.005 0.001 HIS A1241 PHE 0.011 0.002 PHE A 966 TYR 0.022 0.001 TYR A 155 ARG 0.010 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 563) hydrogen bonds : angle 4.25781 ( 1525) covalent geometry : bond 0.00448 (11952) covalent geometry : angle 0.57035 (16882) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 1.844 Fit side-chains REVERT: A 80 CYS cc_start: 0.8469 (t) cc_final: 0.7881 (m) REVERT: A 317 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8209 (tp) REVERT: A 424 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7874 (mmt-90) REVERT: A 619 ILE cc_start: 0.8317 (mm) cc_final: 0.8105 (mp) REVERT: A 942 LYS cc_start: 0.8924 (tppt) cc_final: 0.8637 (mmtm) REVERT: A 952 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: A 968 LYS cc_start: 0.7963 (tmtt) cc_final: 0.7547 (tppp) REVERT: A 976 ARG cc_start: 0.8510 (mtt90) cc_final: 0.7999 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8695 (t0) cc_final: 0.8352 (p0) outliers start: 21 outliers final: 10 residues processed: 80 average time/residue: 1.0063 time to fit residues: 90.2534 Evaluate side-chains 73 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.1980 chunk 126 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.136529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.100297 restraints weight = 20857.122| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.08 r_work: 0.3303 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11952 Z= 0.131 Angle : 0.521 9.866 16882 Z= 0.279 Chirality : 0.037 0.231 2029 Planarity : 0.003 0.052 1639 Dihedral : 20.754 179.422 3191 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.29 % Allowed : 21.70 % Favored : 76.01 % 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: 0.56 (0.25), residues: 1148 helix: 1.29 (0.22), residues: 580 sheet: -0.18 (0.48), residues: 113 loop : -0.62 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.004 0.001 HIS A 982 PHE 0.017 0.001 PHE A 518 TYR 0.017 0.001 TYR A 155 ARG 0.011 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 563) hydrogen bonds : angle 4.06085 ( 1525) covalent geometry : bond 0.00282 (11952) covalent geometry : angle 0.52063 (16882) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 1.217 Fit side-chains REVERT: A 80 CYS cc_start: 0.8424 (t) cc_final: 0.6965 (m) REVERT: A 84 GLU cc_start: 0.8157 (pt0) cc_final: 0.7764 (pm20) REVERT: A 317 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 321 MET cc_start: 0.8882 (mmt) cc_final: 0.8381 (mmt) REVERT: A 424 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7761 (mmt-90) REVERT: A 952 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: A 968 LYS cc_start: 0.7931 (tmtt) cc_final: 0.7526 (tppp) REVERT: A 976 ARG cc_start: 0.8508 (mtt90) cc_final: 0.7977 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8644 (t0) cc_final: 0.8246 (p0) outliers start: 17 outliers final: 11 residues processed: 85 average time/residue: 0.9537 time to fit residues: 91.4196 Evaluate side-chains 76 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 96 optimal weight: 0.0010 chunk 8 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.134662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.098158 restraints weight = 20953.682| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.07 r_work: 0.3266 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11952 Z= 0.185 Angle : 0.558 10.634 16882 Z= 0.298 Chirality : 0.038 0.235 2029 Planarity : 0.004 0.052 1639 Dihedral : 20.837 179.426 3191 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.96 % Allowed : 21.70 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1148 helix: 1.29 (0.22), residues: 579 sheet: -0.22 (0.48), residues: 113 loop : -0.57 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.004 0.001 HIS A 167 PHE 0.009 0.001 PHE A 491 TYR 0.020 0.001 TYR A 155 ARG 0.013 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 563) hydrogen bonds : angle 4.12458 ( 1525) covalent geometry : bond 0.00407 (11952) covalent geometry : angle 0.55829 (16882) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 1.637 Fit side-chains REVERT: A 80 CYS cc_start: 0.8447 (t) cc_final: 0.7815 (m) REVERT: A 317 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8251 (tp) REVERT: A 424 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7821 (mmt-90) REVERT: A 952 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: A 969 ASP cc_start: 0.6988 (t70) cc_final: 0.6367 (m-30) REVERT: A 970 PHE cc_start: 0.5175 (m-80) cc_final: 0.4889 (m-80) REVERT: A 976 ARG cc_start: 0.8501 (mtt90) cc_final: 0.7985 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8696 (t0) cc_final: 0.8343 (p0) outliers start: 22 outliers final: 13 residues processed: 78 average time/residue: 1.2320 time to fit residues: 108.9229 Evaluate side-chains 72 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 10.0000 chunk 91 optimal weight: 0.0020 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 0.0020 chunk 115 optimal weight: 0.5980 chunk 104 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.1554 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.139333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103802 restraints weight = 20985.378| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.11 r_work: 0.3358 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11952 Z= 0.104 Angle : 0.502 9.871 16882 Z= 0.268 Chirality : 0.035 0.226 2029 Planarity : 0.003 0.063 1639 Dihedral : 20.607 179.565 3191 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.89 % Allowed : 22.64 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1148 helix: 1.64 (0.22), residues: 572 sheet: -0.11 (0.49), residues: 111 loop : -0.52 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1126 HIS 0.003 0.001 HIS A 412 PHE 0.018 0.001 PHE A 518 TYR 0.013 0.001 TYR A 594 ARG 0.012 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 563) hydrogen bonds : angle 3.87463 ( 1525) covalent geometry : bond 0.00215 (11952) covalent geometry : angle 0.50180 (16882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.424 Fit side-chains REVERT: A 80 CYS cc_start: 0.8286 (t) cc_final: 0.7712 (m) REVERT: A 317 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 321 MET cc_start: 0.8851 (mmt) cc_final: 0.8489 (mmt) REVERT: A 968 LYS cc_start: 0.7907 (tmtt) cc_final: 0.7506 (tppp) REVERT: A 976 ARG cc_start: 0.8435 (mtt90) cc_final: 0.7899 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8575 (t0) cc_final: 0.8106 (p0) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 1.1132 time to fit residues: 105.4119 Evaluate side-chains 66 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.134537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097876 restraints weight = 20958.581| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.08 r_work: 0.3259 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 11952 Z= 0.205 Angle : 0.573 12.995 16882 Z= 0.305 Chirality : 0.039 0.233 2029 Planarity : 0.004 0.064 1639 Dihedral : 20.825 179.487 3191 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.75 % Allowed : 23.05 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1148 helix: 1.43 (0.22), residues: 579 sheet: -0.21 (0.49), residues: 111 loop : -0.51 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.005 0.001 HIS A 167 PHE 0.019 0.002 PHE A 966 TYR 0.020 0.002 TYR A 155 ARG 0.013 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 563) hydrogen bonds : angle 4.07271 ( 1525) covalent geometry : bond 0.00454 (11952) covalent geometry : angle 0.57304 (16882) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.041 Fit side-chains REVERT: A 80 CYS cc_start: 0.8442 (t) cc_final: 0.7080 (m) REVERT: A 84 GLU cc_start: 0.8144 (pt0) cc_final: 0.7741 (pm20) REVERT: A 317 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8222 (tp) REVERT: A 524 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8524 (tt) REVERT: A 968 LYS cc_start: 0.8026 (tmtt) cc_final: 0.7585 (tppp) REVERT: A 976 ARG cc_start: 0.8513 (mtt90) cc_final: 0.7996 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8703 (t0) cc_final: 0.8356 (p0) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 1.3724 time to fit residues: 110.9376 Evaluate side-chains 69 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 14 optimal weight: 0.0050 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.135475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099166 restraints weight = 20773.381| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.06 r_work: 0.3277 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11952 Z= 0.163 Angle : 0.546 12.024 16882 Z= 0.292 Chirality : 0.038 0.232 2029 Planarity : 0.004 0.067 1639 Dihedral : 20.789 179.700 3191 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.75 % Allowed : 23.05 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1148 helix: 1.43 (0.22), residues: 579 sheet: -0.25 (0.50), residues: 111 loop : -0.51 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.004 0.001 HIS A 167 PHE 0.010 0.001 PHE A1080 TYR 0.021 0.001 TYR A 639 ARG 0.015 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 563) hydrogen bonds : angle 4.06638 ( 1525) covalent geometry : bond 0.00360 (11952) covalent geometry : angle 0.54564 (16882) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.100 Fit side-chains REVERT: A 80 CYS cc_start: 0.8429 (t) cc_final: 0.7031 (m) REVERT: A 84 GLU cc_start: 0.8125 (pt0) cc_final: 0.7705 (pm20) REVERT: A 317 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8340 (tp) REVERT: A 321 MET cc_start: 0.8914 (mmt) cc_final: 0.8368 (mmt) REVERT: A 969 ASP cc_start: 0.7147 (t70) cc_final: 0.6648 (m-30) REVERT: A 976 ARG cc_start: 0.8518 (mtt90) cc_final: 0.7988 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8683 (t0) cc_final: 0.8313 (p0) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.9117 time to fit residues: 74.2727 Evaluate side-chains 68 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 100 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.136087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.099906 restraints weight = 20678.709| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.06 r_work: 0.3288 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11952 Z= 0.147 Angle : 0.540 11.505 16882 Z= 0.287 Chirality : 0.037 0.231 2029 Planarity : 0.004 0.067 1639 Dihedral : 20.698 179.947 3191 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.62 % Allowed : 23.32 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1148 helix: 1.44 (0.22), residues: 584 sheet: -0.23 (0.50), residues: 112 loop : -0.50 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.003 0.001 HIS A 982 PHE 0.014 0.001 PHE A 970 TYR 0.017 0.001 TYR A 639 ARG 0.014 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 563) hydrogen bonds : angle 3.99612 ( 1525) covalent geometry : bond 0.00326 (11952) covalent geometry : angle 0.54049 (16882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11253.29 seconds wall clock time: 205 minutes 49.22 seconds (12349.22 seconds total)