Starting phenix.real_space_refine (version: dev) on Mon Apr 4 16:10:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/04_2022/7n76_24221.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/04_2022/7n76_24221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/04_2022/7n76_24221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/04_2022/7n76_24221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/04_2022/7n76_24221.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/04_2022/7n76_24221.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.023 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7399 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 7399 Classifications: {'water': 3, 'peptide': 1036} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 69, 'TRANS': 963, None: 3, 'PCIS': 3} Not linked: pdbres="PRO A1168 " pdbres="HOH A1201 " Not linked: pdbres="HOH A1201 " pdbres="HOH A1202 " Not linked: pdbres="HOH A1202 " pdbres="HOH A1203 " Chain breaks: 5 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 650 Unresolved non-hydrogen angles: 835 Unresolved non-hydrogen dihedrals: 549 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 6, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 347 Time building chain proxies: 4.76, per 1000 atoms: 0.64 Number of scatterers: 7399 At special positions: 0 Unit cell: (90.214, 102.802, 130.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1327 8.00 N 1280 7.00 C 4748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 52.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 77 removed outlier: 4.194A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.508A pdb=" N MET A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 284 removed outlier: 3.532A pdb=" N SER A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 419 through 445 Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.843A pdb=" N VAL A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 Processing helix chain 'A' and resid 492 through 499 removed outlier: 3.766A pdb=" N ASN A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.011A pdb=" N ARG A 540 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 651 through 659 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 667 through 678 removed outlier: 3.524A pdb=" N ALA A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 removed outlier: 3.704A pdb=" N GLN A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.581A pdb=" N VAL A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 821 through 832 Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 850 through 864 removed outlier: 3.535A pdb=" N THR A 855 " --> pdb=" O PRO A 851 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 884 Processing helix chain 'A' and resid 909 through 949 Processing helix chain 'A' and resid 954 through 964 Processing helix chain 'A' and resid 964 through 974 removed outlier: 3.681A pdb=" N VAL A 969 " --> pdb=" O ILE A 965 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1020 removed outlier: 3.974A pdb=" N ALA A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.827A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1073 through 1093 Processing helix chain 'A' and resid 1109 through 1145 Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1152 through 1164 removed outlier: 3.508A pdb=" N GLN A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.240A pdb=" N ARG A 78 " --> pdb=" O CYS A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.098A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 293 Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.533A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 387 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.660A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490 removed outlier: 5.975A pdb=" N GLY A 887 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N SER A 903 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 889 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 504 " --> pdb=" O GLY A 869 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA A 741 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE A 846 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET A 743 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A 768 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 519 through 525 removed outlier: 4.903A pdb=" N VAL A 520 " --> pdb=" O ARG A 720 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG A 720 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 522 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 718 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG A 631 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE A 625 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 633 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA A 637 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 619 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 579 " --> pdb=" O GLY A 591 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559 removed outlier: 3.503A pdb=" N SER A 557 " --> pdb=" O VAL A 564 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1302 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: 2.85 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2163 1.33 - 1.45: 1028 1.45 - 1.57: 4280 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 7536 Sorted by residual: bond pdb=" CB VAL A 107 " pdb=" CG2 VAL A 107 " ideal model delta sigma weight residual 1.521 1.349 0.172 3.30e-02 9.18e+02 2.73e+01 bond pdb=" CB TYR A 935 " pdb=" CG TYR A 935 " ideal model delta sigma weight residual 1.512 1.437 0.075 2.20e-02 2.07e+03 1.17e+01 bond pdb=" C TYR A 935 " pdb=" N SER A 936 " ideal model delta sigma weight residual 1.335 1.293 0.042 1.31e-02 5.83e+03 1.02e+01 bond pdb=" CG TYR A 935 " pdb=" CD1 TYR A 935 " ideal model delta sigma weight residual 1.389 1.328 0.061 2.10e-02 2.27e+03 8.55e+00 bond pdb=" CG GLN A 108 " pdb=" CD GLN A 108 " ideal model delta sigma weight residual 1.516 1.452 0.064 2.50e-02 1.60e+03 6.54e+00 ... (remaining 7531 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.67: 278 106.67 - 113.51: 4289 113.51 - 120.35: 2727 120.35 - 127.19: 2929 127.19 - 134.03: 81 Bond angle restraints: 10304 Sorted by residual: angle pdb=" CA TYR A 935 " pdb=" CB TYR A 935 " pdb=" CG TYR A 935 " ideal model delta sigma weight residual 113.90 105.40 8.50 1.80e+00 3.09e-01 2.23e+01 angle pdb=" CG1 VAL A 107 " pdb=" CB VAL A 107 " pdb=" CG2 VAL A 107 " ideal model delta sigma weight residual 110.80 102.10 8.70 2.20e+00 2.07e-01 1.57e+01 angle pdb=" CB LEU A 270 " pdb=" CG LEU A 270 " pdb=" CD2 LEU A 270 " ideal model delta sigma weight residual 110.70 122.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA GLN A 108 " pdb=" CB GLN A 108 " pdb=" CG GLN A 108 " ideal model delta sigma weight residual 114.10 106.65 7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 107.75 112.37 -4.62 1.46e+00 4.69e-01 1.00e+01 ... (remaining 10299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4191 17.56 - 35.11: 269 35.11 - 52.67: 39 52.67 - 70.23: 6 70.23 - 87.79: 4 Dihedral angle restraints: 4509 sinusoidal: 1516 harmonic: 2993 Sorted by residual: dihedral pdb=" CA VAL A 964 " pdb=" C VAL A 964 " pdb=" N ILE A 965 " pdb=" CA ILE A 965 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LEU A 934 " pdb=" C LEU A 934 " pdb=" N TYR A 935 " pdb=" CA TYR A 935 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA SER A 889 " pdb=" C SER A 889 " pdb=" N LEU A 890 " pdb=" CA LEU A 890 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.370: 1268 0.370 - 0.741: 0 0.741 - 1.111: 0 1.111 - 1.482: 0 1.482 - 1.852: 1 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CG LEU A 270 " pdb=" CB LEU A 270 " pdb=" CD1 LEU A 270 " pdb=" CD2 LEU A 270 " both_signs ideal model delta sigma weight residual False -2.59 -0.74 -1.85 2.00e-01 2.50e+01 8.58e+01 chirality pdb=" CA TYR A 935 " pdb=" N TYR A 935 " pdb=" C TYR A 935 " pdb=" CB TYR A 935 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU A 158 " pdb=" CB LEU A 158 " pdb=" CD1 LEU A 158 " pdb=" CD2 LEU A 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1266 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 934 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LEU A 934 " 0.070 2.00e-02 2.50e+03 pdb=" O LEU A 934 " -0.026 2.00e-02 2.50e+03 pdb=" N TYR A 935 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 935 " -0.028 2.00e-02 2.50e+03 2.77e-02 1.54e+01 pdb=" CG TYR A 935 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 935 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 935 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 935 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 935 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 935 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 935 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 107 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C VAL A 107 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 107 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN A 108 " 0.015 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 72 2.64 - 3.20: 7035 3.20 - 3.77: 11463 3.77 - 4.33: 15443 4.33 - 4.90: 26475 Nonbonded interactions: 60488 Sorted by model distance: nonbonded pdb=" OH TYR A 359 " pdb=" OG1 THR A 368 " model vdw 2.074 2.440 nonbonded pdb=" OE2 GLU A 172 " pdb=" NE2 GLN A 175 " model vdw 2.159 2.520 nonbonded pdb=" NH1 ARG A 816 " pdb=" O PRO A1167 " model vdw 2.239 2.520 nonbonded pdb=" O ASP A 325 " pdb=" OG1 THR A 391 " model vdw 2.285 2.440 nonbonded pdb=" O PHE A 958 " pdb=" ND2 ASN A 962 " model vdw 2.311 2.520 ... (remaining 60483 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4748 2.51 5 N 1280 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.070 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: 6.100 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 25.000 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.172 7536 Z= 0.339 Angle : 0.643 11.421 10304 Z= 0.341 Chirality : 0.068 1.852 1269 Planarity : 0.004 0.063 1316 Dihedral : 12.160 87.785 2575 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1024 helix: 0.65 (0.23), residues: 501 sheet: 0.25 (0.41), residues: 151 loop : -0.42 (0.32), residues: 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.894 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.1034 time to fit residues: 60.7029 Evaluate side-chains 36 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 50.0000 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 939 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 7536 Z= 0.191 Angle : 0.562 8.990 10304 Z= 0.279 Chirality : 0.042 0.151 1269 Planarity : 0.005 0.055 1316 Dihedral : 4.181 17.138 1099 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1024 helix: 1.46 (0.23), residues: 503 sheet: 0.33 (0.42), residues: 151 loop : 0.02 (0.32), residues: 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.865 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.8929 time to fit residues: 43.3061 Evaluate side-chains 40 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0693 time to fit residues: 1.3271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 40.0000 chunk 29 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 25 optimal weight: 8.9990 chunk 93 optimal weight: 0.1980 chunk 101 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 7536 Z= 0.148 Angle : 0.505 8.695 10304 Z= 0.249 Chirality : 0.040 0.137 1269 Planarity : 0.004 0.050 1316 Dihedral : 3.813 16.282 1099 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1024 helix: 1.84 (0.23), residues: 505 sheet: 0.42 (0.42), residues: 153 loop : 0.22 (0.33), residues: 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.945 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 46 average time/residue: 0.7402 time to fit residues: 38.2705 Evaluate side-chains 42 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0697 time to fit residues: 1.3022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 30.0000 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 7536 Z= 0.153 Angle : 0.491 7.596 10304 Z= 0.241 Chirality : 0.040 0.135 1269 Planarity : 0.004 0.049 1316 Dihedral : 3.663 15.866 1099 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.27), residues: 1024 helix: 2.11 (0.23), residues: 505 sheet: 0.42 (0.41), residues: 159 loop : 0.49 (0.34), residues: 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.873 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 46 average time/residue: 0.8079 time to fit residues: 41.3775 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0681 time to fit residues: 1.3033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 40.0000 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.060 7536 Z= 0.473 Angle : 0.617 9.075 10304 Z= 0.304 Chirality : 0.045 0.187 1269 Planarity : 0.004 0.050 1316 Dihedral : 4.046 16.096 1099 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.27), residues: 1024 helix: 1.92 (0.23), residues: 503 sheet: 0.36 (0.41), residues: 157 loop : 0.48 (0.34), residues: 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.913 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 44 average time/residue: 0.7737 time to fit residues: 38.1138 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0751 time to fit residues: 1.3715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 50.0000 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 7536 Z= 0.405 Angle : 0.594 11.747 10304 Z= 0.290 Chirality : 0.044 0.163 1269 Planarity : 0.004 0.049 1316 Dihedral : 4.040 16.512 1099 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.27), residues: 1024 helix: 1.96 (0.23), residues: 503 sheet: 0.39 (0.41), residues: 157 loop : 0.48 (0.34), residues: 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 39 time to evaluate : 0.896 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 50 average time/residue: 0.7177 time to fit residues: 40.3482 Evaluate side-chains 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.7720 time to fit residues: 3.7566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7536 Z= 0.180 Angle : 0.514 11.865 10304 Z= 0.250 Chirality : 0.041 0.148 1269 Planarity : 0.004 0.048 1316 Dihedral : 3.748 18.704 1099 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.27), residues: 1024 helix: 2.24 (0.23), residues: 503 sheet: 0.38 (0.41), residues: 152 loop : 0.63 (0.33), residues: 369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.874 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 0.8200 time to fit residues: 45.4973 Evaluate side-chains 44 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0725 time to fit residues: 1.4069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 50.0000 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 90 optimal weight: 0.0060 chunk 95 optimal weight: 0.8980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7536 Z= 0.171 Angle : 0.529 11.831 10304 Z= 0.252 Chirality : 0.041 0.166 1269 Planarity : 0.004 0.047 1316 Dihedral : 3.645 16.931 1099 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.27), residues: 1024 helix: 2.34 (0.23), residues: 504 sheet: 0.46 (0.41), residues: 157 loop : 0.62 (0.34), residues: 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.872 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 0.7591 time to fit residues: 39.0334 Evaluate side-chains 43 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.1753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7536 Z= 0.192 Angle : 0.530 10.999 10304 Z= 0.253 Chirality : 0.042 0.216 1269 Planarity : 0.004 0.047 1316 Dihedral : 3.608 16.527 1099 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.27), residues: 1024 helix: 2.42 (0.23), residues: 504 sheet: 0.47 (0.41), residues: 157 loop : 0.64 (0.34), residues: 363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.817 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 0.8374 time to fit residues: 40.8552 Evaluate side-chains 43 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0648 time to fit residues: 1.2778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 50.0000 chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 50.0000 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7536 Z= 0.218 Angle : 0.546 11.548 10304 Z= 0.259 Chirality : 0.042 0.178 1269 Planarity : 0.004 0.046 1316 Dihedral : 3.624 16.655 1099 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.27), residues: 1024 helix: 2.44 (0.23), residues: 504 sheet: 0.49 (0.41), residues: 157 loop : 0.64 (0.34), residues: 363 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.994 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.8349 time to fit residues: 41.6882 Evaluate side-chains 43 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.1736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** 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 = 0.3798 r_free = 0.3798 target = 0.095319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068194 restraints weight = 19283.920| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.80 r_work: 0.3186 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work: 0.3160 rms_B_bonded: 2.58 restraints_weight: 0.1250 r_work: 0.3147 rms_B_bonded: 2.65 restraints_weight: 0.0625 r_work: 0.3134 rms_B_bonded: 2.75 restraints_weight: 0.0312 r_work: 0.3120 rms_B_bonded: 2.87 restraints_weight: 0.0156 r_work: 0.3105 rms_B_bonded: 3.03 restraints_weight: 0.0078 r_work: 0.3090 rms_B_bonded: 3.22 restraints_weight: 0.0039 r_work: 0.3074 rms_B_bonded: 3.43 restraints_weight: 0.0020 r_work: 0.3057 rms_B_bonded: 3.68 restraints_weight: 0.0010 r_work: 0.3039 rms_B_bonded: 3.97 restraints_weight: 0.0005 r_work: 0.3019 rms_B_bonded: 4.29 restraints_weight: 0.0002 r_work: 0.2999 rms_B_bonded: 4.66 restraints_weight: 0.0001 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 7536 Z= 0.160 Angle : 0.524 11.630 10304 Z= 0.249 Chirality : 0.041 0.191 1269 Planarity : 0.004 0.046 1316 Dihedral : 3.530 15.787 1099 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.27), residues: 1024 helix: 2.50 (0.23), residues: 505 sheet: 0.56 (0.41), residues: 156 loop : 0.59 (0.34), residues: 363 =============================================================================== Job complete usr+sys time: 1748.11 seconds wall clock time: 32 minutes 15.02 seconds (1935.02 seconds total)