Starting phenix.real_space_refine on Fri Feb 16 04:11:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/02_2024/7wbu_32406_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/02_2024/7wbu_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_32406/02_2024/7wbu_32406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/02_2024/7wbu_32406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/02_2024/7wbu_32406_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/02_2024/7wbu_32406_updated.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-dev-5238/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: 4.05, per 1000 atoms: 0.56 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: 3.08 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.89 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: 2.53 Time building geometry restraints manager: 3.32 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 1.050 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.470 Find NCS groups from input model: 0.360 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- 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 % Allowed : 0.24 % Favored : 99.39 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 432 HIS 0.003 0.001 HIS A 887 PHE 0.017 0.001 PHE A 107 TYR 0.013 0.001 TYR A 139 ARG 0.003 0.000 ARG A 180 *********************** 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 : 0.827 Fit side-chains REVERT: A 417 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6996 (tm-30) REVERT: A 578 THR cc_start: 0.7833 (m) cc_final: 0.7528 (p) outliers start: 3 outliers final: 2 residues processed: 143 average time/residue: 0.1545 time to fit residues: 31.3720 Evaluate side-chains 103 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 617 ILE 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: 0.0470 chunk 80 optimal weight: 10.0000 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 A 593 HIS ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 7319 Z= 0.119 Angle : 0.482 8.052 9898 Z= 0.236 Chirality : 0.036 0.135 1130 Planarity : 0.004 0.083 1248 Dihedral : 6.968 129.878 960 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.59 % Allowed : 7.81 % Favored : 90.60 % 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: 1.03 (0.29), residues: 894 helix: 1.72 (0.24), residues: 480 sheet: -0.67 (0.53), residues: 109 loop : -0.38 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 432 HIS 0.002 0.000 HIS A 716 PHE 0.021 0.001 PHE A 325 TYR 0.010 0.001 TYR A 288 ARG 0.001 0.000 ARG A 656 *********************** 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: 13 poor density : 124 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.1736 (ttt) cc_final: 0.1109 (tmm) REVERT: A 417 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7111 (tm-30) REVERT: A 736 CYS cc_start: 0.7414 (m) cc_final: 0.6966 (t) outliers start: 13 outliers final: 11 residues processed: 134 average time/residue: 0.1718 time to fit residues: 32.4236 Evaluate side-chains 114 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 67 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.0000 chunk 87 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- 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 887 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1314 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= 0.110 Angle : 0.470 7.751 9898 Z= 0.229 Chirality : 0.036 0.140 1130 Planarity : 0.004 0.067 1248 Dihedral : 6.828 127.042 957 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.71 % Allowed : 9.16 % Favored : 89.13 % 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: 1.20 (0.29), residues: 894 helix: 1.85 (0.24), residues: 476 sheet: -0.73 (0.52), residues: 112 loop : -0.20 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 432 HIS 0.002 0.000 HIS A 155 PHE 0.019 0.001 PHE A 325 TYR 0.008 0.001 TYR A 288 ARG 0.003 0.000 ARG A 180 *********************** 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 131 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 0.778 Fit side-chains REVERT: A 417 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 581 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7306 (mp0) REVERT: A 736 CYS cc_start: 0.7527 (m) cc_final: 0.6929 (t) outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 0.1687 time to fit residues: 29.8378 Evaluate side-chains 108 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 976 ASN 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: 1.9990 chunk 8 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- 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 593 HIS A 803 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7319 Z= 0.234 Angle : 0.531 6.809 9898 Z= 0.263 Chirality : 0.039 0.147 1130 Planarity : 0.004 0.060 1248 Dihedral : 7.191 134.619 957 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.69 % Allowed : 10.99 % Favored : 86.32 % 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: 0.95 (0.29), residues: 894 helix: 1.63 (0.24), residues: 479 sheet: -1.03 (0.51), residues: 111 loop : -0.21 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 494 HIS 0.004 0.001 HIS A 449 PHE 0.022 0.002 PHE A 325 TYR 0.009 0.001 TYR A 124 ARG 0.003 0.000 ARG A 590 *********************** 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 126 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.823 Fit side-chains REVERT: A 581 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7420 (mp0) REVERT: A 725 MET cc_start: 0.7932 (mtt) cc_final: 0.7659 (mtt) outliers start: 22 outliers final: 13 residues processed: 117 average time/residue: 0.1698 time to fit residues: 27.8897 Evaluate side-chains 106 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 391 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7319 Z= 0.342 Angle : 0.630 13.425 9898 Z= 0.311 Chirality : 0.042 0.168 1130 Planarity : 0.004 0.046 1248 Dihedral : 7.771 137.956 957 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.42 % Allowed : 12.33 % Favored : 84.25 % 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: 0.45 (0.29), residues: 894 helix: 1.35 (0.24), residues: 471 sheet: -1.69 (0.52), residues: 99 loop : -0.48 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 494 HIS 0.004 0.001 HIS A 155 PHE 0.026 0.002 PHE A 325 TYR 0.016 0.002 TYR A 124 ARG 0.004 0.001 ARG A 182 *********************** 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 133 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.946 Fit side-chains REVERT: A 371 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 725 MET cc_start: 0.7878 (mtt) cc_final: 0.7543 (mtt) REVERT: A 803 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7000 (m-40) REVERT: A 843 CYS cc_start: 0.7132 (m) cc_final: 0.6830 (m) outliers start: 28 outliers final: 20 residues processed: 123 average time/residue: 0.1488 time to fit residues: 26.7376 Evaluate side-chains 110 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN A 803 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7319 Z= 0.162 Angle : 0.523 9.680 9898 Z= 0.254 Chirality : 0.037 0.144 1130 Planarity : 0.003 0.045 1248 Dihedral : 7.389 150.426 957 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.44 % Allowed : 14.53 % Favored : 83.03 % 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: 0.71 (0.29), residues: 894 helix: 1.57 (0.24), residues: 468 sheet: -1.66 (0.52), residues: 99 loop : -0.33 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 111 HIS 0.002 0.000 HIS A 155 PHE 0.020 0.001 PHE A 325 TYR 0.008 0.001 TYR A 698 ARG 0.002 0.000 ARG A 992 *********************** 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 120 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.828 Fit side-chains REVERT: A 371 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8589 (tt) REVERT: A 431 MET cc_start: 0.8353 (tmm) cc_final: 0.8081 (tmm) REVERT: A 581 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7295 (mp0) REVERT: A 725 MET cc_start: 0.7904 (mtt) cc_final: 0.7523 (mtt) REVERT: A 843 CYS cc_start: 0.6855 (m) cc_final: 0.6543 (m) outliers start: 20 outliers final: 15 residues processed: 114 average time/residue: 0.1560 time to fit residues: 25.7297 Evaluate side-chains 112 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7319 Z= 0.164 Angle : 0.514 9.222 9898 Z= 0.249 Chirality : 0.037 0.144 1130 Planarity : 0.003 0.046 1248 Dihedral : 7.371 156.551 957 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.56 % Allowed : 15.63 % Favored : 81.81 % 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: 0.73 (0.29), residues: 894 helix: 1.57 (0.24), residues: 471 sheet: -1.62 (0.52), residues: 99 loop : -0.34 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 494 HIS 0.003 0.000 HIS A 155 PHE 0.024 0.001 PHE A 325 TYR 0.010 0.001 TYR A 288 ARG 0.002 0.000 ARG A 285 *********************** 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 119 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.865 Fit side-chains REVERT: A 371 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8602 (tt) REVERT: A 581 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7323 (mp0) REVERT: A 590 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7139 (ttp80) REVERT: A 725 MET cc_start: 0.7900 (mtt) cc_final: 0.7508 (mtt) REVERT: A 843 CYS cc_start: 0.6897 (m) cc_final: 0.6582 (m) outliers start: 21 outliers final: 17 residues processed: 113 average time/residue: 0.1606 time to fit residues: 26.1959 Evaluate side-chains 111 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 67 optimal weight: 0.0570 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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: 0.7308 moved from start: 0.2772 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= 0.131 Angle : 0.498 8.675 9898 Z= 0.240 Chirality : 0.036 0.146 1130 Planarity : 0.003 0.046 1248 Dihedral : 7.553 179.878 957 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.95 % Allowed : 16.61 % Favored : 81.44 % 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: 1.57 (0.24), residues: 476 sheet: -1.54 (0.53), residues: 99 loop : -0.26 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 927 HIS 0.002 0.000 HIS A 155 PHE 0.022 0.001 PHE A 325 TYR 0.006 0.001 TYR A 698 ARG 0.002 0.000 ARG A 180 *********************** 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 114 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.916 Fit side-chains REVERT: A 124 TYR cc_start: 0.7608 (t80) cc_final: 0.7086 (t80) REVERT: A 371 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8583 (tt) REVERT: A 435 MET cc_start: 0.8639 (ttm) cc_final: 0.8139 (mtp) REVERT: A 590 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7163 (ttp80) REVERT: A 725 MET cc_start: 0.7925 (mtt) cc_final: 0.7519 (mtt) REVERT: A 843 CYS cc_start: 0.6836 (m) cc_final: 0.6517 (m) outliers start: 16 outliers final: 14 residues processed: 109 average time/residue: 0.1663 time to fit residues: 26.0514 Evaluate side-chains 106 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7319 Z= 0.145 Angle : 0.504 8.474 9898 Z= 0.243 Chirality : 0.037 0.143 1130 Planarity : 0.003 0.044 1248 Dihedral : 5.658 117.282 957 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.08 % Allowed : 16.61 % Favored : 81.32 % 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: 1.60 (0.24), residues: 476 sheet: -1.51 (0.54), residues: 99 loop : -0.25 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 494 HIS 0.003 0.000 HIS A 887 PHE 0.019 0.001 PHE A 325 TYR 0.009 0.001 TYR A 288 ARG 0.002 0.000 ARG A 182 *********************** 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 113 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.868 Fit side-chains REVERT: A 124 TYR cc_start: 0.7579 (t80) cc_final: 0.7088 (t80) REVERT: A 371 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 725 MET cc_start: 0.7936 (mtt) cc_final: 0.7559 (mtt) REVERT: A 843 CYS cc_start: 0.6851 (m) cc_final: 0.6531 (m) outliers start: 17 outliers final: 14 residues processed: 107 average time/residue: 0.1622 time to fit residues: 25.0335 Evaluate side-chains 106 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 0.0980 chunk 7 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 10 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2808 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= 0.129 Angle : 0.514 8.098 9898 Z= 0.248 Chirality : 0.037 0.167 1130 Planarity : 0.003 0.044 1248 Dihedral : 5.004 92.855 957 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.83 % Allowed : 17.34 % Favored : 80.83 % 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: 0.82 (0.29), residues: 894 helix: 1.56 (0.24), residues: 477 sheet: -1.35 (0.52), residues: 109 loop : -0.21 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 927 HIS 0.008 0.001 HIS A 887 PHE 0.021 0.001 PHE A 325 TYR 0.009 0.001 TYR A 288 ARG 0.001 0.000 ARG A 992 ********************** 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 107 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.822 Fit side-chains REVERT: A 124 TYR cc_start: 0.7468 (t80) cc_final: 0.7066 (t80) REVERT: A 228 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7702 (tp) REVERT: A 711 CYS cc_start: 0.7506 (m) cc_final: 0.7291 (m) REVERT: A 725 MET cc_start: 0.7925 (mtt) cc_final: 0.7528 (mtt) REVERT: A 843 CYS cc_start: 0.6834 (m) cc_final: 0.6501 (m) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 0.1578 time to fit residues: 23.4165 Evaluate side-chains 99 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 0.4980 chunk 4 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.171554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.145530 restraints weight = 9942.599| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.71 r_work: 0.3647 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2989 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= 0.210 Angle : 0.552 8.721 9898 Z= 0.268 Chirality : 0.039 0.194 1130 Planarity : 0.004 0.085 1248 Dihedral : 5.334 100.793 957 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.08 % Allowed : 17.09 % Favored : 80.83 % 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: 0.74 (0.29), residues: 894 helix: 1.56 (0.24), residues: 470 sheet: -1.53 (0.52), residues: 109 loop : -0.27 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 494 HIS 0.006 0.001 HIS A 887 PHE 0.027 0.002 PHE A 325 TYR 0.009 0.001 TYR A 124 ARG 0.003 0.000 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.11 seconds wall clock time: 31 minutes 2.82 seconds (1862.82 seconds total)