Starting phenix.real_space_refine on Wed Mar 12 14:07:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iem_35386/03_2025/8iem_35386_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iem_35386/03_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_35386/03_2025/8iem_35386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iem_35386/03_2025/8iem_35386.map" model { file = "/net/cci-nas-00/data/ceres_data/8iem_35386/03_2025/8iem_35386_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iem_35386/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.14 Conformation dependent library (CDL) restraints added in 986.1 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: 0.89 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: 2.29 Time building geometry restraints manager: 2.51 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.220 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- 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 : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.1966 time to fit residues: 27.3890 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 : 0.806 ------------------------------------------------------------------------------- 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: 0.0010 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: 0.1180 ------------------------------------------------------------------------------- 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 = 0.4854 r_free = 0.4854 target = 0.250820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.208842 restraints weight = 12089.993| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 3.73 r_work: 0.4397 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7998 Z= 0.144 Angle : 0.552 11.679 10886 Z= 0.258 Chirality : 0.040 0.166 1295 Planarity : 0.005 0.082 1367 Dihedral : 4.662 54.212 1112 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.43 % Allowed : 21.06 % Favored : 76.50 % 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 (0.27), residues: 999 helix: 1.51 (0.28), residues: 400 sheet: -1.18 (0.71), residues: 64 loop : -2.52 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 100 HIS 0.002 0.000 HIS P 413 PHE 0.006 0.001 PHE P 830 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 127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.871 Fit side-chains REVERT: P 265 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7859 (tt) REVERT: P 615 MET cc_start: 0.5102 (mmp) cc_final: 0.4771 (ptt) outliers start: 21 outliers final: 7 residues processed: 119 average time/residue: 0.1706 time to fit residues: 29.1708 Evaluate side-chains 110 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 519 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: 20.0000 chunk 59 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 0.0570 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 0.0040 chunk 69 optimal weight: 1.9990 overall best weight: 0.7712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 51 HIS P 255 HIS P 497 HIS P 867 GLN P 881 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.219802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.171418 restraints weight = 12073.170| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 4.10 r_work: 0.3981 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 7998 Z= 0.267 Angle : 0.730 10.449 10886 Z= 0.357 Chirality : 0.045 0.193 1295 Planarity : 0.007 0.117 1367 Dihedral : 5.264 58.791 1109 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.91 % Favored : 91.99 % Rotamer: Outliers : 5.32 % Allowed : 20.95 % Favored : 73.73 % 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: -1.31 (0.27), residues: 999 helix: 1.08 (0.28), residues: 407 sheet: -1.36 (0.60), residues: 82 loop : -2.57 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P 100 HIS 0.006 0.001 HIS P 372 PHE 0.020 0.002 PHE P 963 TYR 0.018 0.002 TYR P 442 ARG 0.005 0.001 ARG P 544 *********************** 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 173 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: P 185 VAL cc_start: 0.4263 (OUTLIER) cc_final: 0.4009 (m) REVERT: P 208 ASP cc_start: 0.7283 (t0) cc_final: 0.6872 (t0) REVERT: P 256 TYR cc_start: 0.4668 (OUTLIER) cc_final: 0.3938 (m-80) REVERT: P 390 HIS cc_start: 0.7432 (t-170) cc_final: 0.7118 (t-170) REVERT: P 526 MET cc_start: 0.6885 (tpt) cc_final: 0.6662 (mmt) REVERT: P 615 MET cc_start: 0.5333 (mmp) cc_final: 0.5123 (ptt) REVERT: P 942 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7569 (mp) REVERT: P 951 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7551 (tp) REVERT: P 954 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7613 (mm) REVERT: P 987 LEU cc_start: 0.5560 (tp) cc_final: 0.5077 (tp) REVERT: P 1024 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6527 (mt) outliers start: 46 outliers final: 19 residues processed: 161 average time/residue: 0.1985 time to fit residues: 43.6737 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 413 HIS 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 844 VAL 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 954 ILE Chi-restraints excluded: chain P residue 968 LEU 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 1137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 40 optimal weight: 0.0870 chunk 52 optimal weight: 7.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 HIS P 497 HIS P 508 GLN 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 = 0.4595 r_free = 0.4595 target = 0.217976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.167576 restraints weight = 11920.802| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 4.30 r_work: 0.3966 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7998 Z= 0.172 Angle : 0.602 10.362 10886 Z= 0.283 Chirality : 0.042 0.147 1295 Planarity : 0.005 0.071 1367 Dihedral : 4.908 57.514 1109 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.36 % Allowed : 24.54 % Favored : 72.11 % 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: -1.10 (0.27), residues: 999 helix: 1.35 (0.27), residues: 411 sheet: -1.34 (0.60), residues: 72 loop : -2.54 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 100 HIS 0.002 0.001 HIS P 372 PHE 0.019 0.001 PHE P1029 TYR 0.013 0.001 TYR P1020 ARG 0.004 0.000 ARG P 397 *********************** 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 138 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.946 Fit side-chains REVERT: P 185 VAL cc_start: 0.4383 (OUTLIER) cc_final: 0.3715 (t) REVERT: P 208 ASP cc_start: 0.7442 (t0) cc_final: 0.7217 (t0) REVERT: P 256 TYR cc_start: 0.5008 (OUTLIER) cc_final: 0.4599 (m-10) REVERT: P 283 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7073 (tm-30) REVERT: P 390 HIS cc_start: 0.7343 (t-170) cc_final: 0.7047 (t-170) REVERT: P 777 HIS cc_start: 0.2907 (OUTLIER) cc_final: 0.1717 (t-90) REVERT: P 942 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7576 (mp) REVERT: P 987 LEU cc_start: 0.6111 (tp) cc_final: 0.5553 (tp) REVERT: P 1024 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6903 (mt) REVERT: P 1102 LEU cc_start: 0.5199 (tt) cc_final: 0.4722 (mt) outliers start: 29 outliers final: 17 residues processed: 132 average time/residue: 0.1917 time to fit residues: 35.5459 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 857 GLU Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 968 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: 1.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 626 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.209270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.156966 restraints weight = 11738.458| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 4.13 r_work: 0.3880 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7998 Z= 0.208 Angle : 0.635 10.629 10886 Z= 0.304 Chirality : 0.043 0.145 1295 Planarity : 0.005 0.063 1367 Dihedral : 5.122 56.963 1109 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.75 % Allowed : 23.03 % Favored : 72.22 % 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: -1.05 (0.27), residues: 999 helix: 1.31 (0.27), residues: 417 sheet: -1.35 (0.54), residues: 94 loop : -2.49 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP P1028 HIS 0.003 0.001 HIS P 372 PHE 0.016 0.001 PHE P 830 TYR 0.012 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 151 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.860 Fit side-chains REVERT: P 208 ASP cc_start: 0.7148 (t0) cc_final: 0.6861 (t0) REVERT: P 283 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7141 (tm-30) REVERT: P 306 TRP cc_start: 0.6768 (m100) cc_final: 0.6481 (m100) REVERT: P 390 HIS cc_start: 0.7661 (t-170) cc_final: 0.7320 (t-170) REVERT: P 615 MET cc_start: 0.5826 (ptt) cc_final: 0.5011 (mmt) REVERT: P 777 HIS cc_start: 0.3077 (OUTLIER) cc_final: 0.2040 (t-90) REVERT: P 942 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7615 (mp) REVERT: P 1061 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5552 (mt) REVERT: P 1102 LEU cc_start: 0.5467 (tt) cc_final: 0.5014 (mt) outliers start: 41 outliers final: 24 residues processed: 145 average time/residue: 0.1713 time to fit residues: 35.3005 Evaluate side-chains 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain P residue 376 CYS 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 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 981 THR 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 1097 LEU Chi-restraints excluded: chain P residue 1118 LEU Chi-restraints excluded: chain P residue 1124 VAL 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 22 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.206334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.153612 restraints weight = 11719.201| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 4.07 r_work: 0.3843 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7998 Z= 0.194 Angle : 0.634 16.329 10886 Z= 0.295 Chirality : 0.042 0.176 1295 Planarity : 0.005 0.069 1367 Dihedral : 4.872 52.528 1109 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.32 % Allowed : 23.26 % Favored : 71.41 % 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: 1.36 (0.27), residues: 417 sheet: -1.33 (0.54), residues: 94 loop : -2.41 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP P1028 HIS 0.003 0.001 HIS P 836 PHE 0.009 0.001 PHE P1071 TYR 0.013 0.001 TYR P 183 ARG 0.004 0.000 ARG P 686 *********************** 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 155 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 0.858 Fit side-chains REVERT: P 64 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6993 (mt) REVERT: P 208 ASP cc_start: 0.7199 (t0) cc_final: 0.6877 (t0) REVERT: P 283 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7149 (tm-30) REVERT: P 306 TRP cc_start: 0.6808 (m100) cc_final: 0.6450 (m100) REVERT: P 390 HIS cc_start: 0.7551 (t-170) cc_final: 0.7317 (t-170) REVERT: P 615 MET cc_start: 0.6108 (ptt) cc_final: 0.5102 (mmt) REVERT: P 686 ARG cc_start: 0.6568 (ptm-80) cc_final: 0.6141 (ptm160) REVERT: P 777 HIS cc_start: 0.3504 (OUTLIER) cc_final: 0.2213 (t-170) REVERT: P 871 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: P 942 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7682 (mp) REVERT: P 1061 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5650 (mt) outliers start: 46 outliers final: 26 residues processed: 141 average time/residue: 0.1946 time to fit residues: 38.1210 Evaluate side-chains 133 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 518 LEU Chi-restraints excluded: chain P residue 551 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 841 LEU Chi-restraints excluded: chain P residue 857 GLU Chi-restraints excluded: chain P residue 871 TYR 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 1061 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1124 VAL Chi-restraints excluded: chain P residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 50 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 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 944 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.201743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.150605 restraints weight = 11854.310| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 3.83 r_work: 0.3779 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7998 Z= 0.213 Angle : 0.658 10.679 10886 Z= 0.308 Chirality : 0.043 0.134 1295 Planarity : 0.005 0.064 1367 Dihedral : 4.826 53.704 1109 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.09 % Allowed : 24.42 % 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: -0.94 (0.27), residues: 999 helix: 1.36 (0.27), residues: 418 sheet: -1.34 (0.51), residues: 96 loop : -2.39 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP P1028 HIS 0.005 0.001 HIS P 836 PHE 0.016 0.001 PHE P 963 TYR 0.011 0.001 TYR P 183 ARG 0.003 0.000 ARG P 487 *********************** 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 155 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.876 Fit side-chains REVERT: P 64 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6944 (mt) REVERT: P 208 ASP cc_start: 0.7011 (t0) cc_final: 0.6762 (t0) REVERT: P 283 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7024 (tm-30) REVERT: P 306 TRP cc_start: 0.6971 (m100) cc_final: 0.6532 (m100) REVERT: P 390 HIS cc_start: 0.7760 (t-170) cc_final: 0.7403 (t-170) REVERT: P 686 ARG cc_start: 0.6812 (ptm-80) cc_final: 0.6438 (ptm160) REVERT: P 777 HIS cc_start: 0.3671 (OUTLIER) cc_final: 0.2210 (t-170) REVERT: P 942 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7585 (mp) REVERT: P 1061 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6225 (mt) REVERT: P 1118 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7312 (tt) outliers start: 44 outliers final: 24 residues processed: 145 average time/residue: 0.1762 time to fit residues: 36.4288 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 318 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 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 844 VAL Chi-restraints excluded: chain P residue 857 GLU 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 1061 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 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 881 ASN P1057 GLN P1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.198084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.142745 restraints weight = 11857.831| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.45 r_work: 0.3740 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.6838 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= 0.231 Angle : 0.691 10.716 10886 Z= 0.324 Chirality : 0.044 0.169 1295 Planarity : 0.005 0.068 1367 Dihedral : 4.971 55.054 1109 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 4.40 % Allowed : 25.69 % 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 (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: -0.98 (0.28), residues: 999 helix: 1.31 (0.27), residues: 418 sheet: -1.45 (0.50), residues: 106 loop : -2.38 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P1028 HIS 0.005 0.001 HIS P 836 PHE 0.015 0.001 PHE P 963 TYR 0.016 0.002 TYR P 256 ARG 0.003 0.000 ARG P 370 *********************** 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 140 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.816 Fit side-chains REVERT: P 64 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6938 (mt) REVERT: P 283 GLN cc_start: 0.7903 (tm-30) cc_final: 0.6999 (tm-30) REVERT: P 306 TRP cc_start: 0.7019 (m100) cc_final: 0.6511 (m100) REVERT: P 364 TYR cc_start: 0.6342 (t80) cc_final: 0.6119 (t80) REVERT: P 382 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: P 392 LEU cc_start: 0.8908 (mp) cc_final: 0.8679 (mp) REVERT: P 686 ARG cc_start: 0.6965 (ptm-80) cc_final: 0.6587 (ptm160) REVERT: P 777 HIS cc_start: 0.3771 (OUTLIER) cc_final: 0.2287 (t-170) REVERT: P 870 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7730 (mp10) REVERT: P 942 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7634 (mp) REVERT: P 1061 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6336 (mt) outliers start: 38 outliers final: 23 residues processed: 131 average time/residue: 0.1670 time to fit residues: 31.6003 Evaluate side-chains 126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 237 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 376 CYS Chi-restraints excluded: chain P residue 382 GLN 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 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 844 VAL Chi-restraints excluded: chain P residue 857 GLU Chi-restraints excluded: chain P residue 870 GLN 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 1061 LEU Chi-restraints excluded: chain P residue 1065 VAL 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: 0.7980 chunk 57 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 94 optimal weight: 0.0000 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.199170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.143973 restraints weight = 12112.712| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.48 r_work: 0.3756 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.6962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7998 Z= 0.177 Angle : 0.662 10.636 10886 Z= 0.306 Chirality : 0.042 0.155 1295 Planarity : 0.005 0.063 1367 Dihedral : 4.774 55.750 1109 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.36 % Allowed : 26.62 % 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: -0.85 (0.28), residues: 999 helix: 1.44 (0.27), residues: 418 sheet: -1.46 (0.55), residues: 94 loop : -2.30 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P1028 HIS 0.003 0.001 HIS P 836 PHE 0.012 0.001 PHE P 963 TYR 0.013 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 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 1.087 Fit side-chains REVERT: P 64 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6957 (mt) REVERT: P 283 GLN cc_start: 0.7872 (tm-30) cc_final: 0.6919 (tm-30) REVERT: P 306 TRP cc_start: 0.7020 (m100) cc_final: 0.6538 (m100) REVERT: P 392 LEU cc_start: 0.8897 (mp) cc_final: 0.8675 (mp) REVERT: P 686 ARG cc_start: 0.7043 (ptm-80) cc_final: 0.6662 (ptm160) REVERT: P 777 HIS cc_start: 0.3903 (OUTLIER) cc_final: 0.2429 (t-170) REVERT: P 870 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7740 (mp10) REVERT: P 871 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: P 942 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7733 (mp) REVERT: P 1061 LEU cc_start: 0.6615 (mm) cc_final: 0.6192 (mt) outliers start: 29 outliers final: 22 residues processed: 122 average time/residue: 0.2007 time to fit residues: 34.5549 Evaluate side-chains 122 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 167 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 237 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 376 CYS 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 518 LEU Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 777 HIS Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 857 GLU Chi-restraints excluded: chain P residue 870 GLN Chi-restraints excluded: chain P residue 871 TYR 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 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4399 r_free = 0.4399 target = 0.196007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143934 restraints weight = 11816.390| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.96 r_work: 0.3709 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.7303 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= 0.214 Angle : 0.682 10.634 10886 Z= 0.318 Chirality : 0.043 0.156 1295 Planarity : 0.005 0.069 1367 Dihedral : 4.926 57.648 1109 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.36 % Allowed : 26.74 % 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 (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: -0.86 (0.28), residues: 999 helix: 1.40 (0.27), residues: 418 sheet: -1.45 (0.58), residues: 84 loop : -2.27 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP P1028 HIS 0.004 0.001 HIS P 836 PHE 0.013 0.001 PHE P 963 TYR 0.015 0.001 TYR P 256 ARG 0.005 0.000 ARG P1164 ********************** 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 131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.889 Fit side-chains REVERT: P 64 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6948 (mt) REVERT: P 169 GLN cc_start: 0.8445 (mt0) cc_final: 0.7926 (mt0) REVERT: P 283 GLN cc_start: 0.7899 (tm-30) cc_final: 0.6935 (tm-30) REVERT: P 392 LEU cc_start: 0.8898 (mp) cc_final: 0.8686 (mp) REVERT: P 686 ARG cc_start: 0.7108 (ptm-80) cc_final: 0.6813 (ptm160) REVERT: P 777 HIS cc_start: 0.3968 (OUTLIER) cc_final: 0.2436 (t-170) REVERT: P 870 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: P 942 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7647 (mp) REVERT: P 999 VAL cc_start: 0.8471 (t) cc_final: 0.8082 (t) REVERT: P 1003 SER cc_start: 0.8297 (m) cc_final: 0.7680 (m) REVERT: P 1061 LEU cc_start: 0.6840 (mm) cc_final: 0.6508 (mt) outliers start: 29 outliers final: 21 residues processed: 125 average time/residue: 0.1868 time to fit residues: 32.9231 Evaluate side-chains 123 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain P residue 237 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 413 HIS 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 844 VAL Chi-restraints excluded: chain P residue 857 GLU Chi-restraints excluded: chain P residue 870 GLN 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 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 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 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.196703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143325 restraints weight = 11892.751| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 4.09 r_work: 0.3713 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.7441 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= 0.196 Angle : 0.669 10.616 10886 Z= 0.311 Chirality : 0.043 0.161 1295 Planarity : 0.005 0.067 1367 Dihedral : 4.894 58.762 1109 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.36 % Allowed : 27.20 % 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 (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: -0.79 (0.28), residues: 999 helix: 1.44 (0.27), residues: 419 sheet: -1.48 (0.58), residues: 84 loop : -2.21 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP P1028 HIS 0.004 0.001 HIS P 202 PHE 0.011 0.001 PHE P 963 TYR 0.015 0.001 TYR P 183 ARG 0.004 0.000 ARG P 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4457.13 seconds wall clock time: 76 minutes 51.94 seconds (4611.94 seconds total)