Starting phenix.real_space_refine on Wed Feb 12 13:41:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iem_35386/02_2025/8iem_35386_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iem_35386/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8iem_35386/02_2025/8iem_35386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iem_35386/02_2025/8iem_35386.map" model { file = "/net/cci-nas-00/data/ceres_data/8iem_35386/02_2025/8iem_35386_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iem_35386/02_2025/8iem_35386_trim.cif" } resolution = 3.35 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= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.35, per 1000 atoms: 0.68 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: 2.19 Conformation dependent library (CDL) restraints added in 983.5 milliseconds 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: 1.08 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: 2.42 Time building geometry restraints manager: 2.50 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.870 ------------------------------------------------------------------------------- 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= 0.201 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 (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: -1.00 (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 TRP 0.018 0.001 TRP P 100 HIS 0.002 0.000 HIS P 390 PHE 0.023 0.001 PHE P 963 TYR 0.012 0.001 TYR P 442 ARG 0.008 0.000 ARG P 980 *********************** 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 : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.1884 time to fit residues: 26.2450 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 : 0.817 ------------------------------------------------------------------------------- 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 85 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.0770 chunk 26 optimal weight: 0.0670 chunk 51 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.0470 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 390 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.247442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.204233 restraints weight = 12030.358| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 3.71 r_work: 0.4356 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7998 Z= 0.148 Angle : 0.557 11.888 10886 Z= 0.260 Chirality : 0.040 0.152 1295 Planarity : 0.005 0.081 1367 Dihedral : 4.644 53.426 1112 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.43 % Allowed : 21.30 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % 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: -1.04 (0.27), residues: 999 helix: 1.52 (0.28), residues: 400 sheet: -1.15 (0.71), residues: 64 loop : -2.54 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 100 HIS 0.003 0.000 HIS P 413 PHE 0.007 0.001 PHE P 945 TYR 0.012 0.001 TYR P 442 ARG 0.005 0.000 ARG P 980 *********************** 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 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.915 Fit side-chains REVERT: P 256 TYR cc_start: 0.3125 (OUTLIER) cc_final: 0.2594 (m-10) REVERT: P 265 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7827 (tt) REVERT: P 615 MET cc_start: 0.5022 (mmp) cc_final: 0.4755 (ptt) outliers start: 21 outliers final: 7 residues processed: 123 average time/residue: 0.1723 time to fit residues: 30.4861 Evaluate side-chains 114 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 99 optimal weight: 0.0070 chunk 49 optimal weight: 9.9990 chunk 83 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 HIS P 497 HIS P 881 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.222994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173903 restraints weight = 12171.197| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 4.33 r_work: 0.4034 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 7998 Z= 0.229 Angle : 0.670 9.980 10886 Z= 0.322 Chirality : 0.043 0.215 1295 Planarity : 0.006 0.081 1367 Dihedral : 5.079 59.909 1109 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.21 % Favored : 92.69 % Rotamer: Outliers : 5.09 % Allowed : 20.95 % 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 (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: -1.09 (0.27), residues: 999 helix: 1.37 (0.28), residues: 406 sheet: -1.36 (0.68), residues: 62 loop : -2.50 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 100 HIS 0.005 0.001 HIS P 372 PHE 0.014 0.002 PHE P 963 TYR 0.016 0.002 TYR P 442 ARG 0.004 0.000 ARG P1072 *********************** 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 172 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: P 176 ILE cc_start: 0.8768 (mm) cc_final: 0.8520 (mt) REVERT: P 177 GLU cc_start: 0.8164 (pp20) cc_final: 0.7732 (pm20) REVERT: P 185 VAL cc_start: 0.3956 (OUTLIER) cc_final: 0.3301 (t) REVERT: P 208 ASP cc_start: 0.7260 (t0) cc_final: 0.6864 (t0) REVERT: P 283 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7599 (tt0) REVERT: P 526 MET cc_start: 0.7016 (tpt) cc_final: 0.6745 (mmt) REVERT: P 942 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7588 (mp) REVERT: P 951 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7756 (tp) REVERT: P 987 LEU cc_start: 0.5272 (tp) cc_final: 0.4880 (tp) outliers start: 44 outliers final: 18 residues processed: 161 average time/residue: 0.1942 time to fit residues: 42.4813 Evaluate side-chains 131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 CYS Chi-restraints excluded: chain P residue 172 ARG 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 248 ILE Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU 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 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 1137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 0.4980 chunk 51 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.0870 chunk 49 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 P 881 ASN ** P1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.217685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.166778 restraints weight = 11900.274| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 4.31 r_work: 0.3962 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.3976 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= 0.197 Angle : 0.620 10.186 10886 Z= 0.294 Chirality : 0.042 0.144 1295 Planarity : 0.005 0.067 1367 Dihedral : 5.049 57.821 1109 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.70 % Allowed : 23.84 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % 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: -1.03 (0.28), residues: 999 helix: 1.40 (0.27), residues: 411 sheet: -1.20 (0.60), residues: 82 loop : -2.52 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P1028 HIS 0.004 0.001 HIS P 198 PHE 0.011 0.001 PHE P1029 TYR 0.013 0.001 TYR P1020 ARG 0.003 0.000 ARG P 294 *********************** 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 152 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.819 Fit side-chains REVERT: P 169 GLN cc_start: 0.7068 (tp40) cc_final: 0.6681 (mt0) REVERT: P 185 VAL cc_start: 0.4199 (OUTLIER) cc_final: 0.2618 (p) REVERT: P 208 ASP cc_start: 0.7469 (t0) cc_final: 0.7232 (t0) REVERT: P 250 LEU cc_start: 0.9079 (tp) cc_final: 0.8868 (tp) REVERT: P 283 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7057 (tm-30) REVERT: P 379 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8283 (tt) REVERT: P 390 HIS cc_start: 0.6994 (OUTLIER) cc_final: 0.6690 (t-170) REVERT: P 526 MET cc_start: 0.7172 (tpt) cc_final: 0.6970 (mmt) REVERT: P 615 MET cc_start: 0.5844 (ptt) cc_final: 0.4956 (mmp) REVERT: P 777 HIS cc_start: 0.2959 (OUTLIER) cc_final: 0.1729 (t-90) REVERT: P 942 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7426 (mp) REVERT: P 987 LEU cc_start: 0.6161 (tp) cc_final: 0.5677 (tp) REVERT: P 1024 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6729 (mt) REVERT: P 1102 LEU cc_start: 0.5308 (tt) cc_final: 0.4841 (mt) outliers start: 32 outliers final: 18 residues processed: 145 average time/residue: 0.1944 time to fit residues: 39.1870 Evaluate side-chains 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 390 HIS 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 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 518 LEU 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 857 GLU 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 996 LEU Chi-restraints excluded: chain P residue 1024 LEU Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1124 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 74 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 390 HIS ** P1103 GLN ** 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 = 0.4554 r_free = 0.4554 target = 0.213334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162109 restraints weight = 11791.759| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.98 r_work: 0.3944 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7998 Z= 0.187 Angle : 0.607 10.465 10886 Z= 0.286 Chirality : 0.042 0.143 1295 Planarity : 0.005 0.074 1367 Dihedral : 4.973 51.399 1109 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.63 % Allowed : 23.84 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % 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: -0.96 (0.28), residues: 999 helix: 1.38 (0.27), residues: 415 sheet: -1.36 (0.65), residues: 72 loop : -2.39 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P1028 HIS 0.003 0.001 HIS P 390 PHE 0.011 0.001 PHE P 830 TYR 0.010 0.001 TYR P 442 ARG 0.006 0.000 ARG P 294 *********************** 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 149 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.825 Fit side-chains REVERT: P 64 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6924 (mt) REVERT: P 169 GLN cc_start: 0.7052 (tp40) cc_final: 0.6701 (mt0) REVERT: P 208 ASP cc_start: 0.7423 (t0) cc_final: 0.7070 (t0) REVERT: P 283 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7136 (tm-30) REVERT: P 306 TRP cc_start: 0.6282 (m100) cc_final: 0.6070 (m100) REVERT: P 371 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6867 (tpt-90) REVERT: P 379 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8462 (tt) REVERT: P 615 MET cc_start: 0.5880 (ptt) cc_final: 0.4972 (mmp) REVERT: P 777 HIS cc_start: 0.2936 (OUTLIER) cc_final: 0.2039 (t-90) REVERT: P 942 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7590 (mp) REVERT: P 1024 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7212 (mt) REVERT: P 1102 LEU cc_start: 0.5504 (tt) cc_final: 0.5070 (mt) outliers start: 40 outliers final: 21 residues processed: 141 average time/residue: 0.1885 time to fit residues: 37.8945 Evaluate side-chains 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 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 333 LEU Chi-restraints excluded: chain P residue 371 ARG Chi-restraints excluded: chain P residue 376 CYS Chi-restraints excluded: chain P residue 379 LEU 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 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 518 LEU 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 840 LEU Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 857 GLU 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 1024 LEU Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1097 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.0470 chunk 89 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 626 HIS ** P1103 GLN ** 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 = 0.4547 r_free = 0.4547 target = 0.212321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161040 restraints weight = 11761.944| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 4.14 r_work: 0.3923 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7998 Z= 0.171 Angle : 0.617 16.970 10886 Z= 0.282 Chirality : 0.041 0.159 1295 Planarity : 0.005 0.069 1367 Dihedral : 4.769 51.484 1109 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.86 % Allowed : 24.31 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % 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: -0.92 (0.28), residues: 999 helix: 1.40 (0.27), residues: 416 sheet: -1.30 (0.58), residues: 82 loop : -2.38 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P1028 HIS 0.003 0.001 HIS P 390 PHE 0.009 0.001 PHE P1029 TYR 0.009 0.001 TYR P 183 ARG 0.005 0.000 ARG P 294 *********************** 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 151 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.774 Fit side-chains REVERT: P 64 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6934 (mt) REVERT: P 169 GLN cc_start: 0.7070 (tp40) cc_final: 0.6722 (mt0) REVERT: P 176 ILE cc_start: 0.8722 (mm) cc_final: 0.8344 (mt) REVERT: P 208 ASP cc_start: 0.7203 (t0) cc_final: 0.6869 (t0) REVERT: P 283 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7177 (tm-30) REVERT: P 306 TRP cc_start: 0.6535 (m100) cc_final: 0.6237 (m100) REVERT: P 777 HIS cc_start: 0.3236 (OUTLIER) cc_final: 0.2139 (t-90) REVERT: P 942 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7530 (mp) REVERT: P 1024 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7314 (mt) REVERT: P 1102 LEU cc_start: 0.5333 (tt) cc_final: 0.4972 (mt) outliers start: 42 outliers final: 25 residues processed: 143 average time/residue: 0.1798 time to fit residues: 36.3937 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 : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 LEU 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 318 LEU Chi-restraints excluded: chain P residue 371 ARG 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 435 LEU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 518 LEU 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 840 LEU Chi-restraints excluded: chain P residue 857 GLU 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 1024 LEU Chi-restraints excluded: chain P residue 1092 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 68 optimal weight: 0.0040 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 85 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 HIS P 390 HIS ** P1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.210468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.158042 restraints weight = 11915.698| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 4.18 r_work: 0.3898 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7998 Z= 0.169 Angle : 0.620 12.285 10886 Z= 0.283 Chirality : 0.041 0.216 1295 Planarity : 0.005 0.074 1367 Dihedral : 4.542 52.487 1109 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.40 % Allowed : 24.54 % 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 (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: -0.82 (0.28), residues: 999 helix: 1.47 (0.27), residues: 417 sheet: -1.31 (0.53), residues: 94 loop : -2.31 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P1028 HIS 0.003 0.001 HIS P 390 PHE 0.007 0.001 PHE P 830 TYR 0.008 0.001 TYR P 183 ARG 0.002 0.000 ARG P 294 *********************** 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 148 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.969 Fit side-chains REVERT: P 64 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6903 (mt) REVERT: P 208 ASP cc_start: 0.7190 (t0) cc_final: 0.6870 (t0) REVERT: P 283 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7167 (tm-30) REVERT: P 306 TRP cc_start: 0.6686 (m100) cc_final: 0.6349 (m100) REVERT: P 777 HIS cc_start: 0.3418 (OUTLIER) cc_final: 0.2350 (t-90) REVERT: P 942 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7584 (mp) REVERT: P 1024 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7342 (mt) REVERT: P 1102 LEU cc_start: 0.5591 (tt) cc_final: 0.5187 (mt) outliers start: 38 outliers final: 29 residues processed: 139 average time/residue: 0.1690 time to fit residues: 33.6860 Evaluate side-chains 135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain P residue 232 LEU 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 295 VAL Chi-restraints excluded: chain P residue 318 LEU 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 435 LEU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 518 LEU 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 840 LEU Chi-restraints excluded: chain P residue 857 GLU 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 1017 LEU Chi-restraints excluded: chain P residue 1024 LEU Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1097 LEU Chi-restraints excluded: chain P residue 1118 LEU Chi-restraints excluded: chain P residue 1124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 HIS ** P 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 881 ASN P1026 GLN P1057 GLN P1127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.201257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146930 restraints weight = 11785.248| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.91 r_work: 0.3765 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.6232 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= 0.233 Angle : 0.697 12.049 10886 Z= 0.327 Chirality : 0.044 0.196 1295 Planarity : 0.005 0.068 1367 Dihedral : 4.920 56.451 1109 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.44 % Allowed : 23.84 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % 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: -0.90 (0.28), residues: 999 helix: 1.34 (0.27), residues: 418 sheet: -1.26 (0.55), residues: 94 loop : -2.32 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P1028 HIS 0.006 0.001 HIS P 390 PHE 0.017 0.002 PHE P 103 TYR 0.015 0.002 TYR P 257 ARG 0.003 0.000 ARG P 686 *********************** 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 160 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.848 Fit side-chains REVERT: P 64 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6937 (mt) REVERT: P 169 GLN cc_start: 0.8574 (mt0) cc_final: 0.8308 (mp10) REVERT: P 176 ILE cc_start: 0.8883 (mm) cc_final: 0.8434 (mt) REVERT: P 208 ASP cc_start: 0.7227 (t0) cc_final: 0.6964 (t0) REVERT: P 283 GLN cc_start: 0.7831 (tm-30) cc_final: 0.6940 (tm-30) REVERT: P 306 TRP cc_start: 0.6919 (m100) cc_final: 0.6470 (m100) REVERT: P 686 ARG cc_start: 0.6699 (ptm-80) cc_final: 0.6391 (ptm160) REVERT: P 777 HIS cc_start: 0.3725 (OUTLIER) cc_final: 0.2257 (t-170) REVERT: P 840 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7404 (mm) REVERT: P 942 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7626 (mp) outliers start: 47 outliers final: 28 residues processed: 149 average time/residue: 0.1741 time to fit residues: 37.0170 Evaluate side-chains 133 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 318 LEU Chi-restraints excluded: chain P residue 327 MET Chi-restraints excluded: chain P residue 333 LEU 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 840 LEU Chi-restraints excluded: chain P residue 841 LEU Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 857 GLU 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 1017 LEU Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1111 ILE Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 29 optimal weight: 0.0030 chunk 94 optimal weight: 0.9980 chunk 40 optimal weight: 0.0070 chunk 64 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.2786 ------------------------------------------------------------------------------- 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 ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4471 r_free = 0.4471 target = 0.204071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151278 restraints weight = 12033.206| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.97 r_work: 0.3806 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7998 Z= 0.170 Angle : 0.662 11.231 10886 Z= 0.302 Chirality : 0.042 0.196 1295 Planarity : 0.005 0.068 1367 Dihedral : 4.690 54.726 1109 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.01 % Allowed : 26.85 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % 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 (0.28), residues: 999 helix: 1.50 (0.27), residues: 417 sheet: -1.36 (0.60), residues: 82 loop : -2.15 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P1028 HIS 0.007 0.001 HIS P 390 PHE 0.009 0.001 PHE P 103 TYR 0.012 0.001 TYR P 256 ARG 0.004 0.000 ARG P 370 *********************** 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 136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.888 Fit side-chains REVERT: P 64 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6945 (mt) REVERT: P 176 ILE cc_start: 0.8786 (mm) cc_final: 0.8312 (mt) REVERT: P 283 GLN cc_start: 0.7809 (tm-30) cc_final: 0.6989 (tm-30) REVERT: P 306 TRP cc_start: 0.6919 (m100) cc_final: 0.6476 (m100) REVERT: P 686 ARG cc_start: 0.6731 (ptm-80) cc_final: 0.6400 (ptm160) REVERT: P 777 HIS cc_start: 0.3626 (OUTLIER) cc_final: 0.2139 (t-170) REVERT: P 867 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8320 (mt0) REVERT: P 942 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7624 (mp) REVERT: P 1102 LEU cc_start: 0.5251 (tt) cc_final: 0.4370 (mt) outliers start: 26 outliers final: 19 residues processed: 127 average time/residue: 0.1805 time to fit residues: 32.4127 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 : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU 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 777 HIS Chi-restraints excluded: chain P residue 857 GLU 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 1017 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1092 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 76 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.0030 chunk 37 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 0.0060 overall best weight: 0.3006 ------------------------------------------------------------------------------- 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 ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4470 r_free = 0.4470 target = 0.203677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.151940 restraints weight = 11427.497| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.67 r_work: 0.3821 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.6360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7998 Z= 0.169 Angle : 0.661 11.064 10886 Z= 0.303 Chirality : 0.042 0.175 1295 Planarity : 0.006 0.089 1367 Dihedral : 4.559 55.184 1109 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.89 % Allowed : 26.62 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % 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: -0.66 (0.28), residues: 999 helix: 1.55 (0.27), residues: 417 sheet: -1.38 (0.59), residues: 82 loop : -2.12 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P1028 HIS 0.008 0.001 HIS P 390 PHE 0.007 0.001 PHE P 963 TYR 0.012 0.001 TYR P 256 ARG 0.004 0.000 ARG P 370 ********************** 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 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.814 Fit side-chains REVERT: P 64 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6937 (mt) REVERT: P 169 GLN cc_start: 0.8471 (mt0) cc_final: 0.8056 (mt0) REVERT: P 176 ILE cc_start: 0.8751 (mm) cc_final: 0.8279 (mt) REVERT: P 283 GLN cc_start: 0.7781 (tm-30) cc_final: 0.6956 (tm-30) REVERT: P 306 TRP cc_start: 0.6950 (m100) cc_final: 0.6518 (m100) REVERT: P 686 ARG cc_start: 0.6816 (ptm-80) cc_final: 0.6413 (ptm160) REVERT: P 777 HIS cc_start: 0.3591 (OUTLIER) cc_final: 0.2076 (t-170) REVERT: P 867 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8285 (mt0) REVERT: P 942 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7601 (mp) REVERT: P 1102 LEU cc_start: 0.5311 (tt) cc_final: 0.4446 (mt) outliers start: 25 outliers final: 21 residues processed: 121 average time/residue: 0.2253 time to fit residues: 40.0126 Evaluate side-chains 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 273 LEU 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 529 VAL Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 777 HIS Chi-restraints excluded: chain P residue 857 GLU 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 1017 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 1111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.197405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.144385 restraints weight = 11859.654| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.93 r_work: 0.3716 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7998 Z= 0.241 Angle : 0.716 10.425 10886 Z= 0.333 Chirality : 0.044 0.166 1295 Planarity : 0.006 0.084 1367 Dihedral : 4.759 57.598 1109 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.47 % Allowed : 26.50 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % 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: -0.81 (0.28), residues: 999 helix: 1.53 (0.27), residues: 409 sheet: -1.32 (0.51), residues: 106 loop : -2.31 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP P1028 HIS 0.006 0.001 HIS P 390 PHE 0.013 0.001 PHE P 963 TYR 0.013 0.002 TYR P 183 ARG 0.004 0.000 ARG P 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4451.88 seconds wall clock time: 79 minutes 26.68 seconds (4766.68 seconds total)