Starting phenix.real_space_refine on Fri Aug 22 21:11:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iem_35386/08_2025/8iem_35386_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iem_35386/08_2025/8iem_35386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iem_35386/08_2025/8iem_35386_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iem_35386/08_2025/8iem_35386_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iem_35386/08_2025/8iem_35386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iem_35386/08_2025/8iem_35386.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.031 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 53 5.16 5 Be 1 3.05 5 C 5057 2.51 5 N 1344 2.21 5 O 1370 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7829 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7810 Classifications: {'peptide': 1011} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 67, 'TRANS': 938} Chain breaks: 5 Chain: "P" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' MG': 1, 'BEF': 1, 'SPM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.53, per 1000 atoms: 0.20 Number of scatterers: 7829 At special positions: 0 Unit cell: (107.31, 125.925, 107.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 53 16.00 Mg 1 11.99 F 3 9.00 O 1370 8.00 N 1344 7.00 C 5057 6.00 Be 1 4.00 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: 0.41 Conformation dependent library (CDL) restraints added in 315.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 43.9% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'P' and resid 50 through 58 Processing helix chain 'P' and resid 61 through 66 Processing helix chain 'P' and resid 68 through 77 removed outlier: 3.571A pdb=" N ARG P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU P 77 " --> pdb=" O VAL P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 200 removed outlier: 4.154A pdb=" N HIS P 198 " --> pdb=" O CYS P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 209 through 217 Processing helix chain 'P' and resid 230 through 235 Processing helix chain 'P' and resid 241 through 254 removed outlier: 3.528A pdb=" N LEU P 250 " --> pdb=" O PHE P 246 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP P 254 " --> pdb=" O LEU P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 289 removed outlier: 3.574A pdb=" N ALA P 260 " --> pdb=" O TYR P 256 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER P 270 " --> pdb=" O ILE P 266 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS P 272 " --> pdb=" O SER P 268 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU P 275 " --> pdb=" O ILE P 271 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR P 276 " --> pdb=" O CYS P 272 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN P 281 " --> pdb=" O LYS P 277 " (cutoff:3.500A) Processing helix chain 'P' and resid 402 through 412 removed outlier: 3.752A pdb=" N LEU P 407 " --> pdb=" O ALA P 403 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL P 408 " --> pdb=" O LYS P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 424 through 450 removed outlier: 3.946A pdb=" N PHE P 428 " --> pdb=" O HIS P 424 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU P 438 " --> pdb=" O VAL P 434 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY P 439 " --> pdb=" O LEU P 435 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE P 441 " --> pdb=" O LEU P 437 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN P 450 " --> pdb=" O ILE P 446 " (cutoff:3.500A) Processing helix chain 'P' and resid 456 through 468 removed outlier: 3.613A pdb=" N ARG P 460 " --> pdb=" O GLU P 456 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA P 461 " --> pdb=" O ILE P 457 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL P 468 " --> pdb=" O LEU P 464 " (cutoff:3.500A) Processing helix chain 'P' and resid 472 through 489 removed outlier: 4.347A pdb=" N TYR P 483 " --> pdb=" O VAL P 479 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA P 484 " --> pdb=" O CYS P 480 " (cutoff:3.500A) Processing helix chain 'P' and resid 490 through 492 No H-bonds generated for 'chain 'P' and resid 490 through 492' Processing helix chain 'P' and resid 549 through 558 removed outlier: 4.083A pdb=" N ARG P 553 " --> pdb=" O GLY P 549 " (cutoff:3.500A) Processing helix chain 'P' and resid 573 through 580 Processing helix chain 'P' and resid 656 through 663 Processing helix chain 'P' and resid 673 through 683 removed outlier: 3.952A pdb=" N LEU P 677 " --> pdb=" O PHE P 673 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN P 678 " --> pdb=" O ALA P 674 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER P 679 " --> pdb=" O GLN P 675 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA P 683 " --> pdb=" O SER P 679 " (cutoff:3.500A) Processing helix chain 'P' and resid 696 through 707 Processing helix chain 'P' and resid 731 through 741 removed outlier: 3.786A pdb=" N VAL P 735 " --> pdb=" O GLN P 731 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG P 741 " --> pdb=" O GLN P 737 " (cutoff:3.500A) Processing helix chain 'P' and resid 753 through 765 Processing helix chain 'P' and resid 826 through 834 Processing helix chain 'P' and resid 855 through 868 removed outlier: 3.593A pdb=" N LYS P 859 " --> pdb=" O ALA P 855 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR P 860 " --> pdb=" O PRO P 856 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU P 861 " --> pdb=" O GLU P 857 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS P 868 " --> pdb=" O CYS P 864 " (cutoff:3.500A) Processing helix chain 'P' and resid 914 through 951 removed outlier: 4.030A pdb=" N MET P 918 " --> pdb=" O GLU P 914 " (cutoff:3.500A) Processing helix chain 'P' and resid 952 through 954 No H-bonds generated for 'chain 'P' and resid 952 through 954' Processing helix chain 'P' and resid 959 through 978 removed outlier: 3.921A pdb=" N ALA P 975 " --> pdb=" O THR P 971 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL P 976 " --> pdb=" O THR P 972 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU P 977 " --> pdb=" O THR P 973 " (cutoff:3.500A) Processing helix chain 'P' and resid 979 through 981 No H-bonds generated for 'chain 'P' and resid 979 through 981' Processing helix chain 'P' and resid 998 through 1003 Processing helix chain 'P' and resid 1004 through 1023 removed outlier: 3.581A pdb=" N LEU P1011 " --> pdb=" O LEU P1007 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR P1023 " --> pdb=" O GLY P1019 " (cutoff:3.500A) Processing helix chain 'P' and resid 1024 through 1026 No H-bonds generated for 'chain 'P' and resid 1024 through 1026' Processing helix chain 'P' and resid 1044 through 1065 Processing helix chain 'P' and resid 1078 through 1098 removed outlier: 3.965A pdb=" N VAL P1096 " --> pdb=" O LEU P1092 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL P1098 " --> pdb=" O GLY P1094 " (cutoff:3.500A) Processing helix chain 'P' and resid 1115 through 1138 removed outlier: 3.695A pdb=" N LEU P1119 " --> pdb=" O GLY P1115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE P1132 " --> pdb=" O PHE P1128 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET P1133 " --> pdb=" O VAL P1129 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU P1138 " --> pdb=" O LEU P1134 " (cutoff:3.500A) Processing helix chain 'P' and resid 1141 through 1148 Processing helix chain 'P' and resid 1156 through 1168 removed outlier: 3.792A pdb=" N LYS P1160 " --> pdb=" O LYS P1156 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU P1168 " --> pdb=" O ARG P1164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 40 through 42 removed outlier: 3.651A pdb=" N CYS P 41 " --> pdb=" O ILE P 90 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 90 " --> pdb=" O CYS P 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'P' and resid 104 through 105 removed outlier: 4.119A pdb=" N TYR P 165 " --> pdb=" O VAL P 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 174 through 176 removed outlier: 3.564A pdb=" N TYR P 183 " --> pdb=" O ILE P 174 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE P 176 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA P 181 " --> pdb=" O ILE P 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 294 through 299 removed outlier: 3.702A pdb=" N VAL P 307 " --> pdb=" O VAL P 295 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL P 297 " --> pdb=" O GLU P 305 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU P 305 " --> pdb=" O VAL P 297 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU P 303 " --> pdb=" O ARG P 299 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 317 through 319 Processing sheet with id=AA6, first strand: chain 'P' and resid 351 through 352 removed outlier: 4.169A pdb=" N VAL P 340 " --> pdb=" O VAL P 352 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU P 337 " --> pdb=" O ARG P 384 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET P 339 " --> pdb=" O GLN P 382 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN P 382 " --> pdb=" O MET P 339 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASN P 341 " --> pdb=" O ILE P 380 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE P 380 " --> pdb=" O ASN P 341 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 509 through 512 removed outlier: 3.525A pdb=" N VAL P 510 " --> pdb=" O ARG P 745 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL P 747 " --> pdb=" O VAL P 510 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N PHE P 851 " --> pdb=" O ALA P 746 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N MET P 748 " --> pdb=" O PHE P 851 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 624 through 627 removed outlier: 4.228A pdb=" N HIS P 626 " --> pdb=" O VAL P 640 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL P 640 " --> pdb=" O HIS P 626 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA P 651 " --> pdb=" O LYS P 693 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL P 688 " --> pdb=" O LEU P 721 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU P 721 " --> pdb=" O VAL P 688 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU P 690 " --> pdb=" O LEU P 719 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 893 through 894 292 hydrogen bonds defined for protein. 864 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: 1.09 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1371 1.33 - 1.45: 1888 1.45 - 1.57: 4660 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 7998 Sorted by residual: bond pdb=" CA TYR P 240 " pdb=" C TYR P 240 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" C PRO P 470 " pdb=" O PRO P 470 " ideal model delta sigma weight residual 1.240 1.204 0.036 1.12e-02 7.97e+03 1.04e+01 bond pdb=" CA PRO P 470 " pdb=" C PRO P 470 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.94e+00 bond pdb=" C VAL P 469 " pdb=" O VAL P 469 " ideal model delta sigma weight residual 1.240 1.204 0.035 1.26e-02 6.30e+03 7.87e+00 bond pdb=" CA VAL P 525 " pdb=" C VAL P 525 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.26e-02 6.30e+03 7.84e+00 ... (remaining 7993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 10691 2.23 - 4.45: 152 4.45 - 6.68: 31 6.68 - 8.91: 9 8.91 - 11.13: 3 Bond angle restraints: 10886 Sorted by residual: angle pdb=" C LEU P 546 " pdb=" N PRO P 547 " pdb=" CA PRO P 547 " ideal model delta sigma weight residual 120.98 114.22 6.76 1.07e+00 8.73e-01 4.00e+01 angle pdb=" N TYR P 240 " pdb=" CA TYR P 240 " pdb=" C TYR P 240 " ideal model delta sigma weight residual 113.17 105.29 7.88 1.26e+00 6.30e-01 3.91e+01 angle pdb=" C LEU P 539 " pdb=" N VAL P 540 " pdb=" CA VAL P 540 " ideal model delta sigma weight residual 121.70 132.83 -11.13 1.80e+00 3.09e-01 3.83e+01 angle pdb=" N PRO P 470 " pdb=" CA PRO P 470 " pdb=" C PRO P 470 " ideal model delta sigma weight residual 110.70 117.45 -6.75 1.22e+00 6.72e-01 3.06e+01 angle pdb=" C TYR P 240 " pdb=" N TYR P 241 " pdb=" CA TYR P 241 " ideal model delta sigma weight residual 122.79 113.58 9.21 1.78e+00 3.16e-01 2.68e+01 ... (remaining 10881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4162 17.76 - 35.51: 512 35.51 - 53.27: 138 53.27 - 71.03: 14 71.03 - 88.79: 11 Dihedral angle restraints: 4837 sinusoidal: 1913 harmonic: 2924 Sorted by residual: dihedral pdb=" CA PRO P 229 " pdb=" C PRO P 229 " pdb=" N GLN P 230 " pdb=" CA GLN P 230 " ideal model delta harmonic sigma weight residual -180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA PRO P 239 " pdb=" C PRO P 239 " pdb=" N TYR P 240 " pdb=" CA TYR P 240 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LYS P 514 " pdb=" C LYS P 514 " pdb=" N THR P 515 " pdb=" CA THR P 515 " ideal model delta harmonic sigma weight residual 180.00 160.77 19.23 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 4834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1073 0.051 - 0.102: 193 0.102 - 0.154: 27 0.154 - 0.205: 1 0.205 - 0.256: 1 Chirality restraints: 1295 Sorted by residual: chirality pdb=" CA VAL P 469 " pdb=" N VAL P 469 " pdb=" C VAL P 469 " pdb=" CB VAL P 469 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA ASN P 238 " pdb=" N ASN P 238 " pdb=" C ASN P 238 " pdb=" CB ASN P 238 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CB VAL P 468 " pdb=" CA VAL P 468 " pdb=" CG1 VAL P 468 " pdb=" CG2 VAL P 468 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 1292 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU P 237 " -0.027 2.00e-02 2.50e+03 5.60e-02 3.13e+01 pdb=" C LEU P 237 " 0.097 2.00e-02 2.50e+03 pdb=" O LEU P 237 " -0.038 2.00e-02 2.50e+03 pdb=" N ASN P 238 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR P 228 " -0.086 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO P 229 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO P 229 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO P 229 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 523 " 0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C LEU P 523 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU P 523 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP P 524 " 0.023 2.00e-02 2.50e+03 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 799 2.75 - 3.29: 7407 3.29 - 3.82: 12272 3.82 - 4.36: 12452 4.36 - 4.90: 22439 Nonbonded interactions: 55369 Sorted by model distance: nonbonded pdb=" OG1 THR P 515 " pdb=" F1 BEF P1203 " model vdw 2.211 2.990 nonbonded pdb=" OD1 ASN P 881 " pdb=" F1 BEF P1203 " model vdw 2.282 2.990 nonbonded pdb=" OD1 ASP P 513 " pdb="BE BEF P1203 " model vdw 2.285 2.420 nonbonded pdb=" OG1 THR P 515 " pdb=" F2 BEF P1203 " model vdw 2.291 2.990 nonbonded pdb=" O ASP P 878 " pdb=" OG SER P 896 " model vdw 2.302 3.040 ... (remaining 55364 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: 1.970 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 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 0.054 7998 Z= 0.176 Angle : 0.689 11.135 10886 Z= 0.381 Chirality : 0.041 0.256 1295 Planarity : 0.007 0.128 1367 Dihedral : 16.411 88.786 2949 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.21 % Favored : 93.69 % Rotamer: Outliers : 0.58 % Allowed : 21.99 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.28), residues: 999 helix: 1.39 (0.28), residues: 410 sheet: -0.86 (0.74), residues: 64 loop : -2.48 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 980 TYR 0.012 0.001 TYR P 442 PHE 0.023 0.001 PHE P 963 TRP 0.018 0.001 TRP P 100 HIS 0.002 0.000 HIS P 390 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7998) covalent geometry : angle 0.68927 (10886) hydrogen bonds : bond 0.15465 ( 292) hydrogen bonds : angle 5.88220 ( 864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.0651 time to fit residues: 9.1706 Evaluate side-chains 97 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 524 ASP Chi-restraints excluded: chain P residue 525 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.0050 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 390 HIS P 867 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.235395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.188400 restraints weight = 12039.358| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 3.57 r_work: 0.4222 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7998 Z= 0.141 Angle : 0.613 12.254 10886 Z= 0.292 Chirality : 0.043 0.201 1295 Planarity : 0.006 0.080 1367 Dihedral : 4.822 53.454 1112 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.47 % Allowed : 20.72 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.27), residues: 999 helix: 1.36 (0.28), residues: 401 sheet: -0.99 (0.67), residues: 70 loop : -2.61 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 544 TYR 0.014 0.001 TYR P 442 PHE 0.013 0.001 PHE P1051 TRP 0.015 0.001 TRP P 100 HIS 0.005 0.001 HIS P 372 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7998) covalent geometry : angle 0.61308 (10886) hydrogen bonds : bond 0.03345 ( 292) hydrogen bonds : angle 4.16955 ( 864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.237 Fit side-chains REVERT: P 176 ILE cc_start: 0.8605 (mm) cc_final: 0.8340 (mt) REVERT: P 240 TYR cc_start: 0.8114 (t80) cc_final: 0.7762 (t80) REVERT: P 256 TYR cc_start: 0.3985 (OUTLIER) cc_final: 0.3219 (m-10) REVERT: P 265 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7901 (tt) REVERT: P 287 ASP cc_start: 0.7418 (m-30) cc_final: 0.7103 (m-30) REVERT: P 1005 LEU cc_start: 0.7431 (mm) cc_final: 0.7090 (mt) outliers start: 30 outliers final: 13 residues processed: 137 average time/residue: 0.0720 time to fit residues: 13.9838 Evaluate side-chains 127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 CYS Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 265 LEU Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 392 LEU Chi-restraints excluded: chain P residue 413 HIS Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 1017 LEU Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 30.0000 chunk 57 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 98 optimal weight: 0.4980 chunk 64 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 HIS P 390 HIS P 497 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.226614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.178879 restraints weight = 12034.960| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 4.22 r_work: 0.4079 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7998 Z= 0.129 Angle : 0.591 10.280 10886 Z= 0.277 Chirality : 0.041 0.159 1295 Planarity : 0.005 0.064 1367 Dihedral : 4.805 52.496 1109 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.17 % Allowed : 21.88 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.27), residues: 999 helix: 1.47 (0.28), residues: 406 sheet: -1.37 (0.69), residues: 62 loop : -2.47 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 487 TYR 0.012 0.001 TYR P 442 PHE 0.009 0.001 PHE P 830 TRP 0.017 0.001 TRP P 100 HIS 0.004 0.001 HIS P 198 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7998) covalent geometry : angle 0.59098 (10886) hydrogen bonds : bond 0.03322 ( 292) hydrogen bonds : angle 3.90880 ( 864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: P 169 GLN cc_start: 0.6806 (tp40) cc_final: 0.6342 (mt0) REVERT: P 176 ILE cc_start: 0.8677 (mm) cc_final: 0.8429 (mt) REVERT: P 185 VAL cc_start: 0.3827 (OUTLIER) cc_final: 0.2065 (p) REVERT: P 283 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7501 (tt0) REVERT: P 615 MET cc_start: 0.6013 (ptt) cc_final: 0.5192 (mmp) REVERT: P 942 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7477 (mp) REVERT: P 951 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7602 (tp) REVERT: P 987 LEU cc_start: 0.5330 (tp) cc_final: 0.5047 (tp) REVERT: P 1009 MET cc_start: 0.8212 (mmm) cc_final: 0.7984 (mmm) REVERT: P 1102 LEU cc_start: 0.5079 (tt) cc_final: 0.4229 (mt) outliers start: 36 outliers final: 18 residues processed: 151 average time/residue: 0.0718 time to fit residues: 15.1855 Evaluate side-chains 126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 327 MET Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 521 ASP Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 951 LEU Chi-restraints excluded: chain P residue 1024 LEU Chi-restraints excluded: chain P residue 1061 LEU Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 202 HIS P 255 HIS P 497 HIS P 626 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.211243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.159062 restraints weight = 11942.763| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 4.21 r_work: 0.3890 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7998 Z= 0.150 Angle : 0.667 10.560 10886 Z= 0.320 Chirality : 0.044 0.155 1295 Planarity : 0.005 0.050 1367 Dihedral : 5.294 53.641 1109 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.63 % Allowed : 24.31 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.27), residues: 999 helix: 1.19 (0.27), residues: 415 sheet: -1.29 (0.60), residues: 82 loop : -2.57 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 294 TYR 0.016 0.002 TYR P1020 PHE 0.009 0.001 PHE P 830 TRP 0.038 0.002 TRP P 100 HIS 0.008 0.001 HIS P 390 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7998) covalent geometry : angle 0.66718 (10886) hydrogen bonds : bond 0.04039 ( 292) hydrogen bonds : angle 3.89506 ( 864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.252 Fit side-chains REVERT: P 250 LEU cc_start: 0.9025 (tp) cc_final: 0.8766 (tp) REVERT: P 283 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7121 (tm-30) REVERT: P 390 HIS cc_start: 0.7719 (t-170) cc_final: 0.7317 (t-170) REVERT: P 615 MET cc_start: 0.5747 (ptt) cc_final: 0.4866 (mmt) REVERT: P 777 HIS cc_start: 0.3190 (OUTLIER) cc_final: 0.2011 (t-90) REVERT: P 843 LYS cc_start: 0.6004 (tttm) cc_final: 0.5362 (tmtt) REVERT: P 942 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7673 (mp) REVERT: P 1024 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7215 (mt) outliers start: 40 outliers final: 26 residues processed: 153 average time/residue: 0.0789 time to fit residues: 16.4608 Evaluate side-chains 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 327 MET Chi-restraints excluded: chain P residue 392 LEU Chi-restraints excluded: chain P residue 413 HIS Chi-restraints excluded: chain P residue 435 LEU Chi-restraints excluded: chain P residue 466 THR Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 777 HIS Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 951 LEU Chi-restraints excluded: chain P residue 964 LEU Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1024 LEU Chi-restraints excluded: chain P residue 1032 LEU Chi-restraints excluded: chain P residue 1061 LEU Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1124 VAL Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 202 HIS P 881 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.208320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.157202 restraints weight = 11528.591| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 3.83 r_work: 0.3883 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7998 Z= 0.123 Angle : 0.610 10.603 10886 Z= 0.290 Chirality : 0.042 0.144 1295 Planarity : 0.005 0.071 1367 Dihedral : 5.163 59.511 1109 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.51 % Allowed : 25.12 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.28), residues: 999 helix: 1.31 (0.27), residues: 417 sheet: -1.20 (0.55), residues: 94 loop : -2.49 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 294 TYR 0.010 0.001 TYR P 183 PHE 0.010 0.001 PHE P 830 TRP 0.023 0.002 TRP P 100 HIS 0.002 0.001 HIS P 84 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7998) covalent geometry : angle 0.60961 (10886) hydrogen bonds : bond 0.03389 ( 292) hydrogen bonds : angle 3.74955 ( 864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.210 Fit side-chains REVERT: P 64 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6921 (mt) REVERT: P 208 ASP cc_start: 0.7320 (t0) cc_final: 0.7021 (t0) REVERT: P 283 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7176 (tm-30) REVERT: P 390 HIS cc_start: 0.7427 (t-170) cc_final: 0.7105 (t-170) REVERT: P 777 HIS cc_start: 0.3333 (OUTLIER) cc_final: 0.2141 (t-90) REVERT: P 843 LYS cc_start: 0.5481 (tttm) cc_final: 0.5224 (tmtt) REVERT: P 942 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7641 (mp) REVERT: P 951 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7735 (tp) REVERT: P 1024 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7389 (mt) outliers start: 39 outliers final: 25 residues processed: 138 average time/residue: 0.0694 time to fit residues: 13.6155 Evaluate side-chains 133 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 327 MET Chi-restraints excluded: chain P residue 376 CYS Chi-restraints excluded: chain P residue 392 LEU Chi-restraints excluded: chain P residue 413 HIS Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 777 HIS Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 951 LEU Chi-restraints excluded: chain P residue 1024 LEU Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1097 LEU Chi-restraints excluded: chain P residue 1118 LEU Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 7.9990 chunk 65 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1026 GLN ** P1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.204172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.152472 restraints weight = 11445.096| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 3.76 r_work: 0.3824 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7998 Z= 0.126 Angle : 0.627 10.456 10886 Z= 0.296 Chirality : 0.043 0.194 1295 Planarity : 0.005 0.071 1367 Dihedral : 4.805 52.139 1109 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.86 % Allowed : 25.23 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.28), residues: 999 helix: 1.36 (0.27), residues: 417 sheet: -1.18 (0.56), residues: 92 loop : -2.38 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 294 TYR 0.015 0.001 TYR P 228 PHE 0.010 0.001 PHE P1029 TRP 0.028 0.002 TRP P1028 HIS 0.002 0.001 HIS P 369 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7998) covalent geometry : angle 0.62723 (10886) hydrogen bonds : bond 0.03406 ( 292) hydrogen bonds : angle 3.70410 ( 864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.218 Fit side-chains REVERT: P 64 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6883 (mt) REVERT: P 208 ASP cc_start: 0.7234 (t0) cc_final: 0.6892 (t0) REVERT: P 283 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7129 (tm-30) REVERT: P 777 HIS cc_start: 0.3582 (OUTLIER) cc_final: 0.2238 (t-90) REVERT: P 942 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7609 (mp) REVERT: P 1024 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7519 (mt) outliers start: 42 outliers final: 28 residues processed: 142 average time/residue: 0.0673 time to fit residues: 13.7371 Evaluate side-chains 136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 56 MET Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 327 MET Chi-restraints excluded: chain P residue 376 CYS Chi-restraints excluded: chain P residue 392 LEU Chi-restraints excluded: chain P residue 413 HIS Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 777 HIS Chi-restraints excluded: chain P residue 841 LEU Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 951 LEU Chi-restraints excluded: chain P residue 968 LEU Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1024 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1118 LEU Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 0.0870 chunk 50 optimal weight: 0.0170 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 944 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.205508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.152975 restraints weight = 11848.221| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 4.11 r_work: 0.3827 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7998 Z= 0.110 Angle : 0.629 15.379 10886 Z= 0.288 Chirality : 0.042 0.144 1295 Planarity : 0.005 0.066 1367 Dihedral : 4.721 56.663 1109 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.98 % Allowed : 25.69 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.28), residues: 999 helix: 1.44 (0.27), residues: 417 sheet: -1.24 (0.55), residues: 94 loop : -2.34 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 370 TYR 0.010 0.001 TYR P 183 PHE 0.015 0.001 PHE P 103 TRP 0.029 0.002 TRP P1028 HIS 0.002 0.000 HIS P 836 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7998) covalent geometry : angle 0.62852 (10886) hydrogen bonds : bond 0.03161 ( 292) hydrogen bonds : angle 3.69316 ( 864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.322 Fit side-chains REVERT: P 64 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6947 (mt) REVERT: P 176 ILE cc_start: 0.8785 (mm) cc_final: 0.8339 (mt) REVERT: P 208 ASP cc_start: 0.7099 (t0) cc_final: 0.6791 (t0) REVERT: P 283 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7092 (tm-30) REVERT: P 777 HIS cc_start: 0.3566 (OUTLIER) cc_final: 0.2186 (t-170) REVERT: P 942 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7647 (mp) REVERT: P 1061 LEU cc_start: 0.6252 (mm) cc_final: 0.5630 (mt) outliers start: 43 outliers final: 25 residues processed: 133 average time/residue: 0.0647 time to fit residues: 12.6565 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 56 MET Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 327 MET Chi-restraints excluded: chain P residue 376 CYS Chi-restraints excluded: chain P residue 392 LEU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 777 HIS Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 968 LEU Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1097 LEU Chi-restraints excluded: chain P residue 1111 ILE Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 0.0770 chunk 92 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 75 optimal weight: 0.0470 chunk 55 optimal weight: 0.0470 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 overall best weight: 0.1534 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.207868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155621 restraints weight = 11920.619| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 4.10 r_work: 0.3866 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7998 Z= 0.101 Angle : 0.621 11.273 10886 Z= 0.283 Chirality : 0.041 0.135 1295 Planarity : 0.005 0.068 1367 Dihedral : 4.542 59.944 1109 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.24 % Allowed : 27.31 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.28), residues: 999 helix: 1.65 (0.27), residues: 410 sheet: -1.26 (0.54), residues: 92 loop : -2.30 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 370 TYR 0.010 0.001 TYR P 256 PHE 0.008 0.001 PHE P 963 TRP 0.028 0.002 TRP P 100 HIS 0.002 0.000 HIS P 390 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7998) covalent geometry : angle 0.62061 (10886) hydrogen bonds : bond 0.02683 ( 292) hydrogen bonds : angle 3.65312 ( 864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.172 Fit side-chains REVERT: P 64 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6931 (mt) REVERT: P 176 ILE cc_start: 0.8771 (mm) cc_final: 0.8324 (mt) REVERT: P 208 ASP cc_start: 0.7046 (t0) cc_final: 0.6710 (t0) REVERT: P 283 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7050 (tm-30) REVERT: P 509 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8184 (pt) REVERT: P 777 HIS cc_start: 0.3496 (OUTLIER) cc_final: 0.2095 (t-90) REVERT: P 942 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7654 (mp) REVERT: P 1061 LEU cc_start: 0.6150 (mm) cc_final: 0.5482 (mt) outliers start: 28 outliers final: 18 residues processed: 122 average time/residue: 0.0604 time to fit residues: 10.7331 Evaluate side-chains 127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 56 MET Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 327 MET Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 392 LEU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 777 HIS Chi-restraints excluded: chain P residue 836 HIS Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1097 LEU Chi-restraints excluded: chain P residue 1111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 47 optimal weight: 3.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.205198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.152165 restraints weight = 11834.298| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 4.09 r_work: 0.3823 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7998 Z= 0.107 Angle : 0.630 10.783 10886 Z= 0.288 Chirality : 0.042 0.129 1295 Planarity : 0.005 0.066 1367 Dihedral : 4.482 55.502 1109 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.70 % Allowed : 27.20 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.28), residues: 999 helix: 1.66 (0.27), residues: 411 sheet: -1.35 (0.55), residues: 92 loop : -2.26 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 370 TYR 0.009 0.001 TYR P 256 PHE 0.016 0.001 PHE P 103 TRP 0.029 0.002 TRP P1028 HIS 0.004 0.001 HIS P 390 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7998) covalent geometry : angle 0.62993 (10886) hydrogen bonds : bond 0.02971 ( 292) hydrogen bonds : angle 3.62064 ( 864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: P 62 LEU cc_start: 0.6867 (mt) cc_final: 0.6308 (pp) REVERT: P 64 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6992 (mt) REVERT: P 176 ILE cc_start: 0.8763 (mm) cc_final: 0.8309 (mt) REVERT: P 208 ASP cc_start: 0.7033 (t0) cc_final: 0.6694 (t0) REVERT: P 283 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7063 (tm-30) REVERT: P 452 VAL cc_start: 0.7087 (t) cc_final: 0.6885 (p) REVERT: P 615 MET cc_start: 0.5301 (ptt) cc_final: 0.4215 (mmp) REVERT: P 942 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7613 (mp) REVERT: P 1061 LEU cc_start: 0.6263 (mm) cc_final: 0.5655 (mt) outliers start: 32 outliers final: 25 residues processed: 127 average time/residue: 0.0664 time to fit residues: 12.3253 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 56 MET Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 327 MET Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 392 LEU Chi-restraints excluded: chain P residue 413 HIS Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 777 HIS Chi-restraints excluded: chain P residue 841 LEU Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1097 LEU Chi-restraints excluded: chain P residue 1111 ILE Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 0.0470 chunk 88 optimal weight: 0.7980 chunk 50 optimal weight: 0.0270 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 244 GLN ** P 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.204239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.151532 restraints weight = 11740.316| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 4.16 r_work: 0.3808 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7998 Z= 0.107 Angle : 0.628 10.560 10886 Z= 0.286 Chirality : 0.041 0.128 1295 Planarity : 0.005 0.069 1367 Dihedral : 4.431 53.749 1109 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.47 % Allowed : 27.89 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.28), residues: 999 helix: 1.68 (0.27), residues: 411 sheet: -1.35 (0.54), residues: 92 loop : -2.25 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 370 TYR 0.011 0.001 TYR P 256 PHE 0.011 0.001 PHE P 963 TRP 0.032 0.002 TRP P1028 HIS 0.004 0.001 HIS P 390 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7998) covalent geometry : angle 0.62753 (10886) hydrogen bonds : bond 0.02972 ( 292) hydrogen bonds : angle 3.62745 ( 864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.269 Fit side-chains REVERT: P 176 ILE cc_start: 0.8728 (mm) cc_final: 0.8267 (mt) REVERT: P 208 ASP cc_start: 0.7079 (t0) cc_final: 0.6740 (t0) REVERT: P 283 GLN cc_start: 0.7802 (tm-30) cc_final: 0.6984 (tm-30) REVERT: P 777 HIS cc_start: 0.3618 (OUTLIER) cc_final: 0.2037 (t-170) REVERT: P 942 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7628 (mp) REVERT: P 1061 LEU cc_start: 0.6288 (mm) cc_final: 0.5689 (mt) outliers start: 30 outliers final: 24 residues processed: 123 average time/residue: 0.0680 time to fit residues: 12.2111 Evaluate side-chains 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 56 MET Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 327 MET Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 392 LEU Chi-restraints excluded: chain P residue 413 HIS Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 777 HIS Chi-restraints excluded: chain P residue 841 LEU Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1097 LEU Chi-restraints excluded: chain P residue 1111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.200917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.148984 restraints weight = 11709.110| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.94 r_work: 0.3767 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7998 Z= 0.121 Angle : 0.652 10.479 10886 Z= 0.299 Chirality : 0.042 0.134 1295 Planarity : 0.005 0.064 1367 Dihedral : 4.432 54.824 1109 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.70 % Allowed : 27.66 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.28), residues: 999 helix: 1.67 (0.27), residues: 411 sheet: -1.33 (0.54), residues: 94 loop : -2.23 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 370 TYR 0.011 0.001 TYR P 183 PHE 0.012 0.001 PHE P 963 TRP 0.043 0.003 TRP P 67 HIS 0.005 0.001 HIS P 390 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7998) covalent geometry : angle 0.65187 (10886) hydrogen bonds : bond 0.03349 ( 292) hydrogen bonds : angle 3.60675 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.98 seconds wall clock time: 36 minutes 8.66 seconds (2168.66 seconds total)