Starting phenix.real_space_refine on Sat Dec 28 01:00:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjq_31627/12_2024/7fjq_31627.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjq_31627/12_2024/7fjq_31627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fjq_31627/12_2024/7fjq_31627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjq_31627/12_2024/7fjq_31627.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjq_31627/12_2024/7fjq_31627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjq_31627/12_2024/7fjq_31627.cif" } resolution = 3.6 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= 0.002 sd= 0.080 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4570 2.51 5 N 1203 2.21 5 O 1269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7072 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 67, 'TRANS': 905} Chain breaks: 9 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 534 Unresolved non-hydrogen dihedrals: 372 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 260 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'SPM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.64, per 1000 atoms: 0.65 Number of scatterers: 7086 At special positions: 0 Unit cell: (77.9509, 96.6152, 138.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1269 8.00 N 1203 7.00 C 4570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 317 " distance=2.03 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: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 42.4% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.623A pdb=" N MET A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 257 through 287 removed outlier: 4.197A pdb=" N SER A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.736A pdb=" N VAL A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.850A pdb=" N VAL A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.534A pdb=" N GLN A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 3.782A pdb=" N ASN A 502 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 505 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 removed outlier: 3.610A pdb=" N ALA A 554 " --> pdb=" O PRO A 550 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 4.178A pdb=" N LYS A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 577' Processing helix chain 'A' and resid 577 through 582 removed outlier: 4.523A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 662 removed outlier: 3.535A pdb=" N GLY A 662 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 709 through 713 removed outlier: 3.935A pdb=" N VAL A 712 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.838A pdb=" N ILE A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 737 " --> pdb=" O THR A 733 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 738 " --> pdb=" O PRO A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 765 removed outlier: 3.705A pdb=" N THR A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 834 Processing helix chain 'A' and resid 840 through 844 Processing helix chain 'A' and resid 858 through 866 removed outlier: 3.719A pdb=" N LEU A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS A 864 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 889 removed outlier: 4.390A pdb=" N LYS A 887 " --> pdb=" O CYS A 883 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 888 " --> pdb=" O GLY A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.607A pdb=" N ILE A 920 " --> pdb=" O VAL A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 950 removed outlier: 3.522A pdb=" N TYR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 979 removed outlier: 3.923A pdb=" N VAL A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1025 Processing helix chain 'A' and resid 1044 through 1065 removed outlier: 3.943A pdb=" N THR A1048 " --> pdb=" O ASN A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1077 Processing helix chain 'A' and resid 1078 through 1098 Processing helix chain 'A' and resid 1104 through 1108 removed outlier: 3.969A pdb=" N ALA A1107 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A1108 " --> pdb=" O PRO A1105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1104 through 1108' Processing helix chain 'A' and resid 1116 through 1140 Processing helix chain 'A' and resid 1157 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.643A pdb=" N LEU A 392 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 493 through 495 Processing sheet with id=AA3, first strand: chain 'A' and resid 792 through 794 removed outlier: 4.689A pdb=" N LEU A 773 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 823 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 850 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA A 746 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N PHE A 851 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET A 748 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N MET A 875 " --> pdb=" O ILE A 893 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 530 removed outlier: 5.417A pdb=" N VAL A 525 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG A 725 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A 527 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU A 718 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER A 692 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 641 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG A 636 " --> pdb=" O PRO A 629 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER A 638 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG A 627 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA A 642 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER A 623 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 562 through 564 removed outlier: 3.730A pdb=" N LEU A 564 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 783 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: 2.31 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1025 1.25 - 1.39: 1712 1.39 - 1.53: 3693 1.53 - 1.67: 728 1.67 - 1.81: 65 Bond restraints: 7223 Sorted by residual: bond pdb=" CA TYR A 256 " pdb=" C TYR A 256 " ideal model delta sigma weight residual 1.523 1.308 0.215 1.34e-02 5.57e+03 2.57e+02 bond pdb=" CA HIS A 255 " pdb=" C HIS A 255 " ideal model delta sigma weight residual 1.523 1.347 0.176 1.34e-02 5.57e+03 1.73e+02 bond pdb=" CA ALA A 965 " pdb=" C ALA A 965 " ideal model delta sigma weight residual 1.524 1.363 0.161 1.27e-02 6.20e+03 1.60e+02 bond pdb=" C LEU A 964 " pdb=" O LEU A 964 " ideal model delta sigma weight residual 1.237 1.106 0.131 1.17e-02 7.31e+03 1.25e+02 bond pdb=" CA SER A 941 " pdb=" C SER A 941 " ideal model delta sigma weight residual 1.524 1.386 0.138 1.27e-02 6.20e+03 1.17e+02 ... (remaining 7218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 9458 4.92 - 9.84: 372 9.84 - 14.77: 31 14.77 - 19.69: 6 19.69 - 24.61: 3 Bond angle restraints: 9870 Sorted by residual: angle pdb=" N PRO A1172 " pdb=" CA PRO A1172 " pdb=" C PRO A1172 " ideal model delta sigma weight residual 110.70 86.09 24.61 1.22e+00 6.72e-01 4.07e+02 angle pdb=" N LYS A1117 " pdb=" CA LYS A1117 " pdb=" C LYS A1117 " ideal model delta sigma weight residual 111.71 98.66 13.05 1.15e+00 7.56e-01 1.29e+02 angle pdb=" N ILE A 441 " pdb=" CA ILE A 441 " pdb=" C ILE A 441 " ideal model delta sigma weight residual 111.56 101.88 9.68 8.60e-01 1.35e+00 1.27e+02 angle pdb=" N TRP A 258 " pdb=" CA TRP A 258 " pdb=" C TRP A 258 " ideal model delta sigma weight residual 111.11 123.97 -12.86 1.20e+00 6.94e-01 1.15e+02 angle pdb=" N LEU A1042 " pdb=" CA LEU A1042 " pdb=" C LEU A1042 " ideal model delta sigma weight residual 109.81 133.44 -23.63 2.21e+00 2.05e-01 1.14e+02 ... (remaining 9865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 3961 16.85 - 33.69: 266 33.69 - 50.53: 93 50.53 - 67.37: 17 67.37 - 84.22: 4 Dihedral angle restraints: 4341 sinusoidal: 1536 harmonic: 2805 Sorted by residual: dihedral pdb=" C LEU A1042 " pdb=" N LEU A1042 " pdb=" CA LEU A1042 " pdb=" CB LEU A1042 " ideal model delta harmonic sigma weight residual -122.60 -152.07 29.47 0 2.50e+00 1.60e-01 1.39e+02 dihedral pdb=" N LEU A1042 " pdb=" C LEU A1042 " pdb=" CA LEU A1042 " pdb=" CB LEU A1042 " ideal model delta harmonic sigma weight residual 122.80 151.73 -28.93 0 2.50e+00 1.60e-01 1.34e+02 dihedral pdb=" N GLN A 944 " pdb=" C GLN A 944 " pdb=" CA GLN A 944 " pdb=" CB GLN A 944 " ideal model delta harmonic sigma weight residual 122.80 147.79 -24.99 0 2.50e+00 1.60e-01 1.00e+02 ... (remaining 4338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.265: 1108 0.265 - 0.530: 82 0.530 - 0.795: 26 0.795 - 1.060: 4 1.060 - 1.325: 2 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CA LEU A1042 " pdb=" N LEU A1042 " pdb=" C LEU A1042 " pdb=" CB LEU A1042 " both_signs ideal model delta sigma weight residual False 2.51 1.19 1.33 2.00e-01 2.50e+01 4.39e+01 chirality pdb=" CA GLN A 944 " pdb=" N GLN A 944 " pdb=" C GLN A 944 " pdb=" CB GLN A 944 " both_signs ideal model delta sigma weight residual False 2.51 1.44 1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA LYS A 935 " pdb=" N LYS A 935 " pdb=" C LYS A 935 " pdb=" CB LYS A 935 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 1219 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 966 " -0.040 2.00e-02 2.50e+03 7.67e-02 5.88e+01 pdb=" C ILE A 966 " 0.133 2.00e-02 2.50e+03 pdb=" O ILE A 966 " -0.047 2.00e-02 2.50e+03 pdb=" N ASP A 967 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 967 " -0.039 2.00e-02 2.50e+03 7.29e-02 5.31e+01 pdb=" C ASP A 967 " 0.126 2.00e-02 2.50e+03 pdb=" O ASP A 967 " -0.045 2.00e-02 2.50e+03 pdb=" N LEU A 968 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 969 " 0.032 2.00e-02 2.50e+03 6.23e-02 3.89e+01 pdb=" C VAL A 969 " -0.108 2.00e-02 2.50e+03 pdb=" O VAL A 969 " 0.039 2.00e-02 2.50e+03 pdb=" N ILE A 970 " 0.036 2.00e-02 2.50e+03 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 147 2.56 - 3.15: 5519 3.15 - 3.73: 10784 3.73 - 4.32: 14168 4.32 - 4.90: 22826 Nonbonded interactions: 53444 Sorted by model distance: nonbonded pdb=" CB HIS A 255 " pdb=" N TYR A 256 " model vdw 1.980 2.816 nonbonded pdb=" CB TYR A 256 " pdb=" N TYR A 257 " model vdw 2.063 2.816 nonbonded pdb=" N SER A1055 " pdb=" OG SER A1055 " model vdw 2.181 2.496 nonbonded pdb=" O TYR A 256 " pdb=" N TRP A 258 " model vdw 2.204 3.120 nonbonded pdb=" O TYR A 256 " pdb=" C TYR A 257 " model vdw 2.294 3.270 ... (remaining 53439 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.210 Find NCS groups from input model: 0.070 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.019 0.215 7223 Z= 1.242 Angle : 2.025 24.610 9870 Z= 1.333 Chirality : 0.171 1.325 1222 Planarity : 0.014 0.144 1250 Dihedral : 13.671 84.216 2522 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 1.68 % Allowed : 10.18 % Favored : 88.14 % Rotamer: Outliers : 6.77 % Allowed : 9.94 % Favored : 83.29 % Cbeta Deviations : 4.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.67 (0.24), residues: 953 helix: -1.36 (0.25), residues: 398 sheet: -2.71 (0.50), residues: 71 loop : -3.45 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1171 HIS 0.009 0.001 HIS A 255 PHE 0.066 0.004 PHE A 945 TYR 0.035 0.003 TYR A 940 ARG 0.003 0.001 ARG A1158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ILE cc_start: 0.8701 (pp) cc_final: 0.8493 (mm) REVERT: A 854 MET cc_start: 0.8812 (mmm) cc_final: 0.8491 (mmm) REVERT: A 918 MET cc_start: 0.8317 (ptp) cc_final: 0.7981 (ptp) REVERT: A 937 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (mmt) REVERT: A 941 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.9060 (t) REVERT: A 942 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 1008 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7960 (tt0) outliers start: 49 outliers final: 25 residues processed: 156 average time/residue: 0.1847 time to fit residues: 39.6543 Evaluate side-chains 95 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1080 PRO Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.0170 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 497 HIS A 870 GLN A1047 ASN ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7223 Z= 0.234 Angle : 0.818 11.373 9870 Z= 0.411 Chirality : 0.049 0.311 1222 Planarity : 0.008 0.136 1250 Dihedral : 9.159 56.297 1091 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.65 % Favored : 89.82 % Rotamer: Outliers : 4.97 % Allowed : 14.78 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -3.29 (0.25), residues: 953 helix: -1.27 (0.26), residues: 385 sheet: -2.13 (0.50), residues: 74 loop : -3.03 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1171 HIS 0.005 0.001 HIS A 255 PHE 0.017 0.002 PHE A 963 TYR 0.025 0.002 TYR A 936 ARG 0.007 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 918 MET cc_start: 0.8217 (ptp) cc_final: 0.8016 (ptp) REVERT: A 920 ILE cc_start: 0.8917 (pp) cc_final: 0.8663 (pt) REVERT: A 937 MET cc_start: 0.8290 (tpp) cc_final: 0.7836 (mmm) REVERT: A 1047 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7719 (t0) REVERT: A 1133 MET cc_start: 0.7076 (mmm) cc_final: 0.6852 (mmp) outliers start: 36 outliers final: 15 residues processed: 103 average time/residue: 0.1798 time to fit residues: 25.8947 Evaluate side-chains 81 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1067 LYS Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 73 optimal weight: 0.0040 chunk 59 optimal weight: 0.0980 chunk 24 optimal weight: 30.0000 chunk 88 optimal weight: 0.9980 chunk 95 optimal weight: 0.0170 chunk 78 optimal weight: 0.0870 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7223 Z= 0.177 Angle : 0.729 10.661 9870 Z= 0.360 Chirality : 0.046 0.280 1222 Planarity : 0.006 0.072 1250 Dihedral : 7.643 59.377 1057 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.34 % Favored : 90.14 % Rotamer: Outliers : 4.01 % Allowed : 16.71 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.91 (0.26), residues: 953 helix: -0.90 (0.26), residues: 395 sheet: -1.40 (0.57), residues: 66 loop : -2.99 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1028 HIS 0.002 0.000 HIS A 198 PHE 0.017 0.001 PHE A 963 TYR 0.015 0.001 TYR A 936 ARG 0.005 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.852 Fit side-chains REVERT: A 794 MET cc_start: 0.6596 (mtt) cc_final: 0.6185 (mtt) REVERT: A 920 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8596 (pt) REVERT: A 937 MET cc_start: 0.8281 (tpp) cc_final: 0.7915 (mmm) REVERT: A 1140 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6356 (mp10) outliers start: 29 outliers final: 10 residues processed: 100 average time/residue: 0.1520 time to fit residues: 22.7239 Evaluate side-chains 76 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1140 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.0010 chunk 93 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7223 Z= 0.200 Angle : 0.728 10.791 9870 Z= 0.353 Chirality : 0.045 0.318 1222 Planarity : 0.007 0.106 1250 Dihedral : 6.520 58.465 1043 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.44 % Favored : 90.24 % Rotamer: Outliers : 4.14 % Allowed : 17.82 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.48 (0.26), residues: 953 helix: -0.45 (0.27), residues: 394 sheet: -1.07 (0.60), residues: 66 loop : -2.85 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1171 HIS 0.002 0.000 HIS A 198 PHE 0.016 0.001 PHE A 963 TYR 0.014 0.001 TYR A 166 ARG 0.004 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.846 Fit side-chains REVERT: A 920 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8663 (pt) REVERT: A 970 ILE cc_start: 0.8856 (mt) cc_final: 0.8579 (mt) REVERT: A 1009 MET cc_start: 0.8412 (mmm) cc_final: 0.8167 (tpp) outliers start: 30 outliers final: 14 residues processed: 91 average time/residue: 0.1522 time to fit residues: 21.0763 Evaluate side-chains 80 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 chunk 47 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS A 962 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7223 Z= 0.410 Angle : 0.830 12.606 9870 Z= 0.408 Chirality : 0.049 0.248 1222 Planarity : 0.007 0.102 1250 Dihedral : 6.636 56.857 1041 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.97 % Favored : 89.61 % Rotamer: Outliers : 4.28 % Allowed : 18.09 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.37 (0.27), residues: 953 helix: -0.46 (0.26), residues: 393 sheet: -1.00 (0.60), residues: 67 loop : -2.70 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1171 HIS 0.004 0.001 HIS A 255 PHE 0.024 0.002 PHE A 168 TYR 0.019 0.002 TYR A1076 ARG 0.004 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 724 MET cc_start: 0.7076 (mmp) cc_final: 0.6522 (mmm) outliers start: 31 outliers final: 16 residues processed: 95 average time/residue: 0.1662 time to fit residues: 22.9426 Evaluate side-chains 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1012 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 0.0870 chunk 7 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7223 Z= 0.185 Angle : 0.726 11.831 9870 Z= 0.349 Chirality : 0.045 0.335 1222 Planarity : 0.006 0.089 1250 Dihedral : 6.257 49.704 1041 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.13 % Favored : 90.45 % Rotamer: Outliers : 2.90 % Allowed : 20.99 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.03 (0.27), residues: 953 helix: -0.06 (0.27), residues: 394 sheet: -0.72 (0.63), residues: 66 loop : -2.63 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1171 HIS 0.003 0.000 HIS A 413 PHE 0.010 0.001 PHE A 963 TYR 0.015 0.001 TYR A 936 ARG 0.004 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 724 MET cc_start: 0.6899 (mmp) cc_final: 0.6553 (mmm) REVERT: A 1009 MET cc_start: 0.8596 (mmm) cc_final: 0.8378 (mmm) REVERT: A 1140 GLN cc_start: 0.6732 (OUTLIER) cc_final: 0.6127 (mp10) outliers start: 21 outliers final: 17 residues processed: 87 average time/residue: 0.1439 time to fit residues: 18.8638 Evaluate side-chains 83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1140 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 52 optimal weight: 0.0170 chunk 93 optimal weight: 0.9980 chunk 58 optimal weight: 0.0370 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 0.0020 chunk 37 optimal weight: 0.9990 overall best weight: 0.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7223 Z= 0.168 Angle : 0.702 12.067 9870 Z= 0.337 Chirality : 0.045 0.355 1222 Planarity : 0.006 0.085 1250 Dihedral : 5.853 49.978 1041 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.02 % Favored : 90.66 % Rotamer: Outliers : 2.49 % Allowed : 21.55 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.77 (0.28), residues: 953 helix: 0.28 (0.28), residues: 394 sheet: -0.58 (0.65), residues: 66 loop : -2.61 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1028 HIS 0.002 0.000 HIS A 413 PHE 0.015 0.001 PHE A 168 TYR 0.012 0.001 TYR A 936 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 724 MET cc_start: 0.6788 (mmp) cc_final: 0.6485 (mmt) REVERT: A 970 ILE cc_start: 0.8630 (mt) cc_final: 0.8346 (mt) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 0.1387 time to fit residues: 19.8781 Evaluate side-chains 84 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 81 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7223 Z= 0.192 Angle : 0.708 11.092 9870 Z= 0.341 Chirality : 0.045 0.292 1222 Planarity : 0.006 0.083 1250 Dihedral : 5.740 46.366 1041 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.60 % Favored : 91.08 % Rotamer: Outliers : 1.93 % Allowed : 22.24 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.61 (0.28), residues: 953 helix: 0.44 (0.28), residues: 393 sheet: -0.50 (0.67), residues: 65 loop : -2.53 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 643 HIS 0.003 0.000 HIS A 413 PHE 0.012 0.001 PHE A 963 TYR 0.015 0.001 TYR A 166 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.887 Fit side-chains REVERT: A 273 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8115 (mm) REVERT: A 724 MET cc_start: 0.6800 (mmp) cc_final: 0.6518 (mmt) outliers start: 14 outliers final: 13 residues processed: 81 average time/residue: 0.1501 time to fit residues: 18.3068 Evaluate side-chains 82 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7223 Z= 0.198 Angle : 0.725 11.634 9870 Z= 0.345 Chirality : 0.045 0.310 1222 Planarity : 0.006 0.083 1250 Dihedral : 5.719 46.865 1041 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.50 % Favored : 91.19 % Rotamer: Outliers : 2.21 % Allowed : 22.79 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.50 (0.28), residues: 953 helix: 0.51 (0.28), residues: 394 sheet: -0.63 (0.66), residues: 66 loop : -2.43 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1171 HIS 0.004 0.000 HIS A 413 PHE 0.015 0.001 PHE A 168 TYR 0.017 0.001 TYR A 166 ARG 0.003 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.820 Fit side-chains REVERT: A 273 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8115 (mm) REVERT: A 724 MET cc_start: 0.6770 (mmp) cc_final: 0.6562 (mmt) REVERT: A 970 ILE cc_start: 0.8557 (mt) cc_final: 0.8345 (mt) outliers start: 16 outliers final: 13 residues processed: 80 average time/residue: 0.1650 time to fit residues: 19.6483 Evaluate side-chains 81 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.0060 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 0.0370 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7223 Z= 0.182 Angle : 0.718 14.324 9870 Z= 0.340 Chirality : 0.045 0.289 1222 Planarity : 0.005 0.084 1250 Dihedral : 5.591 47.658 1039 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.18 % Favored : 91.50 % Rotamer: Outliers : 1.80 % Allowed : 23.34 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.38 (0.28), residues: 953 helix: 0.60 (0.28), residues: 397 sheet: -0.46 (0.65), residues: 65 loop : -2.38 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1171 HIS 0.003 0.000 HIS A 413 PHE 0.013 0.001 PHE A 168 TYR 0.013 0.001 TYR A 166 ARG 0.004 0.000 ARG A 636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.891 Fit side-chains REVERT: A 273 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8105 (mm) REVERT: A 724 MET cc_start: 0.6625 (mmp) cc_final: 0.6394 (mmm) outliers start: 13 outliers final: 12 residues processed: 83 average time/residue: 0.1484 time to fit residues: 18.5268 Evaluate side-chains 85 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.0570 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.0270 chunk 14 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 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 = 0.4273 r_free = 0.4273 target = 0.177835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111956 restraints weight = 10581.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113468 restraints weight = 7028.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114446 restraints weight = 5170.139| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7223 Z= 0.182 Angle : 0.715 12.807 9870 Z= 0.340 Chirality : 0.045 0.299 1222 Planarity : 0.006 0.082 1250 Dihedral : 5.516 46.583 1039 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.39 % Favored : 91.29 % Rotamer: Outliers : 2.21 % Allowed : 23.07 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.28 (0.28), residues: 953 helix: 0.64 (0.28), residues: 398 sheet: -0.52 (0.65), residues: 66 loop : -2.28 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 643 HIS 0.002 0.000 HIS A 413 PHE 0.025 0.001 PHE A 168 TYR 0.022 0.001 TYR A 166 ARG 0.003 0.000 ARG A 636 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1593.53 seconds wall clock time: 30 minutes 39.62 seconds (1839.62 seconds total)