Starting phenix.real_space_refine on Fri Dec 27 12:01:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2c_44103/12_2024/9b2c_44103.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2c_44103/12_2024/9b2c_44103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2c_44103/12_2024/9b2c_44103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2c_44103/12_2024/9b2c_44103.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2c_44103/12_2024/9b2c_44103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2c_44103/12_2024/9b2c_44103.cif" } resolution = 3.0 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= 0.001 sd= 0.118 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 26 5.16 5 C 2973 2.51 5 N 805 2.21 5 O 792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4596 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 761 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 1, 'TRANS': 108} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "L" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1535 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 57 Chain: "N" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 759 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "H" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1488 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.65, per 1000 atoms: 0.79 Number of scatterers: 4596 At special positions: 0 Unit cell: (64, 81, 120, 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 26 16.00 O 792 8.00 N 805 7.00 C 2973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.13 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.00 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.02 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.02 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 501 " - " ASN A 331 " " NAG B 1 " - " ASN A 311 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 741.6 milliseconds 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 16 sheets defined 8.1% alpha, 50.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.706A pdb=" N VAL A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 188 through 192 Processing helix chain 'N' and resid 63 through 66 Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 207 through 210 Processing sheet with id=AA1, first strand: chain 'A' and resid 320 through 328 removed outlier: 5.029A pdb=" N ALA A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP A 317 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU A 323 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS A 315 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 320 through 328 removed outlier: 5.029A pdb=" N ALA A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP A 317 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU A 323 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS A 315 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 335 removed outlier: 8.004A pdb=" N GLN A 376 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N GLN A 412 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 11.719A pdb=" N CYS A 378 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N GLU A 410 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 12.031A pdb=" N SER A 380 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N ALA A 408 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 400 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL A 392 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN A 402 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 390 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 353 " --> pdb=" O THR A 393 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.591A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.188A pdb=" N ALA L 135 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 158 through 159 Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.501A pdb=" N SER N 26 " --> pdb=" O GLN N 4 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.520A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL N 51 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET N 35 " --> pdb=" O VAL N 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.848A pdb=" N THR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.669A pdb=" N PHE H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.875A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.875A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 157 through 160 removed outlier: 4.321A pdb=" N TYR H 200 " --> pdb=" O VAL H 217 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 828 1.32 - 1.45: 1256 1.45 - 1.58: 2586 1.58 - 1.70: 2 1.70 - 1.83: 36 Bond restraints: 4708 Sorted by residual: bond pdb=" N PRO H 208 " pdb=" CD PRO H 208 " ideal model delta sigma weight residual 1.473 1.614 -0.141 1.40e-02 5.10e+03 1.01e+02 bond pdb=" N PRO L 45 " pdb=" CD PRO L 45 " ideal model delta sigma weight residual 1.473 1.403 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" CA SER N 36 " pdb=" CB SER N 36 " ideal model delta sigma weight residual 1.534 1.471 0.063 1.60e-02 3.91e+03 1.57e+01 bond pdb=" C CYS L 23 " pdb=" O CYS L 23 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.18e-02 7.18e+03 1.17e+01 bond pdb=" N VAL A 395 " pdb=" CA VAL A 395 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.17e+01 ... (remaining 4703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 6027 2.96 - 5.92: 377 5.92 - 8.88: 46 8.88 - 11.85: 5 11.85 - 14.81: 1 Bond angle restraints: 6456 Sorted by residual: angle pdb=" C CYS H 202 " pdb=" CA CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sigma weight residual 111.30 96.49 14.81 1.70e+00 3.46e-01 7.59e+01 angle pdb=" C GLY H 124 " pdb=" N PRO H 125 " pdb=" CA PRO H 125 " ideal model delta sigma weight residual 119.85 127.47 -7.62 1.01e+00 9.80e-01 5.70e+01 angle pdb=" C GLY L 104 " pdb=" N PRO L 105 " pdb=" CA PRO L 105 " ideal model delta sigma weight residual 119.32 127.54 -8.22 1.14e+00 7.69e-01 5.20e+01 angle pdb=" C GLN L 17 " pdb=" N PRO L 18 " pdb=" CA PRO L 18 " ideal model delta sigma weight residual 120.03 126.80 -6.77 9.90e-01 1.02e+00 4.67e+01 angle pdb=" C LYS A 338 " pdb=" N PRO A 339 " pdb=" CA PRO A 339 " ideal model delta sigma weight residual 119.56 126.53 -6.97 1.02e+00 9.61e-01 4.66e+01 ... (remaining 6451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 2636 21.04 - 42.09: 84 42.09 - 63.13: 30 63.13 - 84.17: 11 84.17 - 105.21: 5 Dihedral angle restraints: 2766 sinusoidal: 880 harmonic: 1886 Sorted by residual: dihedral pdb=" CD ARG N 73 " pdb=" NE ARG N 73 " pdb=" CZ ARG N 73 " pdb=" NH1 ARG N 73 " ideal model delta sinusoidal sigma weight residual 0.00 82.47 -82.47 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS H 146 " pdb=" SG CYS H 146 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual 93.00 158.52 -65.52 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" C CYS H 202 " pdb=" N CYS H 202 " pdb=" CA CYS H 202 " pdb=" CB CYS H 202 " ideal model delta harmonic sigma weight residual -122.60 -104.12 -18.48 0 2.50e+00 1.60e-01 5.46e+01 ... (remaining 2763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 555 0.084 - 0.168: 150 0.168 - 0.252: 38 0.252 - 0.336: 5 0.336 - 0.421: 5 Chirality restraints: 753 Sorted by residual: chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.64e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.42e+01 chirality pdb=" CA CYS H 202 " pdb=" N CYS H 202 " pdb=" C CYS H 202 " pdb=" CB CYS H 202 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 750 not shown) Planarity restraints: 839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 73 " -1.124 9.50e-02 1.11e+02 5.04e-01 1.53e+02 pdb=" NE ARG N 73 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG N 73 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG N 73 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG N 73 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 113 " 0.566 9.50e-02 1.11e+02 2.54e-01 3.93e+01 pdb=" NE ARG L 113 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG L 113 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG L 113 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG L 113 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 30 " -0.028 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C SER H 30 " 0.091 2.00e-02 2.50e+03 pdb=" O SER H 30 " -0.032 2.00e-02 2.50e+03 pdb=" N HIS H 31 " -0.031 2.00e-02 2.50e+03 ... (remaining 836 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1761 2.89 - 3.40: 3691 3.40 - 3.90: 7450 3.90 - 4.40: 8468 4.40 - 4.90: 14724 Nonbonded interactions: 36094 Sorted by model distance: nonbonded pdb=" O PRO L 8 " pdb=" CG2 THR L 107 " model vdw 2.392 3.460 nonbonded pdb=" O CYS H 202 " pdb=" CB CYS H 202 " model vdw 2.410 2.752 nonbonded pdb=" O LEU L 38 " pdb=" O TYR L 54 " model vdw 2.421 3.040 nonbonded pdb=" O TYR L 54 " pdb=" N VAL L 56 " model vdw 2.439 3.120 nonbonded pdb=" NH2 ARG L 51 " pdb=" O LEU H 103 " model vdw 2.441 3.120 ... (remaining 36089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.000 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.011 0.141 4708 Z= 0.744 Angle : 1.606 14.807 6456 Z= 1.099 Chirality : 0.087 0.421 753 Planarity : 0.025 0.504 837 Dihedral : 13.713 105.210 1536 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.77 % Allowed : 2.63 % Favored : 96.60 % Rotamer: Outliers : 3.41 % Allowed : 3.12 % Favored : 93.47 % Cbeta Deviations : 1.16 % Peptide Plane: Cis-proline : 13.79 % 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: -0.08 (0.32), residues: 647 helix: -2.74 (0.94), residues: 12 sheet: -0.09 (0.29), residues: 296 loop : 0.26 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP H 109 HIS 0.006 0.001 HIS H 31 PHE 0.015 0.003 PHE H 108 TYR 0.042 0.004 TYR L 54 ARG 0.006 0.001 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.494 Fit side-chains REVERT: L 94 MET cc_start: 0.7619 (tmt) cc_final: 0.7122 (tmt) REVERT: L 148 GLU cc_start: 0.7866 (mp0) cc_final: 0.7258 (pp20) REVERT: L 165 GLN cc_start: 0.8031 (mt0) cc_final: 0.7822 (mt0) outliers start: 12 outliers final: 0 residues processed: 66 average time/residue: 1.2010 time to fit residues: 82.8197 Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4708 Z= 0.222 Angle : 0.646 8.162 6456 Z= 0.335 Chirality : 0.047 0.165 753 Planarity : 0.005 0.043 837 Dihedral : 7.796 60.185 786 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.47 % Favored : 97.37 % Rotamer: Outliers : 1.70 % Allowed : 8.52 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.14 (0.33), residues: 647 helix: -2.31 (0.76), residues: 20 sheet: 0.23 (0.29), residues: 301 loop : 0.29 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS L 194 PHE 0.015 0.002 PHE A 374 TYR 0.030 0.002 TYR L 54 ARG 0.004 0.001 ARG N 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.467 Fit side-chains REVERT: A 354 MET cc_start: 0.8204 (ttp) cc_final: 0.7950 (ttp) REVERT: L 112 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8378 (ptpt) REVERT: L 152 GLN cc_start: 0.7995 (tt0) cc_final: 0.7718 (mt0) outliers start: 6 outliers final: 0 residues processed: 44 average time/residue: 1.1087 time to fit residues: 51.3354 Evaluate side-chains 34 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 112 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN L 204 GLN H 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 4708 Z= 0.293 Angle : 0.618 6.434 6456 Z= 0.323 Chirality : 0.046 0.153 753 Planarity : 0.005 0.043 837 Dihedral : 5.542 37.267 786 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.84 % Allowed : 9.94 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.00 (0.33), residues: 647 helix: -1.77 (0.94), residues: 20 sheet: 0.16 (0.29), residues: 306 loop : 0.13 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS L 194 PHE 0.019 0.002 PHE N 48 TYR 0.030 0.002 TYR L 54 ARG 0.005 0.001 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.500 Fit side-chains REVERT: A 354 MET cc_start: 0.8270 (ttp) cc_final: 0.8027 (ttp) REVERT: L 112 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8443 (ptpt) REVERT: L 152 GLN cc_start: 0.8018 (tt0) cc_final: 0.7790 (mt0) outliers start: 10 outliers final: 4 residues processed: 43 average time/residue: 1.0602 time to fit residues: 48.1074 Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 58 optimal weight: 0.0040 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 152 GLN L 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 4708 Z= 0.294 Angle : 0.605 6.375 6456 Z= 0.315 Chirality : 0.046 0.155 753 Planarity : 0.004 0.044 837 Dihedral : 5.090 33.493 786 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.12 % Allowed : 11.36 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.33), residues: 647 helix: -2.03 (0.89), residues: 22 sheet: 0.07 (0.28), residues: 316 loop : 0.03 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 194 PHE 0.017 0.002 PHE N 48 TYR 0.027 0.002 TYR L 54 ARG 0.003 0.000 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.468 Fit side-chains REVERT: A 354 MET cc_start: 0.8268 (ttp) cc_final: 0.8032 (ttp) REVERT: L 112 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8496 (ptpt) REVERT: L 160 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7428 (mm-40) outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 1.1208 time to fit residues: 48.3666 Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4708 Z= 0.261 Angle : 0.583 6.236 6456 Z= 0.303 Chirality : 0.045 0.152 753 Planarity : 0.004 0.043 837 Dihedral : 4.856 31.757 786 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.69 % Allowed : 11.36 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.33), residues: 647 helix: -1.66 (0.98), residues: 22 sheet: 0.07 (0.28), residues: 306 loop : -0.03 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 PHE 0.014 0.002 PHE N 48 TYR 0.026 0.002 TYR L 54 ARG 0.006 0.001 ARG L 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 354 MET cc_start: 0.8260 (ttp) cc_final: 0.8056 (ttp) REVERT: A 357 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6606 (ptt180) REVERT: L 112 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8477 (ptpt) REVERT: L 160 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7450 (mm-40) outliers start: 13 outliers final: 8 residues processed: 41 average time/residue: 1.1813 time to fit residues: 50.7654 Evaluate side-chains 42 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 4708 Z= 0.310 Angle : 0.602 6.480 6456 Z= 0.313 Chirality : 0.046 0.159 753 Planarity : 0.005 0.043 837 Dihedral : 4.870 31.353 786 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.26 % Allowed : 11.36 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.23 (0.34), residues: 647 helix: -1.73 (0.97), residues: 23 sheet: 0.03 (0.28), residues: 316 loop : -0.06 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS L 98 PHE 0.015 0.002 PHE N 48 TYR 0.026 0.002 TYR L 54 ARG 0.006 0.001 ARG L 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 354 MET cc_start: 0.8263 (ttp) cc_final: 0.8055 (ttp) REVERT: A 357 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6715 (ptt180) REVERT: L 112 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8549 (ptpt) REVERT: L 160 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7462 (mm-40) outliers start: 15 outliers final: 7 residues processed: 42 average time/residue: 1.0719 time to fit residues: 47.4451 Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4708 Z= 0.278 Angle : 0.584 6.084 6456 Z= 0.304 Chirality : 0.045 0.158 753 Planarity : 0.004 0.043 837 Dihedral : 4.803 31.056 786 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.98 % Allowed : 13.07 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.22 (0.34), residues: 647 helix: -1.60 (1.02), residues: 23 sheet: 0.04 (0.28), residues: 316 loop : -0.06 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 PHE 0.013 0.002 PHE N 48 TYR 0.026 0.002 TYR L 54 ARG 0.007 0.001 ARG L 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6723 (ptt180) REVERT: L 112 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8539 (ptpt) REVERT: L 160 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7481 (mm-40) outliers start: 14 outliers final: 7 residues processed: 43 average time/residue: 1.1371 time to fit residues: 51.4122 Evaluate side-chains 39 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 53 optimal weight: 0.2980 chunk 57 optimal weight: 0.0070 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 4708 Z= 0.147 Angle : 0.527 5.070 6456 Z= 0.275 Chirality : 0.043 0.148 753 Planarity : 0.004 0.042 837 Dihedral : 4.512 30.187 786 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.22 % Rotamer: Outliers : 3.12 % Allowed : 13.92 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.03 (0.34), residues: 647 helix: -1.34 (1.06), residues: 23 sheet: 0.20 (0.29), residues: 305 loop : 0.01 (0.38), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 PHE 0.010 0.001 PHE L 214 TYR 0.024 0.001 TYR L 54 ARG 0.007 0.000 ARG L 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: L 160 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7387 (mm-40) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 1.0007 time to fit residues: 48.6785 Evaluate side-chains 39 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.0020 chunk 37 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 152 GLN L 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4708 Z= 0.215 Angle : 0.553 5.303 6456 Z= 0.288 Chirality : 0.045 0.201 753 Planarity : 0.004 0.042 837 Dihedral : 4.526 31.243 786 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.12 % Allowed : 14.20 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.02 (0.34), residues: 647 helix: -1.34 (1.06), residues: 23 sheet: 0.22 (0.29), residues: 306 loop : 0.00 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 PHE 0.010 0.001 PHE L 144 TYR 0.027 0.002 TYR L 54 ARG 0.008 0.001 ARG L 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6643 (ptt180) REVERT: L 160 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7513 (mm-40) outliers start: 11 outliers final: 6 residues processed: 39 average time/residue: 1.1252 time to fit residues: 46.3379 Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.0270 chunk 39 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 overall best weight: 0.8418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 152 GLN L 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 4708 Z= 0.296 Angle : 0.589 5.840 6456 Z= 0.307 Chirality : 0.046 0.246 753 Planarity : 0.005 0.043 837 Dihedral : 4.667 31.896 786 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 1.99 % Allowed : 15.91 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.14 (0.34), residues: 647 helix: -1.46 (1.04), residues: 23 sheet: 0.09 (0.29), residues: 318 loop : -0.02 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 98 PHE 0.013 0.002 PHE N 48 TYR 0.027 0.002 TYR L 54 ARG 0.008 0.001 ARG L 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6680 (ptt180) REVERT: L 160 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7530 (mm-40) outliers start: 7 outliers final: 6 residues processed: 38 average time/residue: 1.0653 time to fit residues: 42.7270 Evaluate side-chains 39 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.153639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118853 restraints weight = 4811.812| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.31 r_work: 0.3191 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4708 Z= 0.216 Angle : 0.557 5.420 6456 Z= 0.290 Chirality : 0.045 0.209 753 Planarity : 0.004 0.042 837 Dihedral : 4.553 31.917 786 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 1.70 % Allowed : 16.19 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.13 (0.34), residues: 647 helix: -1.40 (1.05), residues: 23 sheet: 0.09 (0.29), residues: 318 loop : -0.00 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS L 98 PHE 0.009 0.001 PHE H 29 TYR 0.026 0.002 TYR L 54 ARG 0.008 0.001 ARG L 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1799.10 seconds wall clock time: 32 minutes 56.47 seconds (1976.47 seconds total)