Starting phenix.real_space_refine on Mon Mar 11 09:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iem_35386/03_2024/8iem_35386_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iem_35386/03_2024/8iem_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iem_35386/03_2024/8iem_35386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iem_35386/03_2024/8iem_35386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iem_35386/03_2024/8iem_35386_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iem_35386/03_2024/8iem_35386_trim_updated.pdb" } 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 Residue "P GLU 177": "OE1" <-> "OE2" Residue "P GLU 311": "OE1" <-> "OE2" Residue "P GLU 542": "OE1" <-> "OE2" Residue "P GLU 771": "OE1" <-> "OE2" Residue "P GLU 1046": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.69, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 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... running ksdssp... Secondary structure from input PDB file: 30 helices and 8 sheets defined 39.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'P' and resid 51 through 59 removed outlier: 3.750A pdb=" N GLY P 59 " --> pdb=" O TRP P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 65 Processing helix chain 'P' and resid 69 through 76 removed outlier: 3.571A pdb=" N ARG P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 199 Processing helix chain 'P' and resid 210 through 216 Processing helix chain 'P' and resid 229 through 234 removed outlier: 3.648A pdb=" N LEU P 232 " --> pdb=" O PRO P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 253 removed outlier: 3.528A pdb=" N LEU P 250 " --> pdb=" O PHE P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 288 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 403 through 411 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 425 through 450 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 457 through 468 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 473 through 491 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) removed outlier: 3.628A pdb=" N ARG P 490 " --> pdb=" O SER P 486 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN P 491 " --> pdb=" O ARG P 487 " (cutoff:3.500A) Processing helix chain 'P' and resid 550 through 556 Processing helix chain 'P' and resid 573 through 581 removed outlier: 4.086A pdb=" N THR P 581 " --> pdb=" O MET P 577 " (cutoff:3.500A) Processing helix chain 'P' and resid 657 through 662 Processing helix chain 'P' and resid 674 through 683 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 697 through 706 Processing helix chain 'P' and resid 730 through 742 Proline residue: P 734 - end of helix removed outlier: 3.587A pdb=" N ARG P 741 " --> pdb=" O GLN P 737 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR P 742 " --> pdb=" O ALA P 738 " (cutoff:3.500A) Processing helix chain 'P' and resid 754 through 764 Processing helix chain 'P' and resid 827 through 833 Processing helix chain 'P' and resid 856 through 869 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) removed outlier: 3.820A pdb=" N LEU P 869 " --> pdb=" O GLU P 865 " (cutoff:3.500A) Processing helix chain 'P' and resid 913 through 952 Proline residue: P 917 - end of helix removed outlier: 3.527A pdb=" N ILE P 950 " --> pdb=" O SER P 947 " (cutoff:3.500A) Processing helix chain 'P' and resid 960 through 980 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) removed outlier: 5.426A pdb=" N SER P 979 " --> pdb=" O ALA P 975 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG P 980 " --> pdb=" O VAL P 976 " (cutoff:3.500A) Processing helix chain 'P' and resid 999 through 1002 No H-bonds generated for 'chain 'P' and resid 999 through 1002' Processing helix chain 'P' and resid 1005 through 1025 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) removed outlier: 4.650A pdb=" N LEU P1024 " --> pdb=" O TYR P1020 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA P1025 " --> pdb=" O PHE P1021 " (cutoff:3.500A) Processing helix chain 'P' and resid 1045 through 1064 Processing helix chain 'P' and resid 1079 through 1097 removed outlier: 3.965A pdb=" N VAL P1096 " --> pdb=" O LEU P1092 " (cutoff:3.500A) Processing helix chain 'P' and resid 1116 through 1137 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) Processing helix chain 'P' and resid 1142 through 1147 Processing helix chain 'P' and resid 1157 through 1167 Processing sheet with id= A, 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= A Processing sheet with id= B, 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= C, 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= D, first strand: chain 'P' and resid 317 through 319 Processing sheet with id= E, first strand: chain 'P' and resid 509 through 512 removed outlier: 7.123A pdb=" N ARG P 745 " --> pdb=" O VAL P 510 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE P 512 " --> pdb=" O ARG P 745 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL P 747 " --> pdb=" O PHE P 512 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'P' and resid 717 through 723 removed outlier: 6.290A pdb=" N LEU P 690 " --> pdb=" O LEU P 719 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU P 721 " --> pdb=" O VAL P 688 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL P 688 " --> pdb=" O LEU P 721 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA P 651 " --> pdb=" O LYS P 693 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL P 640 " --> pdb=" O HIS P 626 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS P 626 " --> pdb=" O VAL P 640 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'P' and resid 337 through 340 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) Processing sheet with id= H, first strand: chain 'P' and resid 823 through 825 removed outlier: 7.158A pdb=" N LEU P 825 " --> pdb=" O THR P 849 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE P 851 " --> pdb=" O LEU P 825 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 3.23 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: 100.50 - 107.38: 364 107.38 - 114.26: 4713 114.26 - 121.14: 3582 121.14 - 128.02: 2158 128.02 - 134.90: 69 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: 7469 3.29 - 3.82: 12291 3.82 - 4.36: 12508 4.36 - 4.90: 22450 Nonbonded interactions: 55517 Sorted by model distance: nonbonded pdb=" OG1 THR P 515 " pdb=" F1 BEF P1203 " model vdw 2.211 2.390 nonbonded pdb=" OD1 ASN P 881 " pdb=" F1 BEF P1203 " model vdw 2.282 2.390 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 2.390 nonbonded pdb=" O ASP P 878 " pdb=" OG SER P 896 " model vdw 2.302 2.440 ... (remaining 55512 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: 1.510 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: 5.430 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 24.870 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- 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= 0.188 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 fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.1833 time to fit residues: 25.4490 Evaluate side-chains 97 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 0.8980 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.2980 chunk 79 optimal weight: 0.0470 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 179 GLN P 184 GLN P 390 HIS P 867 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7998 Z= 0.172 Angle : 0.584 12.715 10886 Z= 0.280 Chirality : 0.041 0.167 1295 Planarity : 0.006 0.072 1367 Dihedral : 4.604 52.412 1112 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.82 % Allowed : 21.64 % Favored : 74.54 % 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: -1.41 (0.27), residues: 999 helix: 1.00 (0.27), residues: 393 sheet: -1.34 (0.69), residues: 66 loop : -2.51 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 100 HIS 0.003 0.001 HIS P 372 PHE 0.011 0.001 PHE P1051 TYR 0.015 0.001 TYR P 442 ARG 0.006 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 150 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 0.863 Fit side-chains REVERT: P 256 TYR cc_start: 0.3006 (OUTLIER) cc_final: 0.2458 (m-10) outliers start: 33 outliers final: 12 residues processed: 140 average time/residue: 0.1843 time to fit residues: 35.9246 Evaluate side-chains 120 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 509 LEU Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 949 LEU Chi-restraints excluded: chain P residue 1017 LEU Chi-restraints excluded: chain P residue 1032 LEU Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 0.0470 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.0020 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.5286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 184 GLN P 497 HIS ** P 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 881 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7998 Z= 0.188 Angle : 0.620 9.780 10886 Z= 0.296 Chirality : 0.042 0.164 1295 Planarity : 0.006 0.061 1367 Dihedral : 4.770 57.234 1109 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.51 % Allowed : 22.34 % Favored : 73.15 % 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: -1.39 (0.27), residues: 999 helix: 0.94 (0.27), residues: 402 sheet: -1.52 (0.67), residues: 66 loop : -2.46 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P1028 HIS 0.004 0.001 HIS P 255 PHE 0.021 0.001 PHE P1029 TYR 0.013 0.001 TYR P 442 ARG 0.004 0.000 ARG P 201 *********************** 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 162 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: P 544 ARG cc_start: 0.5678 (ptt180) cc_final: 0.5275 (ptt180) REVERT: P 951 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7665 (tp) outliers start: 39 outliers final: 18 residues processed: 153 average time/residue: 0.1897 time to fit residues: 39.5118 Evaluate side-chains 124 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 172 ARG Chi-restraints excluded: chain P residue 204 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 327 MET 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 759 THR Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 951 LEU Chi-restraints excluded: chain P residue 1024 LEU Chi-restraints excluded: chain P residue 1032 LEU Chi-restraints excluded: chain P residue 1033 ASN 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 69 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.0050 chunk 97 optimal weight: 0.4980 chunk 48 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 184 GLN P 390 HIS P 497 HIS P 731 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.3250 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= 0.141 Angle : 0.554 10.432 10886 Z= 0.259 Chirality : 0.040 0.143 1295 Planarity : 0.005 0.048 1367 Dihedral : 4.574 55.781 1109 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.05 % Allowed : 23.96 % Favored : 71.99 % 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: -1.33 (0.27), residues: 999 helix: 0.92 (0.27), residues: 408 sheet: -1.44 (0.61), residues: 76 loop : -2.41 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP P1028 HIS 0.002 0.000 HIS P 390 PHE 0.004 0.001 PHE P 837 TYR 0.012 0.001 TYR P1020 ARG 0.002 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 139 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: P 185 VAL cc_start: 0.3938 (OUTLIER) cc_final: 0.2179 (p) outliers start: 35 outliers final: 20 residues processed: 131 average time/residue: 0.1993 time to fit residues: 35.6612 Evaluate side-chains 120 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 185 VAL 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 327 MET Chi-restraints excluded: chain P residue 352 VAL 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 521 ASP Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 1024 LEU Chi-restraints excluded: chain P residue 1033 ASN Chi-restraints excluded: chain P residue 1061 LEU Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7998 Z= 0.271 Angle : 0.732 11.926 10886 Z= 0.351 Chirality : 0.045 0.150 1295 Planarity : 0.006 0.056 1367 Dihedral : 5.626 57.947 1109 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 5.67 % Allowed : 23.50 % 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: -1.62 (0.27), residues: 999 helix: 0.63 (0.27), residues: 408 sheet: -1.49 (0.56), residues: 79 loop : -2.56 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P1028 HIS 0.006 0.001 HIS P 777 PHE 0.014 0.002 PHE P1071 TYR 0.019 0.002 TYR P1020 ARG 0.019 0.001 ARG P 783 *********************** 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 162 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 113 time to evaluate : 0.917 Fit side-chains REVERT: P 62 LEU cc_start: 0.6048 (mt) cc_final: 0.5678 (pp) REVERT: P 544 ARG cc_start: 0.5877 (ptt180) cc_final: 0.5668 (ptt180) REVERT: P 942 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7616 (mp) outliers start: 49 outliers final: 29 residues processed: 154 average time/residue: 0.1767 time to fit residues: 38.4848 Evaluate side-chains 128 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 CYS Chi-restraints excluded: chain P residue 56 MET 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 327 MET Chi-restraints excluded: chain P residue 352 VAL 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 584 VAL Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 951 LEU Chi-restraints excluded: chain P residue 968 LEU Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1002 LEU Chi-restraints excluded: chain P residue 1032 LEU Chi-restraints excluded: chain P residue 1033 ASN Chi-restraints excluded: chain P residue 1044 ASN 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 1118 LEU Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 51 optimal weight: 0.0970 chunk 94 optimal weight: 0.2980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1057 GLN P1127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.5595 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= 0.176 Angle : 0.618 10.395 10886 Z= 0.292 Chirality : 0.042 0.152 1295 Planarity : 0.006 0.074 1367 Dihedral : 5.306 59.730 1109 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.70 % Allowed : 26.62 % Favored : 69.68 % 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: -1.35 (0.27), residues: 999 helix: 0.87 (0.27), residues: 407 sheet: -1.42 (0.56), residues: 79 loop : -2.40 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP P1028 HIS 0.002 0.001 HIS P 777 PHE 0.008 0.001 PHE P1071 TYR 0.009 0.001 TYR P 442 ARG 0.009 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 144 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 0.921 Fit side-chains REVERT: P 62 LEU cc_start: 0.5951 (mt) cc_final: 0.5577 (pp) REVERT: P 100 TRP cc_start: 0.6266 (m-90) cc_final: 0.6061 (m-90) REVERT: P 686 ARG cc_start: 0.6437 (ptm-80) cc_final: 0.6184 (ptm160) REVERT: P 942 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7644 (mp) REVERT: P 1061 LEU cc_start: 0.7170 (mm) cc_final: 0.6475 (mt) outliers start: 32 outliers final: 22 residues processed: 134 average time/residue: 0.1873 time to fit residues: 35.0300 Evaluate side-chains 127 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 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 844 VAL Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 996 LEU Chi-restraints excluded: chain P residue 1033 ASN Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1097 LEU Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.0020 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.0270 chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 overall best weight: 0.5646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 777 HIS ** P1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7998 Z= 0.187 Angle : 0.646 15.658 10886 Z= 0.300 Chirality : 0.042 0.162 1295 Planarity : 0.006 0.070 1367 Dihedral : 4.884 52.409 1109 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.17 % Allowed : 26.27 % Favored : 69.56 % 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: -1.33 (0.27), residues: 999 helix: 0.88 (0.27), residues: 409 sheet: -1.43 (0.56), residues: 79 loop : -2.39 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP P1028 HIS 0.012 0.001 HIS P 777 PHE 0.008 0.001 PHE P1029 TYR 0.016 0.001 TYR P 183 ARG 0.005 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 140 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 0.970 Fit side-chains REVERT: P 62 LEU cc_start: 0.5971 (mt) cc_final: 0.5612 (pp) REVERT: P 686 ARG cc_start: 0.6584 (ptm-80) cc_final: 0.6255 (ptm160) REVERT: P 942 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7581 (mp) REVERT: P 1061 LEU cc_start: 0.7478 (mm) cc_final: 0.6855 (mt) outliers start: 36 outliers final: 25 residues processed: 132 average time/residue: 0.1988 time to fit residues: 36.1801 Evaluate side-chains 125 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 56 MET Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 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 844 VAL Chi-restraints excluded: chain P residue 910 MET Chi-restraints excluded: chain P residue 939 LEU Chi-restraints excluded: chain P residue 942 LEU Chi-restraints excluded: chain P residue 954 ILE Chi-restraints excluded: chain P residue 968 LEU Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1033 ASN Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1097 LEU Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.0670 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 424 HIS ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.6317 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= 0.178 Angle : 0.632 10.631 10886 Z= 0.296 Chirality : 0.042 0.134 1295 Planarity : 0.006 0.074 1367 Dihedral : 4.534 53.107 1109 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.63 % Allowed : 26.62 % Favored : 68.75 % 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: -1.26 (0.27), residues: 999 helix: 0.95 (0.27), residues: 407 sheet: -1.45 (0.56), residues: 79 loop : -2.35 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP P1028 HIS 0.003 0.000 HIS P 390 PHE 0.009 0.001 PHE P1029 TYR 0.012 0.001 TYR P 183 ARG 0.005 0.000 ARG P 294 *********************** 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 147 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 107 time to evaluate : 0.936 Fit side-chains REVERT: P 62 LEU cc_start: 0.5962 (mt) cc_final: 0.5614 (pp) REVERT: P 686 ARG cc_start: 0.6686 (ptm-80) cc_final: 0.6419 (ptm160) REVERT: P 731 GLN cc_start: 0.6217 (OUTLIER) cc_final: 0.5696 (pt0) REVERT: P 870 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: P 942 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7581 (mp) REVERT: P 1003 SER cc_start: 0.7751 (m) cc_final: 0.7525 (m) REVERT: P 1061 LEU cc_start: 0.7369 (mm) cc_final: 0.6777 (mt) outliers start: 40 outliers final: 26 residues processed: 136 average time/residue: 0.1809 time to fit residues: 34.6375 Evaluate side-chains 131 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 56 MET Chi-restraints excluded: chain P residue 172 ARG Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 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 435 LEU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 584 VAL Chi-restraints excluded: chain P residue 731 GLN Chi-restraints excluded: chain P residue 742 THR Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 870 GLN 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 981 THR Chi-restraints excluded: chain P residue 1033 ASN Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1097 LEU Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 424 HIS P 626 HIS P 867 GLN ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.6770 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= 0.198 Angle : 0.668 10.832 10886 Z= 0.309 Chirality : 0.042 0.136 1295 Planarity : 0.006 0.069 1367 Dihedral : 4.405 53.597 1109 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.94 % Allowed : 26.97 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.24 (0.27), residues: 999 helix: 0.97 (0.27), residues: 407 sheet: -1.56 (0.51), residues: 91 loop : -2.31 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP P1028 HIS 0.003 0.001 HIS P 836 PHE 0.010 0.001 PHE P 103 TYR 0.015 0.001 TYR P 183 ARG 0.005 0.000 ARG P 294 *********************** 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 138 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 0.868 Fit side-chains REVERT: P 435 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5887 (tt) REVERT: P 686 ARG cc_start: 0.7010 (ptm-80) cc_final: 0.6656 (ptm160) REVERT: P 731 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6082 (pt0) REVERT: P 870 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7774 (mp10) REVERT: P 942 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7665 (mp) REVERT: P 1003 SER cc_start: 0.7877 (m) cc_final: 0.7585 (m) REVERT: P 1061 LEU cc_start: 0.7593 (mm) cc_final: 0.7031 (mt) outliers start: 34 outliers final: 22 residues processed: 129 average time/residue: 0.1936 time to fit residues: 34.9096 Evaluate side-chains 126 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 56 MET Chi-restraints excluded: chain P residue 172 ARG 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 327 MET Chi-restraints excluded: chain P residue 376 CYS 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 584 VAL Chi-restraints excluded: chain P residue 731 GLN Chi-restraints excluded: chain P residue 742 THR Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 870 GLN 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 981 THR Chi-restraints excluded: chain P residue 1033 ASN Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 184 GLN ** P 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.7016 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= 0.199 Angle : 0.665 10.520 10886 Z= 0.312 Chirality : 0.042 0.137 1295 Planarity : 0.006 0.074 1367 Dihedral : 4.517 54.097 1109 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.59 % Allowed : 27.78 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.27), residues: 999 helix: 0.99 (0.27), residues: 406 sheet: -1.59 (0.51), residues: 91 loop : -2.29 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 67 HIS 0.003 0.001 HIS P 390 PHE 0.013 0.001 PHE P 963 TYR 0.015 0.001 TYR P1076 ARG 0.004 0.000 ARG P 294 ********************** 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 136 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 0.952 Fit side-chains REVERT: P 435 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.6033 (tt) REVERT: P 686 ARG cc_start: 0.6916 (ptm-80) cc_final: 0.6672 (ptm160) REVERT: P 731 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6092 (pt0) REVERT: P 870 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7753 (mp10) REVERT: P 942 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7659 (mp) REVERT: P 1003 SER cc_start: 0.7908 (m) cc_final: 0.7633 (m) REVERT: P 1028 TRP cc_start: 0.7084 (p-90) cc_final: 0.6759 (p-90) REVERT: P 1061 LEU cc_start: 0.7436 (mm) cc_final: 0.6929 (mt) outliers start: 31 outliers final: 22 residues processed: 128 average time/residue: 0.2056 time to fit residues: 35.8685 Evaluate side-chains 126 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 56 MET Chi-restraints excluded: chain P residue 172 ARG 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 327 MET Chi-restraints excluded: chain P residue 376 CYS 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 584 VAL Chi-restraints excluded: chain P residue 731 GLN Chi-restraints excluded: chain P residue 742 THR Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 870 GLN 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 981 THR Chi-restraints excluded: chain P residue 1033 ASN Chi-restraints excluded: chain P residue 1092 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0000 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1057 GLN ** 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 = 0.4418 r_free = 0.4418 target = 0.198388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.143697 restraints weight = 11612.455| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.40 r_work: 0.3743 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7998 Z= 0.176 Angle : 0.652 10.783 10886 Z= 0.305 Chirality : 0.042 0.135 1295 Planarity : 0.006 0.066 1367 Dihedral : 4.461 54.094 1109 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.47 % Allowed : 27.89 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.17 (0.27), residues: 999 helix: 0.99 (0.27), residues: 410 sheet: -1.64 (0.50), residues: 91 loop : -2.23 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 67 HIS 0.002 0.000 HIS P 836 PHE 0.014 0.001 PHE P 963 TYR 0.012 0.001 TYR P 183 ARG 0.004 0.000 ARG P1164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.27 seconds wall clock time: 36 minutes 4.13 seconds (2164.13 seconds total)