Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 10:01:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/07_2023/7wbu_32406_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/07_2023/7wbu_32406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/07_2023/7wbu_32406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/07_2023/7wbu_32406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/07_2023/7wbu_32406_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/07_2023/7wbu_32406_updated.pdb" } resolution = 3.42 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7170 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 77 5.16 5 C 4558 2.51 5 N 1189 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 986": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 7170 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Unusual residues: {'ADP': 1} Classifications: {'peptide': 898, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 868, None: 1} Not linked: pdbres="VAL A 996 " pdbres="ADP A1001 " Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.76, per 1000 atoms: 0.52 Number of scatterers: 7170 At special positions: 0 Unit cell: (84.66, 90.885, 117.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 2 15.00 O 1344 8.00 N 1189 7.00 C 4558 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: 2.70 Conformation dependent library (CDL) restraints added in 959.3 milliseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 3 sheets defined 50.1% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 98 through 112 removed outlier: 3.921A pdb=" N GLU A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 202 through 209 removed outlier: 4.710A pdb=" N ASP A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 removed outlier: 4.417A pdb=" N GLN A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Proline residue: A 224 - end of helix Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 319 through 330 Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.846A pdb=" N GLN A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 357 Processing helix chain 'A' and resid 368 through 383 Processing helix chain 'A' and resid 389 through 408 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.829A pdb=" N TYR A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 485 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 505 through 515 Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 539 through 542 No H-bonds generated for 'chain 'A' and resid 539 through 542' Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 559 through 568 removed outlier: 3.718A pdb=" N PHE A 568 " --> pdb=" O GLN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 589 Processing helix chain 'A' and resid 616 through 632 removed outlier: 4.029A pdb=" N ALA A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 631 " --> pdb=" O CYS A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 676 through 688 Processing helix chain 'A' and resid 704 through 714 Processing helix chain 'A' and resid 733 through 745 removed outlier: 3.989A pdb=" N ASP A 738 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 771 Processing helix chain 'A' and resid 790 through 800 removed outlier: 4.086A pdb=" N ASP A 794 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 828 removed outlier: 4.213A pdb=" N VAL A 821 " --> pdb=" O LYS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 859 removed outlier: 3.974A pdb=" N VAL A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 857 " --> pdb=" O ALA A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 886 Processing helix chain 'A' and resid 904 through 914 removed outlier: 3.802A pdb=" N GLU A 908 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 912 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 914 " --> pdb=" O ALA A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 943 Processing helix chain 'A' and resid 961 through 973 Processing helix chain 'A' and resid 985 through 992 Processing sheet with id= A, first strand: chain 'A' and resid 294 through 298 removed outlier: 6.697A pdb=" N THR A 151 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE A 297 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL A 153 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 152 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 278 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE A 185 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE A 230 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE A 187 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASP A 232 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 189 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 438 through 440 Processing sheet with id= C, first strand: chain 'A' and resid 571 through 576 removed outlier: 6.475A pdb=" N LYS A 597 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE A 574 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS A 599 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE A 576 " --> pdb=" O HIS A 599 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS A 601 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 638 " --> pdb=" O PHE A 598 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU A 600 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN A 640 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N MET A 602 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP A 642 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS A 667 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU A 641 " --> pdb=" O LYS A 667 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 669 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS A 694 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N CYS A 670 " --> pdb=" O HIS A 694 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN A 696 " --> pdb=" O CYS A 670 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU A 723 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 751 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A 780 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE A 808 " --> pdb=" O LEU A 781 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU A 837 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR A 865 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASN A 894 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS A 922 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 951 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 978 " --> pdb=" O LEU A 952 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 275 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1196 1.31 - 1.44: 1881 1.44 - 1.56: 4134 1.56 - 1.69: 5 1.69 - 1.82: 103 Bond restraints: 7319 Sorted by residual: bond pdb=" C ASN A 615 " pdb=" O ASN A 615 " ideal model delta sigma weight residual 1.235 1.183 0.052 1.26e-02 6.30e+03 1.73e+01 bond pdb=" C LYS A 619 " pdb=" O LYS A 619 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.61e+01 bond pdb=" C GLU A 618 " pdb=" O GLU A 618 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.17e-02 7.31e+03 1.58e+01 bond pdb=" CA LYS A 619 " pdb=" C LYS A 619 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.27e-02 6.20e+03 1.52e+01 bond pdb=" N LYS A 619 " pdb=" CA LYS A 619 " ideal model delta sigma weight residual 1.459 1.425 0.035 1.19e-02 7.06e+03 8.52e+00 ... (remaining 7314 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.86: 127 105.86 - 113.37: 4088 113.37 - 120.88: 3631 120.88 - 128.40: 1994 128.40 - 135.91: 58 Bond angle restraints: 9898 Sorted by residual: angle pdb=" CA PRO A 98 " pdb=" N PRO A 98 " pdb=" CD PRO A 98 " ideal model delta sigma weight residual 112.00 102.09 9.91 1.40e+00 5.10e-01 5.01e+01 angle pdb=" CA PRO A 254 " pdb=" N PRO A 254 " pdb=" CD PRO A 254 " ideal model delta sigma weight residual 112.00 104.23 7.77 1.40e+00 5.10e-01 3.08e+01 angle pdb=" N ASN A 615 " pdb=" CA ASN A 615 " pdb=" CB ASN A 615 " ideal model delta sigma weight residual 110.49 119.62 -9.13 1.69e+00 3.50e-01 2.92e+01 angle pdb=" N THR A 616 " pdb=" CA THR A 616 " pdb=" C THR A 616 " ideal model delta sigma weight residual 111.28 116.43 -5.15 1.09e+00 8.42e-01 2.23e+01 angle pdb=" N GLU A 454 " pdb=" CA GLU A 454 " pdb=" CB GLU A 454 " ideal model delta sigma weight residual 110.39 116.67 -6.28 1.66e+00 3.63e-01 1.43e+01 ... (remaining 9893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.27: 4192 26.27 - 52.54: 220 52.54 - 78.81: 16 78.81 - 105.08: 6 105.08 - 131.35: 2 Dihedral angle restraints: 4436 sinusoidal: 1793 harmonic: 2643 Sorted by residual: dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual 300.00 168.65 131.35 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual 300.00 176.19 123.81 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" N ASN A 615 " pdb=" C ASN A 615 " pdb=" CA ASN A 615 " pdb=" CB ASN A 615 " ideal model delta harmonic sigma weight residual 122.80 132.69 -9.89 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 4433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 967 0.055 - 0.110: 149 0.110 - 0.164: 11 0.164 - 0.219: 0 0.219 - 0.274: 3 Chirality restraints: 1130 Sorted by residual: chirality pdb=" CA THR A 616 " pdb=" N THR A 616 " pdb=" C THR A 616 " pdb=" CB THR A 616 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ASN A 615 " pdb=" N ASN A 615 " pdb=" C ASN A 615 " pdb=" CB ASN A 615 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PRO A 98 " pdb=" N PRO A 98 " pdb=" C PRO A 98 " pdb=" CB PRO A 98 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1127 not shown) Planarity restraints: 1248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 253 " 0.096 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO A 254 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 97 " 0.065 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 98 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 432 " -0.015 2.00e-02 2.50e+03 1.62e-02 6.56e+00 pdb=" CG TRP A 432 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 432 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 432 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 432 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 432 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 432 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 432 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 432 " -0.000 2.00e-02 2.50e+03 ... (remaining 1245 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 133 2.70 - 3.25: 7165 3.25 - 3.80: 11321 3.80 - 4.35: 14800 4.35 - 4.90: 23960 Nonbonded interactions: 57379 Sorted by model distance: nonbonded pdb=" O VAL A 605 " pdb=" NZ LYS A 619 " model vdw 2.145 2.520 nonbonded pdb=" OD1 ASP A 875 " pdb=" OG SER A 906 " model vdw 2.249 2.440 nonbonded pdb=" NE1 TRP A 210 " pdb=" OG SER A 214 " model vdw 2.256 2.520 nonbonded pdb=" O LEU A 309 " pdb=" ND1 HIS A 313 " model vdw 2.308 2.520 nonbonded pdb=" OH TYR A 99 " pdb=" O VAL A 186 " model vdw 2.327 2.440 ... (remaining 57374 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 1.220 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.950 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 0.144 7319 Z= 0.212 Angle : 0.590 9.912 9898 Z= 0.314 Chirality : 0.040 0.274 1130 Planarity : 0.006 0.140 1248 Dihedral : 15.373 131.352 2706 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.29), residues: 894 helix: 1.57 (0.24), residues: 476 sheet: -0.68 (0.53), residues: 109 loop : -0.38 (0.36), residues: 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.782 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 143 average time/residue: 0.1617 time to fit residues: 33.0197 Evaluate side-chains 102 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0655 time to fit residues: 1.3659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 287 ASN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 7319 Z= 0.144 Angle : 0.492 7.769 9898 Z= 0.241 Chirality : 0.037 0.135 1130 Planarity : 0.004 0.083 1248 Dihedral : 7.020 131.030 957 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.29), residues: 894 helix: 1.68 (0.24), residues: 480 sheet: -0.81 (0.52), residues: 111 loop : -0.35 (0.37), residues: 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.1648 time to fit residues: 30.9244 Evaluate side-chains 115 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0697 time to fit residues: 2.6852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS A 887 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 7319 Z= 0.139 Angle : 0.484 7.635 9898 Z= 0.236 Chirality : 0.037 0.142 1130 Planarity : 0.004 0.068 1248 Dihedral : 6.980 130.638 957 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.29), residues: 894 helix: 1.75 (0.24), residues: 480 sheet: -0.89 (0.52), residues: 111 loop : -0.30 (0.38), residues: 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.886 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 121 average time/residue: 0.1892 time to fit residues: 32.0968 Evaluate side-chains 106 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0705 time to fit residues: 1.5590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 529 GLN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7319 Z= 0.223 Angle : 0.532 6.611 9898 Z= 0.262 Chirality : 0.039 0.148 1130 Planarity : 0.004 0.061 1248 Dihedral : 7.268 135.983 957 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.29), residues: 894 helix: 1.62 (0.24), residues: 480 sheet: -1.13 (0.50), residues: 111 loop : -0.27 (0.38), residues: 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.844 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.1594 time to fit residues: 26.5753 Evaluate side-chains 106 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0721 time to fit residues: 2.7672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 7319 Z= 0.212 Angle : 0.533 12.434 9898 Z= 0.259 Chirality : 0.039 0.146 1130 Planarity : 0.003 0.045 1248 Dihedral : 7.339 137.387 957 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.29), residues: 894 helix: 1.56 (0.24), residues: 478 sheet: -1.44 (0.51), residues: 101 loop : -0.36 (0.36), residues: 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.793 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 0.1549 time to fit residues: 24.4050 Evaluate side-chains 96 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0707 time to fit residues: 1.3564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7312 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 7319 Z= 0.158 Angle : 0.502 9.460 9898 Z= 0.246 Chirality : 0.037 0.144 1130 Planarity : 0.003 0.045 1248 Dihedral : 7.254 141.341 957 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.29), residues: 894 helix: 1.61 (0.24), residues: 476 sheet: -1.38 (0.51), residues: 102 loop : -0.28 (0.37), residues: 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.896 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 107 average time/residue: 0.1795 time to fit residues: 27.0483 Evaluate side-chains 94 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0695 time to fit residues: 1.5466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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: 0.7296 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7319 Z= 0.140 Angle : 0.495 8.373 9898 Z= 0.239 Chirality : 0.036 0.143 1130 Planarity : 0.003 0.044 1248 Dihedral : 7.192 143.853 957 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.29), residues: 894 helix: 1.67 (0.24), residues: 476 sheet: -1.37 (0.52), residues: 102 loop : -0.28 (0.37), residues: 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.760 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 103 average time/residue: 0.1626 time to fit residues: 24.3161 Evaluate side-chains 95 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0842 time to fit residues: 1.4309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 67 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7315 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7319 Z= 0.165 Angle : 0.511 8.167 9898 Z= 0.248 Chirality : 0.037 0.145 1130 Planarity : 0.003 0.044 1248 Dihedral : 7.216 145.045 957 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.29), residues: 894 helix: 1.59 (0.24), residues: 477 sheet: -1.43 (0.52), residues: 101 loop : -0.32 (0.37), residues: 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.902 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.1682 time to fit residues: 24.6159 Evaluate side-chains 99 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0695 time to fit residues: 1.7097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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: 0.7326 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7319 Z= 0.178 Angle : 0.534 8.405 9898 Z= 0.258 Chirality : 0.038 0.145 1130 Planarity : 0.003 0.044 1248 Dihedral : 7.266 145.793 957 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.29), residues: 894 helix: 1.56 (0.24), residues: 476 sheet: -1.29 (0.51), residues: 109 loop : -0.28 (0.37), residues: 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.764 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 0.1596 time to fit residues: 23.4082 Evaluate side-chains 98 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0747 time to fit residues: 1.7784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7319 Z= 0.173 Angle : 0.540 7.861 9898 Z= 0.260 Chirality : 0.038 0.148 1130 Planarity : 0.004 0.080 1248 Dihedral : 7.238 148.145 957 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.29), residues: 894 helix: 1.56 (0.24), residues: 475 sheet: -1.35 (0.52), residues: 109 loop : -0.30 (0.37), residues: 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.875 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 101 average time/residue: 0.1677 time to fit residues: 24.5942 Evaluate side-chains 93 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0805 time to fit residues: 1.2735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 859 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.171678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144433 restraints weight = 9889.015| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.81 r_work: 0.3629 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7319 Z= 0.209 Angle : 0.575 14.581 9898 Z= 0.274 Chirality : 0.039 0.147 1130 Planarity : 0.004 0.076 1248 Dihedral : 7.316 150.454 957 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.29), residues: 894 helix: 1.56 (0.24), residues: 471 sheet: -1.40 (0.52), residues: 109 loop : -0.31 (0.36), residues: 314 =============================================================================== Job complete usr+sys time: 1552.68 seconds wall clock time: 29 minutes 8.59 seconds (1748.59 seconds total)