Starting phenix.real_space_refine on Wed Mar 12 01:23:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gud_34273/03_2025/8gud_34273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gud_34273/03_2025/8gud_34273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gud_34273/03_2025/8gud_34273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gud_34273/03_2025/8gud_34273.map" model { file = "/net/cci-nas-00/data/ceres_data/8gud_34273/03_2025/8gud_34273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gud_34273/03_2025/8gud_34273.cif" } resolution = 2.62 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 62 5.16 5 C 4360 2.51 5 N 1159 2.21 5 O 1230 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6814 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6784 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 835, 6784 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 8 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'1LT': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AILE A 932 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE A 932 " occ=0.50 residue: pdb=" N AASP A 933 " occ=0.50 ... (6 atoms not shown) pdb=" OD2AASP A 933 " occ=0.50 residue: pdb=" N APHE A 934 " occ=0.50 ... (9 atoms not shown) pdb=" CZ APHE A 934 " occ=0.50 residue: pdb=" N AGLY A 935 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY A 935 " occ=0.50 Time building chain proxies: 4.76, per 1000 atoms: 0.70 Number of scatterers: 6814 At special positions: 0 Unit cell: (74.97, 87.822, 101.745, 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 62 16.00 F 3 9.00 O 1230 8.00 N 1159 7.00 C 4360 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 853.1 milliseconds 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1594 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 47.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.605A pdb=" N PHE A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.507A pdb=" N VAL A 151 " --> pdb=" O CYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 305 through 309 removed outlier: 4.440A pdb=" N ARG A 309 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 497 Processing helix chain 'A' and resid 528 through 536 removed outlier: 3.705A pdb=" N LYS A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 3.632A pdb=" N PHE A 550 " --> pdb=" O GLN A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.599A pdb=" N VAL A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 608 through 622 removed outlier: 3.580A pdb=" N LYS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 5.041A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 662 through 674 Processing helix chain 'A' and resid 677 through 692 removed outlier: 4.422A pdb=" N GLN A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 686 " --> pdb=" O GLN A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 720 removed outlier: 3.818A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 741 Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.514A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.973A pdb=" N CYS A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 823 Processing helix chain 'A' and resid 857 through 862 Processing helix chain 'A' and resid 875 through 884 Processing helix chain 'A' and resid 889 through 899 removed outlier: 3.651A pdb=" N ALA A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 894 " --> pdb=" O TYR A 890 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.531A pdb=" N VAL A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 959 through 965 removed outlier: 3.930A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 964 " --> pdb=" O PHE A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 992 removed outlier: 3.557A pdb=" N GLU A 978 " --> pdb=" O THR A 974 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 988 " --> pdb=" O CYS A 984 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.830A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1027 removed outlier: 3.788A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1047 removed outlier: 4.339A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A1038 " --> pdb=" O GLU A1034 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A1042 " --> pdb=" O TYR A1038 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A1047 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 212 removed outlier: 8.953A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TRP A 195 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N ALA A 289 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 392 removed outlier: 4.090A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE A 338 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU A 476 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS A 340 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA4, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AA5, first strand: chain 'A' and resid 921 through 923 removed outlier: 3.535A pdb=" N MET A 922 " --> pdb=" O PHE A 930 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 930 " --> pdb=" O MET A 922 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 241 hydrogen bonds defined for protein. 693 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1128 1.30 - 1.43: 1781 1.43 - 1.56: 3957 1.56 - 1.69: 6 1.69 - 1.81: 94 Bond restraints: 6966 Sorted by residual: bond pdb=" C9 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.738 1.530 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.734 1.529 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.569 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C5 1LT A1101 " pdb=" C6 1LT A1101 " ideal model delta sigma weight residual 1.525 1.352 0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " ideal model delta sigma weight residual 1.291 1.416 -0.125 2.00e-02 2.50e+03 3.89e+01 ... (remaining 6961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 9381 3.81 - 7.61: 34 7.61 - 11.42: 3 11.42 - 15.22: 1 15.22 - 19.03: 2 Bond angle restraints: 9421 Sorted by residual: angle pdb=" N1 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 118.47 137.50 -19.03 3.00e+00 1.11e-01 4.02e+01 angle pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " pdb=" C9 1LT A1101 " ideal model delta sigma weight residual 88.90 107.71 -18.81 3.00e+00 1.11e-01 3.93e+01 angle pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 126.74 114.54 12.20 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CA TYR A 392 " pdb=" CB TYR A 392 " pdb=" CG TYR A 392 " ideal model delta sigma weight residual 113.90 119.10 -5.20 1.80e+00 3.09e-01 8.35e+00 angle pdb=" CB MET A 583 " pdb=" CG MET A 583 " pdb=" SD MET A 583 " ideal model delta sigma weight residual 112.70 104.36 8.34 3.00e+00 1.11e-01 7.72e+00 ... (remaining 9416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3763 17.55 - 35.11: 377 35.11 - 52.66: 71 52.66 - 70.21: 8 70.21 - 87.77: 11 Dihedral angle restraints: 4230 sinusoidal: 1777 harmonic: 2453 Sorted by residual: dihedral pdb=" CA GLU A 642 " pdb=" C GLU A 642 " pdb=" N GLN A 643 " pdb=" CA GLN A 643 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASN A 647 " pdb=" C ASN A 647 " pdb=" N LEU A 648 " pdb=" CA LEU A 648 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASN A 145 " pdb=" C ASN A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 162.49 17.51 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 822 0.055 - 0.110: 179 0.110 - 0.165: 22 0.165 - 0.220: 3 0.220 - 0.276: 1 Chirality restraints: 1027 Sorted by residual: chirality pdb=" CG LEU A 404 " pdb=" CB LEU A 404 " pdb=" CD1 LEU A 404 " pdb=" CD2 LEU A 404 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CG LEU A 719 " pdb=" CB LEU A 719 " pdb=" CD1 LEU A 719 " pdb=" CD2 LEU A 719 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA ILE A 848 " pdb=" N ILE A 848 " pdb=" C ILE A 848 " pdb=" CB ILE A 848 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 1024 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA AGLY A 935 " 0.036 2.00e-02 2.50e+03 7.39e-02 5.46e+01 pdb=" C AGLY A 935 " -0.128 2.00e-02 2.50e+03 pdb=" O AGLY A 935 " 0.048 2.00e-02 2.50e+03 pdb=" N HIS A 936 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 383 " -0.023 2.00e-02 2.50e+03 2.08e-02 1.09e+01 pdb=" CG TRP A 383 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 383 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 383 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 383 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 383 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 383 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 383 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 383 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 383 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 216 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO A 217 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.032 5.00e-02 4.00e+02 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 155 2.67 - 3.23: 6724 3.23 - 3.79: 10827 3.79 - 4.34: 15470 4.34 - 4.90: 24096 Nonbonded interactions: 57272 Sorted by model distance: nonbonded pdb=" NH1 ARG A 398 " pdb=" OH TYR A 644 " model vdw 2.116 3.120 nonbonded pdb=" O ILE A 633 " pdb=" NE2 GLN A 637 " model vdw 2.138 3.120 nonbonded pdb=" O ASP A 603 " pdb=" NH2 ARG A 612 " model vdw 2.143 3.120 nonbonded pdb=" OH TYR A 165 " pdb=" O CYS A 695 " model vdw 2.172 3.040 nonbonded pdb=" O LYS A1024 " pdb=" OH TYR A1038 " model vdw 2.197 3.040 ... (remaining 57267 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=0.50 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 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 : 0.008 0.208 6966 Z= 0.515 Angle : 0.788 19.031 9421 Z= 0.373 Chirality : 0.047 0.276 1027 Planarity : 0.006 0.074 1203 Dihedral : 14.854 87.766 2636 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.29), residues: 817 helix: -1.47 (0.26), residues: 364 sheet: -1.93 (0.54), residues: 85 loop : -1.00 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 383 HIS 0.003 0.001 HIS A 701 PHE 0.019 0.002 PHE A 937 TYR 0.037 0.002 TYR A 392 ARG 0.005 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.4741 (ttt180) cc_final: 0.4329 (tpp-160) REVERT: A 299 MET cc_start: 0.3812 (mtt) cc_final: 0.3512 (mtp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 1.1861 time to fit residues: 119.0697 Evaluate side-chains 75 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN A 660 ASN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.260868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.226449 restraints weight = 6757.115| |-----------------------------------------------------------------------------| r_work (start): 0.4712 rms_B_bonded: 2.17 r_work: 0.4587 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4594 r_free = 0.4594 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4593 r_free = 0.4593 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6966 Z= 0.226 Angle : 0.623 7.987 9421 Z= 0.313 Chirality : 0.043 0.139 1027 Planarity : 0.005 0.058 1203 Dihedral : 5.750 43.177 917 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.85 % Allowed : 11.61 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.57 (0.30), residues: 817 helix: -0.92 (0.26), residues: 376 sheet: -1.54 (0.56), residues: 86 loop : -0.85 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 383 HIS 0.004 0.001 HIS A 665 PHE 0.016 0.001 PHE A 937 TYR 0.030 0.002 TYR A 392 ARG 0.003 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.659 Fit side-chains REVERT: A 115 ARG cc_start: 0.4320 (ttt180) cc_final: 0.3383 (tpp-160) REVERT: A 121 ILE cc_start: 0.4901 (OUTLIER) cc_final: 0.4314 (mp) REVERT: A 138 ASP cc_start: 0.5898 (t0) cc_final: 0.5264 (t0) REVERT: A 182 TYR cc_start: 0.7099 (t80) cc_final: 0.6886 (t80) REVERT: A 264 LYS cc_start: 0.7188 (tppp) cc_final: 0.6462 (tptp) REVERT: A 432 TYR cc_start: 0.4416 (p90) cc_final: 0.3352 (p90) REVERT: A 642 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5247 (mt-10) REVERT: A 665 HIS cc_start: 0.6579 (t70) cc_final: 0.5990 (t70) REVERT: A 700 LYS cc_start: 0.4858 (mttp) cc_final: 0.4556 (tptt) REVERT: A 717 ASP cc_start: 0.6332 (t0) cc_final: 0.6105 (t0) REVERT: A 765 ARG cc_start: 0.7396 (tpm170) cc_final: 0.7184 (tpm170) outliers start: 14 outliers final: 6 residues processed: 95 average time/residue: 1.0982 time to fit residues: 110.8410 Evaluate side-chains 90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 833 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.260144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.226080 restraints weight = 6698.691| |-----------------------------------------------------------------------------| r_work (start): 0.4706 rms_B_bonded: 2.12 r_work: 0.4585 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4585 r_free = 0.4585 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4585 r_free = 0.4585 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6966 Z= 0.232 Angle : 0.608 8.119 9421 Z= 0.305 Chirality : 0.043 0.166 1027 Planarity : 0.005 0.061 1203 Dihedral : 5.581 42.406 917 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.64 % Allowed : 13.06 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.47 (0.30), residues: 817 helix: -0.82 (0.26), residues: 375 sheet: -1.41 (0.57), residues: 86 loop : -0.82 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 383 HIS 0.006 0.001 HIS A 665 PHE 0.016 0.002 PHE A 937 TYR 0.027 0.002 TYR A 392 ARG 0.003 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.678 Fit side-chains REVERT: A 115 ARG cc_start: 0.4395 (ttt180) cc_final: 0.3428 (tpp-160) REVERT: A 121 ILE cc_start: 0.4916 (OUTLIER) cc_final: 0.4237 (mp) REVERT: A 182 TYR cc_start: 0.7097 (t80) cc_final: 0.6877 (t80) REVERT: A 264 LYS cc_start: 0.7289 (tppp) cc_final: 0.6584 (tptp) REVERT: A 432 TYR cc_start: 0.4361 (p90) cc_final: 0.3385 (p90) REVERT: A 642 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5184 (tt0) REVERT: A 665 HIS cc_start: 0.6651 (t70) cc_final: 0.6171 (t-170) REVERT: A 700 LYS cc_start: 0.4772 (mttp) cc_final: 0.4468 (tptt) outliers start: 20 outliers final: 9 residues processed: 97 average time/residue: 1.1238 time to fit residues: 115.5801 Evaluate side-chains 91 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 896 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.0470 chunk 17 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 875 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.263105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.230720 restraints weight = 7032.701| |-----------------------------------------------------------------------------| r_work (start): 0.4802 rms_B_bonded: 2.14 r_work: 0.4726 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4616 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.4616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4621 r_free = 0.4621 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4621 r_free = 0.4621 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5573 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6966 Z= 0.245 Angle : 0.614 8.218 9421 Z= 0.307 Chirality : 0.043 0.151 1027 Planarity : 0.005 0.062 1203 Dihedral : 5.570 42.153 917 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.30 % Allowed : 15.17 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.42 (0.30), residues: 817 helix: -0.77 (0.26), residues: 374 sheet: -1.35 (0.58), residues: 86 loop : -0.83 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 383 HIS 0.005 0.001 HIS A 665 PHE 0.021 0.002 PHE A 430 TYR 0.024 0.002 TYR A 392 ARG 0.003 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.667 Fit side-chains REVERT: A 115 ARG cc_start: 0.4554 (ttt180) cc_final: 0.3598 (tpp-160) REVERT: A 121 ILE cc_start: 0.5240 (OUTLIER) cc_final: 0.5038 (mp) REVERT: A 138 ASP cc_start: 0.5924 (t0) cc_final: 0.5356 (t0) REVERT: A 141 ARG cc_start: 0.5618 (OUTLIER) cc_final: 0.5262 (tmm160) REVERT: A 165 TYR cc_start: 0.5934 (t80) cc_final: 0.4999 (t80) REVERT: A 182 TYR cc_start: 0.7055 (t80) cc_final: 0.6840 (t80) REVERT: A 432 TYR cc_start: 0.4505 (p90) cc_final: 0.3336 (p90) REVERT: A 665 HIS cc_start: 0.6762 (t70) cc_final: 0.6128 (t-170) REVERT: A 689 GLU cc_start: 0.6559 (mt-10) cc_final: 0.6259 (mp0) REVERT: A 697 MET cc_start: 0.5205 (ttt) cc_final: 0.4580 (ttm) outliers start: 25 outliers final: 10 residues processed: 102 average time/residue: 1.1202 time to fit residues: 120.9210 Evaluate side-chains 92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 896 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.263534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.232343 restraints weight = 7033.156| |-----------------------------------------------------------------------------| r_work (start): 0.4787 rms_B_bonded: 2.08 r_work: 0.4712 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4602 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4625 r_free = 0.4625 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4626 r_free = 0.4626 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6966 Z= 0.229 Angle : 0.604 8.153 9421 Z= 0.300 Chirality : 0.042 0.150 1027 Planarity : 0.005 0.062 1203 Dihedral : 5.478 41.948 917 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.17 % Allowed : 17.15 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.32 (0.30), residues: 817 helix: -0.68 (0.26), residues: 377 sheet: -1.37 (0.57), residues: 86 loop : -0.75 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 383 HIS 0.005 0.001 HIS A 665 PHE 0.015 0.001 PHE A 937 TYR 0.024 0.002 TYR A 392 ARG 0.003 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.4468 (ttt180) cc_final: 0.3535 (tpp-160) REVERT: A 141 ARG cc_start: 0.5613 (OUTLIER) cc_final: 0.5198 (tmm160) REVERT: A 432 TYR cc_start: 0.4552 (p90) cc_final: 0.3277 (p90) REVERT: A 546 GLN cc_start: 0.5614 (OUTLIER) cc_final: 0.4816 (tm-30) REVERT: A 665 HIS cc_start: 0.6746 (t70) cc_final: 0.6201 (t-170) REVERT: A 689 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6310 (mp0) REVERT: A 700 LYS cc_start: 0.4649 (tptt) cc_final: 0.4394 (mttp) outliers start: 24 outliers final: 13 residues processed: 100 average time/residue: 1.1086 time to fit residues: 117.5663 Evaluate side-chains 97 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 44 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.265399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.234777 restraints weight = 7035.711| |-----------------------------------------------------------------------------| r_work (start): 0.4784 rms_B_bonded: 2.02 r_work: 0.4707 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4598 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4628 r_free = 0.4628 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4628 r_free = 0.4628 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5594 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6966 Z= 0.251 Angle : 0.617 8.263 9421 Z= 0.307 Chirality : 0.043 0.149 1027 Planarity : 0.005 0.062 1203 Dihedral : 5.538 42.301 917 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.69 % Allowed : 18.21 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.30), residues: 817 helix: -0.62 (0.26), residues: 374 sheet: -1.38 (0.57), residues: 86 loop : -0.82 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 383 HIS 0.006 0.001 HIS A 665 PHE 0.015 0.002 PHE A 937 TYR 0.023 0.002 TYR A 392 ARG 0.003 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.4524 (ttt180) cc_final: 0.3573 (tpp-160) REVERT: A 141 ARG cc_start: 0.5620 (OUTLIER) cc_final: 0.5091 (tmm160) REVERT: A 182 TYR cc_start: 0.6899 (t80) cc_final: 0.6673 (t80) REVERT: A 455 LEU cc_start: 0.2800 (OUTLIER) cc_final: 0.2298 (pp) REVERT: A 546 GLN cc_start: 0.5633 (OUTLIER) cc_final: 0.4790 (tm-30) REVERT: A 665 HIS cc_start: 0.6846 (t70) cc_final: 0.6004 (t-170) outliers start: 28 outliers final: 14 residues processed: 103 average time/residue: 1.0294 time to fit residues: 112.7720 Evaluate side-chains 98 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 46 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 0.0010 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.267861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.237099 restraints weight = 6900.632| |-----------------------------------------------------------------------------| r_work (start): 0.4815 rms_B_bonded: 2.02 r_work: 0.4737 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4628 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4656 r_free = 0.4656 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4656 r_free = 0.4656 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6966 Z= 0.210 Angle : 0.600 8.292 9421 Z= 0.298 Chirality : 0.042 0.144 1027 Planarity : 0.004 0.061 1203 Dihedral : 5.364 41.561 917 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.03 % Allowed : 19.66 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.30), residues: 817 helix: -0.55 (0.27), residues: 378 sheet: -1.36 (0.57), residues: 86 loop : -0.73 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 383 HIS 0.006 0.001 HIS A 665 PHE 0.014 0.001 PHE A 430 TYR 0.021 0.002 TYR A1038 ARG 0.002 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.4454 (ttt180) cc_final: 0.3523 (tpp-160) REVERT: A 141 ARG cc_start: 0.5531 (OUTLIER) cc_final: 0.5008 (tmm160) REVERT: A 182 TYR cc_start: 0.6956 (t80) cc_final: 0.6732 (t80) REVERT: A 532 LYS cc_start: 0.7794 (mmmm) cc_final: 0.7497 (mmmt) REVERT: A 546 GLN cc_start: 0.5533 (OUTLIER) cc_final: 0.4711 (tm-30) outliers start: 23 outliers final: 12 residues processed: 98 average time/residue: 1.0795 time to fit residues: 112.3904 Evaluate side-chains 95 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 922 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 75 optimal weight: 0.0570 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 68 optimal weight: 6.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.268344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.237765 restraints weight = 7002.369| |-----------------------------------------------------------------------------| r_work (start): 0.4847 rms_B_bonded: 2.02 r_work: 0.4762 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4654 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4659 r_free = 0.4659 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4659 r_free = 0.4659 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5489 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6966 Z= 0.199 Angle : 0.587 8.083 9421 Z= 0.291 Chirality : 0.042 0.145 1027 Planarity : 0.004 0.061 1203 Dihedral : 5.234 40.305 917 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.03 % Allowed : 20.45 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.06 (0.30), residues: 817 helix: -0.40 (0.27), residues: 375 sheet: -1.33 (0.57), residues: 86 loop : -0.70 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 383 HIS 0.004 0.001 HIS A 665 PHE 0.013 0.001 PHE A 430 TYR 0.022 0.002 TYR A1038 ARG 0.002 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.4407 (ttt180) cc_final: 0.3473 (tpp-160) REVERT: A 141 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.5023 (tmm160) REVERT: A 182 TYR cc_start: 0.6944 (t80) cc_final: 0.6701 (t80) REVERT: A 532 LYS cc_start: 0.7682 (mmmm) cc_final: 0.7373 (mmmt) REVERT: A 610 MET cc_start: 0.5331 (tpp) cc_final: 0.5103 (tpp) REVERT: A 700 LYS cc_start: 0.4636 (mttp) cc_final: 0.4359 (tptt) outliers start: 23 outliers final: 14 residues processed: 99 average time/residue: 1.1197 time to fit residues: 117.5055 Evaluate side-chains 95 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 665 HIS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 922 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.0030 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.0030 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.269731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.238985 restraints weight = 6943.452| |-----------------------------------------------------------------------------| r_work (start): 0.4858 rms_B_bonded: 2.04 r_work: 0.4775 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4669 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4673 r_free = 0.4673 target_work(ls_wunit_k1) = 0.218 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4673 r_free = 0.4673 target_work(ls_wunit_k1) = 0.218 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6966 Z= 0.185 Angle : 0.606 15.699 9421 Z= 0.294 Chirality : 0.041 0.145 1027 Planarity : 0.004 0.060 1203 Dihedral : 5.072 38.967 917 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.64 % Allowed : 20.98 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.30), residues: 817 helix: -0.26 (0.27), residues: 375 sheet: -1.25 (0.57), residues: 86 loop : -0.61 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 383 HIS 0.005 0.001 HIS A 665 PHE 0.012 0.001 PHE A 430 TYR 0.024 0.002 TYR A1038 ARG 0.002 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.4483 (ttt180) cc_final: 0.3528 (tpp-160) REVERT: A 141 ARG cc_start: 0.5435 (OUTLIER) cc_final: 0.4985 (tmm160) REVERT: A 182 TYR cc_start: 0.6974 (t80) cc_final: 0.6737 (t80) REVERT: A 264 LYS cc_start: 0.7097 (tppp) cc_final: 0.6411 (tptp) REVERT: A 532 LYS cc_start: 0.7688 (mmmm) cc_final: 0.7389 (mmmt) REVERT: A 610 MET cc_start: 0.5311 (tpp) cc_final: 0.5105 (tpp) REVERT: A 700 LYS cc_start: 0.4639 (mttp) cc_final: 0.4387 (tptt) REVERT: A 717 ASP cc_start: 0.6906 (t0) cc_final: 0.6596 (t0) outliers start: 20 outliers final: 12 residues processed: 98 average time/residue: 1.2495 time to fit residues: 129.0765 Evaluate side-chains 94 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 665 HIS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.268408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.237007 restraints weight = 7048.242| |-----------------------------------------------------------------------------| r_work (start): 0.4837 rms_B_bonded: 2.07 r_work: 0.4753 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4646 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4654 r_free = 0.4654 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4654 r_free = 0.4654 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5507 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6966 Z= 0.208 Angle : 0.628 15.706 9421 Z= 0.305 Chirality : 0.042 0.148 1027 Planarity : 0.004 0.060 1203 Dihedral : 5.187 39.304 917 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.51 % Allowed : 21.50 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.96 (0.30), residues: 817 helix: -0.34 (0.27), residues: 378 sheet: -1.22 (0.57), residues: 86 loop : -0.63 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 383 HIS 0.004 0.001 HIS A 665 PHE 0.014 0.001 PHE A 937 TYR 0.027 0.002 TYR A1038 ARG 0.003 0.000 ARG A 704 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.4398 (ttt180) cc_final: 0.3430 (tpp-160) REVERT: A 141 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.5063 (tmm160) REVERT: A 532 LYS cc_start: 0.7724 (mmmm) cc_final: 0.7419 (mmmt) REVERT: A 610 MET cc_start: 0.5224 (tpp) cc_final: 0.5000 (tpp) REVERT: A 700 LYS cc_start: 0.4583 (mttp) cc_final: 0.4363 (tptt) REVERT: A 717 ASP cc_start: 0.7020 (t0) cc_final: 0.6816 (t0) REVERT: A 732 MET cc_start: 0.6299 (mmt) cc_final: 0.5750 (mtt) outliers start: 19 outliers final: 13 residues processed: 92 average time/residue: 1.1705 time to fit residues: 113.8549 Evaluate side-chains 93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 665 HIS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 906 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 0.0060 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5076 r_free = 0.5076 target = 0.268091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.237407 restraints weight = 7038.892| |-----------------------------------------------------------------------------| r_work (start): 0.4848 rms_B_bonded: 2.05 r_work: 0.4765 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4658 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4674 r_free = 0.4674 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4674 r_free = 0.4674 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6966 Z= 0.206 Angle : 0.621 15.269 9421 Z= 0.303 Chirality : 0.042 0.145 1027 Planarity : 0.004 0.060 1203 Dihedral : 5.155 39.229 917 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.24 % Allowed : 21.90 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.96 (0.30), residues: 817 helix: -0.33 (0.27), residues: 378 sheet: -1.21 (0.57), residues: 86 loop : -0.64 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 383 HIS 0.003 0.001 HIS A 665 PHE 0.013 0.001 PHE A 937 TYR 0.027 0.002 TYR A1038 ARG 0.003 0.000 ARG A 704 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5940.06 seconds wall clock time: 101 minutes 38.42 seconds (6098.42 seconds total)