Starting phenix.real_space_refine on Fri Dec 8 05:09:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/12_2023/8sgt_40467.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/12_2023/8sgt_40467.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/12_2023/8sgt_40467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/12_2023/8sgt_40467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/12_2023/8sgt_40467.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/12_2023/8sgt_40467.pdb" } 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= 0.003 sd= 0.033 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 Ca 6 9.91 5 S 30 5.16 5 C 4600 2.51 5 N 1145 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7119 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5356 Classifications: {'peptide': 687} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 663} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 4.05, per 1000 atoms: 0.57 Number of scatterers: 7119 At special positions: 0 Unit cell: (120.35, 96.28, 145.25, 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) Ca 6 19.99 S 30 16.00 O 1338 8.00 N 1145 7.00 C 4600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 39.1% alpha, 25.3% 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 36 through 72 removed outlier: 3.565A pdb=" N ILE A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.638A pdb=" N LEU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 124 Processing helix chain 'A' and resid 130 through 145 Processing helix chain 'A' and resid 145 through 155 removed outlier: 4.033A pdb=" N VAL A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 189 removed outlier: 3.787A pdb=" N TYR A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.979A pdb=" N ILE A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 607 removed outlier: 3.567A pdb=" N LEU A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 665 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.595A pdb=" N PHE A 713 " --> pdb=" O TRP A 709 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 754 removed outlier: 5.178A pdb=" N PHE A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TRP A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 761 through 764 removed outlier: 3.697A pdb=" N ASN A 764 " --> pdb=" O GLU A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 764' Processing helix chain 'A' and resid 765 through 795 removed outlier: 3.617A pdb=" N VAL A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 828 through 845 removed outlier: 3.710A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 843 " --> pdb=" O ASN A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 861 removed outlier: 3.703A pdb=" N ALA A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 893 removed outlier: 4.585A pdb=" N LEU A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 932 removed outlier: 3.577A pdb=" N LEU A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 4.175A pdb=" N PHE A 865 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443 removed outlier: 3.528A pdb=" N CYS A 485 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 384 removed outlier: 6.871A pdb=" N CYS A 383 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 492 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 458 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 454 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL A 458 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A 412 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU A 460 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ARG A 410 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASN A 462 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 408 " --> pdb=" O ASN A 462 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 568 through 573 removed outlier: 3.555A pdb=" N VAL A 573 " --> pdb=" O MET A 521 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.200A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.200A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.873A pdb=" N GLN A 623 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS A 618 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 625 " --> pdb=" O THR A 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.560A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.507A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1044 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: 2.46 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1159 1.31 - 1.44: 2049 1.44 - 1.56: 4028 1.56 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 7279 Sorted by residual: bond pdb=" C ALA A 931 " pdb=" O ALA A 931 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.26e-02 6.30e+03 1.39e+01 bond pdb=" CA ALA A 931 " pdb=" C ALA A 931 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.35e-02 5.49e+03 8.40e+00 bond pdb=" CA CYS A 933 " pdb=" C CYS A 933 " ideal model delta sigma weight residual 1.527 1.490 0.037 1.30e-02 5.92e+03 7.96e+00 bond pdb=" CA TYR A 932 " pdb=" CB TYR A 932 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.46e-02 4.69e+03 5.51e+00 bond pdb=" C TYR A 932 " pdb=" O TYR A 932 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.28e-02 6.10e+03 4.41e+00 ... (remaining 7274 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.69: 169 106.69 - 113.59: 3985 113.59 - 120.49: 2836 120.49 - 127.40: 2821 127.40 - 134.30: 80 Bond angle restraints: 9891 Sorted by residual: angle pdb=" CA ARG A 632 " pdb=" CB ARG A 632 " pdb=" CG ARG A 632 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 angle pdb=" C THR A 654 " pdb=" N SER A 655 " pdb=" CA SER A 655 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLY L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C ARG A 632 " pdb=" CA ARG A 632 " pdb=" CB ARG A 632 " ideal model delta sigma weight residual 110.35 116.41 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" N ALA A 931 " pdb=" CA ALA A 931 " pdb=" C ALA A 931 " ideal model delta sigma weight residual 111.82 108.26 3.56 1.16e+00 7.43e-01 9.42e+00 ... (remaining 9886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3861 17.93 - 35.86: 287 35.86 - 53.79: 40 53.79 - 71.72: 8 71.72 - 89.65: 11 Dihedral angle restraints: 4207 sinusoidal: 1589 harmonic: 2618 Sorted by residual: dihedral pdb=" CA THR A 528 " pdb=" C THR A 528 " pdb=" N SER A 529 " pdb=" CA SER A 529 " ideal model delta harmonic sigma weight residual 180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.11 34.89 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N THR A 528 " pdb=" CA THR A 528 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 4204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 931 0.061 - 0.121: 178 0.121 - 0.182: 24 0.182 - 0.242: 1 0.242 - 0.303: 3 Chirality restraints: 1137 Sorted by residual: chirality pdb=" CA CYS A 933 " pdb=" N CYS A 933 " pdb=" C CYS A 933 " pdb=" CB CYS A 933 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE A 935 " pdb=" N ILE A 935 " pdb=" C ILE A 935 " pdb=" CB ILE A 935 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE A 615 " pdb=" CA ILE A 615 " pdb=" CG1 ILE A 615 " pdb=" CG2 ILE A 615 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1134 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 593 " 0.053 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO A 594 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO A 133 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 422 " -0.018 2.00e-02 2.50e+03 1.76e-02 6.21e+00 pdb=" CG TYR A 422 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 422 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 422 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 422 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 422 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 422 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 422 " -0.001 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 104 2.65 - 3.21: 6365 3.21 - 3.78: 10632 3.78 - 4.34: 15000 4.34 - 4.90: 25014 Nonbonded interactions: 57115 Sorted by model distance: nonbonded pdb=" OD2 ASP A 421 " pdb="CA CA A1001 " model vdw 2.090 2.510 nonbonded pdb=" OE1 GLU A 385 " pdb="CA CA A1003 " model vdw 2.219 2.510 nonbonded pdb=" OE2 GLU A 385 " pdb="CA CA A1004 " model vdw 2.236 2.510 nonbonded pdb=" OD1 ASP A 413 " pdb=" OH TYR A 422 " model vdw 2.243 2.440 nonbonded pdb=" O THR A 135 " pdb=" OG SER A 139 " model vdw 2.258 2.440 ... (remaining 57110 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: 3.730 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: 9.910 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.500 Find NCS groups from input model: 0.190 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 7279 Z= 0.323 Angle : 0.750 8.186 9891 Z= 0.402 Chirality : 0.050 0.303 1137 Planarity : 0.007 0.079 1240 Dihedral : 13.355 89.651 2520 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.14 (0.25), residues: 900 helix: -0.86 (0.24), residues: 314 sheet: -0.32 (0.33), residues: 250 loop : -0.72 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 215 HIS 0.012 0.002 HIS A 674 PHE 0.030 0.002 PHE A 505 TYR 0.044 0.002 TYR A 422 ARG 0.013 0.001 ARG L 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2208 time to fit residues: 39.5709 Evaluate side-chains 58 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7279 Z= 0.221 Angle : 0.617 7.492 9891 Z= 0.329 Chirality : 0.044 0.157 1137 Planarity : 0.005 0.049 1240 Dihedral : 4.776 20.782 972 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.83 % Allowed : 7.96 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.16 (0.27), residues: 900 helix: 1.04 (0.27), residues: 328 sheet: -0.15 (0.33), residues: 250 loop : -0.49 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 182 HIS 0.005 0.001 HIS A 674 PHE 0.024 0.002 PHE A 782 TYR 0.013 0.001 TYR H 60 ARG 0.003 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.2017 time to fit residues: 22.7531 Evaluate side-chains 64 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0684 time to fit residues: 2.2546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 81 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN L 80 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7279 Z= 0.407 Angle : 0.656 7.370 9891 Z= 0.352 Chirality : 0.046 0.269 1137 Planarity : 0.005 0.073 1240 Dihedral : 4.994 21.391 972 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.83 % Allowed : 11.23 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.21 (0.27), residues: 900 helix: 1.42 (0.27), residues: 324 sheet: -0.50 (0.32), residues: 248 loop : -0.51 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 750 HIS 0.006 0.001 HIS A 674 PHE 0.037 0.003 PHE A 562 TYR 0.025 0.002 TYR H 60 ARG 0.009 0.001 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 56 average time/residue: 0.1887 time to fit residues: 15.0533 Evaluate side-chains 49 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0687 time to fit residues: 2.0878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 50.0000 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7279 Z= 0.248 Angle : 0.552 9.103 9891 Z= 0.294 Chirality : 0.043 0.183 1137 Planarity : 0.004 0.041 1240 Dihedral : 4.668 21.144 972 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.96 % Allowed : 12.66 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.48 (0.28), residues: 900 helix: 1.67 (0.28), residues: 324 sheet: -0.35 (0.32), residues: 250 loop : -0.38 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 182 HIS 0.005 0.001 HIS A 674 PHE 0.023 0.002 PHE A 754 TYR 0.012 0.001 TYR H 60 ARG 0.003 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 62 average time/residue: 0.1804 time to fit residues: 16.0285 Evaluate side-chains 51 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1024 time to fit residues: 2.4978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 20.0000 chunk 1 optimal weight: 0.0980 chunk 65 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 60 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 7279 Z= 0.536 Angle : 0.691 9.079 9891 Z= 0.370 Chirality : 0.046 0.189 1137 Planarity : 0.005 0.080 1240 Dihedral : 5.200 22.222 972 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.00 % Favored : 94.89 % Rotamer: Outliers : 1.96 % Allowed : 15.54 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.20 (0.28), residues: 900 helix: 1.65 (0.28), residues: 324 sheet: -0.63 (0.32), residues: 244 loop : -0.69 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 36 HIS 0.005 0.001 HIS A 674 PHE 0.037 0.003 PHE A 562 TYR 0.020 0.002 TYR H 60 ARG 0.005 0.001 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.809 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 48 average time/residue: 0.1460 time to fit residues: 11.0522 Evaluate side-chains 48 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0713 time to fit residues: 2.5064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 40.0000 chunk 51 optimal weight: 0.0050 chunk 21 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.0570 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.9314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7279 Z= 0.186 Angle : 0.539 7.006 9891 Z= 0.288 Chirality : 0.042 0.165 1137 Planarity : 0.004 0.042 1240 Dihedral : 4.685 20.548 972 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.52 % Allowed : 16.84 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.28), residues: 900 helix: 1.92 (0.28), residues: 317 sheet: -0.57 (0.32), residues: 239 loop : -0.49 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 182 HIS 0.003 0.001 HIS A 459 PHE 0.019 0.001 PHE A 769 TYR 0.012 0.001 TYR A 46 ARG 0.003 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.1990 time to fit residues: 13.3757 Evaluate side-chains 43 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0661 time to fit residues: 1.3364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 7279 Z= 0.486 Angle : 0.643 8.212 9891 Z= 0.347 Chirality : 0.045 0.208 1137 Planarity : 0.005 0.071 1240 Dihedral : 5.118 22.286 972 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.61 % Allowed : 16.71 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.17 (0.28), residues: 900 helix: 1.78 (0.28), residues: 321 sheet: -0.85 (0.32), residues: 240 loop : -0.68 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 111 HIS 0.004 0.001 HIS A 674 PHE 0.029 0.002 PHE A 505 TYR 0.016 0.002 TYR H 60 ARG 0.005 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 39 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 54 average time/residue: 0.1617 time to fit residues: 13.3656 Evaluate side-chains 50 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0768 time to fit residues: 2.8664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 0.0670 chunk 59 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 68 optimal weight: 0.0970 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 overall best weight: 1.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 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: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7279 Z= 0.235 Angle : 0.549 7.809 9891 Z= 0.296 Chirality : 0.042 0.184 1137 Planarity : 0.004 0.042 1240 Dihedral : 4.767 20.701 972 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.04 % Allowed : 16.32 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.39 (0.28), residues: 900 helix: 1.97 (0.28), residues: 319 sheet: -0.77 (0.32), residues: 240 loop : -0.50 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 182 HIS 0.004 0.001 HIS A 459 PHE 0.013 0.001 PHE A 562 TYR 0.010 0.001 TYR H 52 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.1659 time to fit residues: 13.0889 Evaluate side-chains 45 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0727 time to fit residues: 1.4315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7279 Z= 0.324 Angle : 0.576 7.478 9891 Z= 0.311 Chirality : 0.043 0.175 1137 Planarity : 0.004 0.047 1240 Dihedral : 4.817 21.056 972 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.91 % Allowed : 17.23 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.37 (0.28), residues: 900 helix: 1.99 (0.28), residues: 319 sheet: -0.86 (0.32), residues: 232 loop : -0.50 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 851 HIS 0.004 0.001 HIS A 674 PHE 0.033 0.002 PHE A 64 TYR 0.012 0.001 TYR H 52 ARG 0.006 0.001 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 50 average time/residue: 0.1672 time to fit residues: 12.3969 Evaluate side-chains 48 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0669 time to fit residues: 1.9007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.1980 chunk 60 optimal weight: 30.0000 chunk 90 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7279 Z= 0.164 Angle : 0.536 8.725 9891 Z= 0.288 Chirality : 0.042 0.172 1137 Planarity : 0.004 0.038 1240 Dihedral : 4.566 23.781 972 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 17.23 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.58 (0.28), residues: 900 helix: 2.06 (0.28), residues: 319 sheet: -0.65 (0.33), residues: 231 loop : -0.35 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 851 HIS 0.004 0.001 HIS A 459 PHE 0.054 0.001 PHE A 64 TYR 0.012 0.001 TYR H 52 ARG 0.006 0.000 ARG A 547 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1910 time to fit residues: 13.4798 Evaluate side-chains 43 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 74 optimal weight: 0.0170 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 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 = 0.4383 r_free = 0.4383 target = 0.132165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.091233 restraints weight = 21492.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.086671 restraints weight = 14420.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.087451 restraints weight = 11125.777| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 7279 Z= 0.417 Angle : 0.612 9.212 9891 Z= 0.331 Chirality : 0.043 0.167 1137 Planarity : 0.005 0.056 1240 Dihedral : 4.831 21.897 972 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.39 % Allowed : 17.49 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.43 (0.28), residues: 900 helix: 2.06 (0.28), residues: 318 sheet: -0.87 (0.33), residues: 231 loop : -0.46 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 851 HIS 0.004 0.001 HIS A 459 PHE 0.025 0.002 PHE A 505 TYR 0.012 0.002 TYR L 33 ARG 0.006 0.001 ARG A 547 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1515.40 seconds wall clock time: 28 minutes 29.18 seconds (1709.18 seconds total)