Starting phenix.real_space_refine on Thu Nov 14 08:18:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgp_43220/11_2024/8vgp_43220.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgp_43220/11_2024/8vgp_43220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgp_43220/11_2024/8vgp_43220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgp_43220/11_2024/8vgp_43220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgp_43220/11_2024/8vgp_43220.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgp_43220/11_2024/8vgp_43220.cif" } resolution = 2.7 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= 0.011 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 1 9.91 5 S 34 5.16 5 C 3157 2.51 5 N 838 2.21 5 O 1016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5046 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 210} Conformer: "B" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 210} bond proxies already assigned to first conformer: 1796 Chain: "H" Number of atoms: 1624 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1613 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1613 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1643 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1609 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 24} Link IDs: {None: 24} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 400 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 400 " occ=0.50 residue: pdb=" N AARG H 19 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG H 19 " occ=0.50 Time building chain proxies: 5.59, per 1000 atoms: 1.11 Number of scatterers: 5046 At special positions: 0 Unit cell: (115.875, 64.1452, 95.1832, 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 1 19.99 S 34 16.00 O 1016 8.00 N 838 7.00 C 3157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 313 " distance=2.02 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 435 " distance=2.04 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 450 " distance=2.02 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS H 151 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG CYS H 153 " distance=2.03 Simple disulfide: pdb=" SG CYS H 126 " - pdb=" SG CYS L 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 141 " - pdb=" SG CYS L 116 " distance=2.04 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 165 " distance=2.03 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 171 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 1.0 seconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 13 sheets defined 13.6% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 316 through 320 removed outlier: 4.322A pdb=" N GLY A 319 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.814A pdb=" N PHE L 83 " --> pdb=" O CYS L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 301 removed outlier: 25.594A pdb=" N GLU A 308 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 20.837A pdb=" N ARG A 328 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 14.326A pdb=" N LYS A 310 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N GLN A 326 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR A 312 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET A 489 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG A 327 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A 487 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR A 369 " --> pdb=" O HIS A 389 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS A 389 " --> pdb=" O TYR A 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.467A pdb=" N MET A 489 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG A 327 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A 487 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR A 369 " --> pdb=" O HIS A 389 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS A 389 " --> pdb=" O TYR A 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.715A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.052A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL H 96 " --> pdb=" O MET H 100C" (cutoff:3.500A) removed outlier: 5.906A pdb=" N MET H 100C" --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 131 removed outlier: 6.599A pdb=" N CYS H 141 " --> pdb=" O PRO H 130 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 124 through 131 removed outlier: 6.599A pdb=" N CYS H 141 " --> pdb=" O PRO H 130 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 159 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.525A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.833A pdb=" N LEU L 28 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 12.058A pdb=" N SER L 65 " --> pdb=" O LEU L 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.321A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.761A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 153 through 154 225 hydrogen bonds defined for protein. 562 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: 2.09 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1552 1.34 - 1.46: 1255 1.46 - 1.58: 2279 1.58 - 1.71: 0 1.71 - 1.83: 42 Bond restraints: 5128 Sorted by residual: bond pdb=" C THR H 170 " pdb=" N PHE H 171 " ideal model delta sigma weight residual 1.340 1.228 0.112 5.87e-02 2.90e+02 3.67e+00 bond pdb=" CG LEU A 375 " pdb=" CD1 LEU A 375 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.40e+00 bond pdb=" CD LYS A 478 " pdb=" CE LYS A 478 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.23e+00 bond pdb=" CG LEU L 175 " pdb=" CD1 LEU L 175 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.52e+00 bond pdb=" CB BARG A 400 " pdb=" CG BARG A 400 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.47e+00 ... (remaining 5123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 6751 2.60 - 5.20: 182 5.20 - 7.80: 21 7.80 - 10.40: 4 10.40 - 13.00: 1 Bond angle restraints: 6959 Sorted by residual: angle pdb=" N PHE A 447 " pdb=" CA PHE A 447 " pdb=" C PHE A 447 " ideal model delta sigma weight residual 112.89 118.86 -5.97 1.24e+00 6.50e-01 2.32e+01 angle pdb=" CA LEU L 73 " pdb=" CB LEU L 73 " pdb=" CG LEU L 73 " ideal model delta sigma weight residual 116.30 129.30 -13.00 3.50e+00 8.16e-02 1.38e+01 angle pdb=" N GLN A 462 " pdb=" CA GLN A 462 " pdb=" C GLN A 462 " ideal model delta sigma weight residual 112.34 116.82 -4.48 1.30e+00 5.92e-01 1.19e+01 angle pdb=" C GLU H 152 " pdb=" N CYS H 153 " pdb=" CA CYS H 153 " ideal model delta sigma weight residual 121.80 129.92 -8.12 2.44e+00 1.68e-01 1.11e+01 angle pdb=" CA CYS L 124 " pdb=" CB CYS L 124 " pdb=" SG CYS L 124 " ideal model delta sigma weight residual 114.40 107.12 7.28 2.30e+00 1.89e-01 1.00e+01 ... (remaining 6954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2790 17.67 - 35.35: 183 35.35 - 53.02: 37 53.02 - 70.69: 10 70.69 - 88.37: 15 Dihedral angle restraints: 3035 sinusoidal: 1174 harmonic: 1861 Sorted by residual: dihedral pdb=" CD BARG H 19 " pdb=" NE BARG H 19 " pdb=" CZ BARG H 19 " pdb=" NH1BARG H 19 " ideal model delta sinusoidal sigma weight residual 0.00 -74.63 74.63 1 1.00e+01 1.00e-02 7.06e+01 dihedral pdb=" CD BARG A 400 " pdb=" NE BARG A 400 " pdb=" CZ BARG A 400 " pdb=" NH1BARG A 400 " ideal model delta sinusoidal sigma weight residual 0.00 71.95 -71.95 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CA PHE H 98 " pdb=" C PHE H 98 " pdb=" N LEU H 99 " pdb=" CA LEU H 99 " ideal model delta harmonic sigma weight residual -180.00 -150.97 -29.03 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 3032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 433 0.050 - 0.099: 226 0.099 - 0.149: 78 0.149 - 0.199: 11 0.199 - 0.248: 2 Chirality restraints: 750 Sorted by residual: chirality pdb=" CA TYR A 476 " pdb=" N TYR A 476 " pdb=" C TYR A 476 " pdb=" CB TYR A 476 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA TYR H 100A" pdb=" N TYR H 100A" pdb=" C TYR H 100A" pdb=" CB TYR H 100A" both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE A 324 " pdb=" CA ILE A 324 " pdb=" CG1 ILE A 324 " pdb=" CG2 ILE A 324 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 747 not shown) Planarity restraints: 890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD BARG H 19 " 0.904 9.50e-02 1.11e+02 4.06e-01 1.11e+02 pdb=" NE BARG H 19 " -0.075 2.00e-02 2.50e+03 pdb=" CZ BARG H 19 " 0.046 2.00e-02 2.50e+03 pdb=" NH1BARG H 19 " -0.013 2.00e-02 2.50e+03 pdb=" NH2BARG H 19 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD BARG A 400 " 0.874 9.50e-02 1.11e+02 3.93e-01 1.05e+02 pdb=" NE BARG A 400 " -0.074 2.00e-02 2.50e+03 pdb=" CZ BARG A 400 " 0.048 2.00e-02 2.50e+03 pdb=" NH1BARG A 400 " -0.014 2.00e-02 2.50e+03 pdb=" NH2BARG A 400 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD AARG A 400 " 0.243 9.50e-02 1.11e+02 1.10e-01 9.11e+00 pdb=" NE AARG A 400 " -0.022 2.00e-02 2.50e+03 pdb=" CZ AARG A 400 " 0.020 2.00e-02 2.50e+03 pdb=" NH1AARG A 400 " -0.010 2.00e-02 2.50e+03 pdb=" NH2AARG A 400 " 0.001 2.00e-02 2.50e+03 ... (remaining 887 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 183 2.70 - 3.25: 4731 3.25 - 3.80: 7880 3.80 - 4.35: 11345 4.35 - 4.90: 18704 Nonbonded interactions: 42843 Sorted by model distance: nonbonded pdb=" O GLY A 451 " pdb=" O HOH A 701 " model vdw 2.148 3.040 nonbonded pdb=" O HOH A 714 " pdb=" O HOH A 722 " model vdw 2.176 3.040 nonbonded pdb=" OG SER L 7 " pdb=" O HOH L 301 " model vdw 2.219 3.040 nonbonded pdb=" NZ LYS L 190 " pdb=" OD1 ASN L 210 " model vdw 2.250 3.120 nonbonded pdb=" O HOH A 709 " pdb=" O HOH A 716 " model vdw 2.250 3.040 ... (remaining 42838 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 17.980 Find NCS groups from input model: 0.090 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:15.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 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 : 0.010 0.112 5128 Z= 0.631 Angle : 1.019 12.996 6959 Z= 0.548 Chirality : 0.063 0.248 750 Planarity : 0.021 0.406 890 Dihedral : 14.339 88.368 1818 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.00 % Favored : 94.84 % Rotamer: Outliers : 0.91 % Allowed : 5.99 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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: -0.76 (0.32), residues: 646 helix: -2.77 (0.56), residues: 42 sheet: 0.45 (0.31), residues: 266 loop : -0.98 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP H 33 HIS 0.013 0.003 HIS H 35 PHE 0.024 0.004 PHE H 98 TYR 0.022 0.005 TYR A 353 ARG 0.019 0.004 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: H 141 CYS cc_start: 0.7481 (m) cc_final: 0.6963 (m) outliers start: 4 outliers final: 0 residues processed: 92 average time/residue: 1.6904 time to fit residues: 160.5853 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5128 Z= 0.250 Angle : 0.684 9.496 6959 Z= 0.362 Chirality : 0.046 0.137 750 Planarity : 0.004 0.048 890 Dihedral : 5.476 26.440 704 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.09 % Allowed : 10.53 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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: 0.01 (0.34), residues: 646 helix: -1.90 (0.64), residues: 45 sheet: 0.71 (0.31), residues: 276 loop : -0.25 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 33 HIS 0.006 0.001 HIS A 402 PHE 0.021 0.002 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.008 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: L 123 GLU cc_start: 0.8920 (mp0) cc_final: 0.8586 (mp0) REVERT: L 125 LEU cc_start: 0.8585 (mm) cc_final: 0.8203 (mt) REVERT: L 167 ASP cc_start: 0.8921 (t0) cc_final: 0.8720 (t0) outliers start: 5 outliers final: 1 residues processed: 71 average time/residue: 1.8333 time to fit residues: 134.6861 Evaluate side-chains 63 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5128 Z= 0.250 Angle : 0.639 9.451 6959 Z= 0.338 Chirality : 0.045 0.159 750 Planarity : 0.004 0.046 890 Dihedral : 5.142 26.009 704 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.09 % Allowed : 12.16 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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: 0.19 (0.34), residues: 646 helix: -1.40 (0.70), residues: 46 sheet: 0.77 (0.31), residues: 276 loop : -0.13 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.004 0.001 HIS A 402 PHE 0.023 0.002 PHE H 98 TYR 0.010 0.001 TYR A 391 ARG 0.008 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 458 MET cc_start: 0.8788 (mmm) cc_final: 0.8573 (mmp) REVERT: L 123 GLU cc_start: 0.8956 (mp0) cc_final: 0.8619 (mp0) REVERT: L 167 ASP cc_start: 0.8871 (t0) cc_final: 0.8669 (t0) outliers start: 6 outliers final: 2 residues processed: 72 average time/residue: 1.6331 time to fit residues: 121.8978 Evaluate side-chains 64 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.0010 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS H 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5128 Z= 0.270 Angle : 0.635 9.484 6959 Z= 0.334 Chirality : 0.045 0.161 750 Planarity : 0.004 0.044 890 Dihedral : 5.044 28.163 704 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.63 % Allowed : 13.61 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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: 0.27 (0.35), residues: 646 helix: -1.36 (0.71), residues: 46 sheet: 0.86 (0.32), residues: 276 loop : -0.11 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.003 0.001 HIS A 402 PHE 0.020 0.002 PHE H 98 TYR 0.011 0.001 TYR H 91 ARG 0.007 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: L 123 GLU cc_start: 0.8957 (mp0) cc_final: 0.8577 (mp0) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 1.6061 time to fit residues: 116.5292 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 0.0000 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5128 Z= 0.189 Angle : 0.603 9.540 6959 Z= 0.318 Chirality : 0.043 0.157 750 Planarity : 0.004 0.044 890 Dihedral : 4.832 29.348 704 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Rotamer: Outliers : 2.00 % Allowed : 13.43 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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: 0.41 (0.35), residues: 646 helix: -1.29 (0.71), residues: 47 sheet: 0.95 (0.32), residues: 272 loop : 0.01 (0.38), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 354 HIS 0.002 0.000 HIS A 402 PHE 0.022 0.001 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.007 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 315 MET cc_start: 0.8096 (mmp) cc_final: 0.7726 (mmt) outliers start: 11 outliers final: 3 residues processed: 70 average time/residue: 1.7698 time to fit residues: 128.3897 Evaluate side-chains 64 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN H 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5128 Z= 0.254 Angle : 0.640 9.187 6959 Z= 0.335 Chirality : 0.045 0.206 750 Planarity : 0.004 0.040 890 Dihedral : 4.950 39.765 704 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 2.18 % Allowed : 13.61 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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: 0.39 (0.35), residues: 646 helix: -1.45 (0.69), residues: 47 sheet: 1.00 (0.32), residues: 272 loop : -0.04 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS A 402 PHE 0.021 0.001 PHE H 98 TYR 0.010 0.001 TYR H 91 ARG 0.009 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8141 (mmp) cc_final: 0.7770 (mmt) REVERT: H 197 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8331 (tp-100) REVERT: L 80 CYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7562 (m) outliers start: 12 outliers final: 4 residues processed: 69 average time/residue: 1.7296 time to fit residues: 123.8849 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 122 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN H 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 5128 Z= 0.344 Angle : 0.673 8.890 6959 Z= 0.352 Chirality : 0.046 0.177 750 Planarity : 0.004 0.043 890 Dihedral : 5.078 35.338 704 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.09 % Rotamer: Outliers : 1.81 % Allowed : 13.97 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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: 0.36 (0.35), residues: 646 helix: -1.08 (0.75), residues: 40 sheet: 1.00 (0.32), residues: 276 loop : -0.19 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.002 PHE H 98 TYR 0.013 0.001 TYR H 91 ARG 0.010 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: H 197 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8334 (tp-100) outliers start: 10 outliers final: 4 residues processed: 70 average time/residue: 1.5062 time to fit residues: 109.3773 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 122 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN H 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5128 Z= 0.284 Angle : 0.676 10.505 6959 Z= 0.353 Chirality : 0.045 0.145 750 Planarity : 0.004 0.048 890 Dihedral : 5.030 33.437 704 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 1.45 % Allowed : 14.70 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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: 0.42 (0.35), residues: 646 helix: -1.06 (0.74), residues: 40 sheet: 0.93 (0.31), residues: 288 loop : -0.07 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.002 PHE H 98 TYR 0.011 0.001 TYR H 91 ARG 0.012 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 197 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8321 (tp-100) outliers start: 8 outliers final: 5 residues processed: 66 average time/residue: 1.5425 time to fit residues: 105.6469 Evaluate side-chains 66 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN H 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 5128 Z= 0.353 Angle : 0.702 11.128 6959 Z= 0.366 Chirality : 0.046 0.147 750 Planarity : 0.005 0.050 890 Dihedral : 5.083 31.716 704 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 1.63 % Allowed : 14.70 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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: 0.34 (0.35), residues: 646 helix: -1.43 (0.69), residues: 46 sheet: 0.95 (0.31), residues: 288 loop : -0.13 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.002 PHE H 98 TYR 0.013 0.001 TYR H 91 ARG 0.013 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 2.0367 time to fit residues: 140.2071 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN H 204 ASN L 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5128 Z= 0.267 Angle : 0.682 11.000 6959 Z= 0.356 Chirality : 0.045 0.141 750 Planarity : 0.004 0.055 890 Dihedral : 4.998 30.656 704 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 1.63 % Allowed : 15.06 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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: 0.45 (0.35), residues: 646 helix: -0.85 (0.76), residues: 40 sheet: 0.98 (0.31), residues: 288 loop : -0.11 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.019 0.001 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.013 0.001 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 197 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8384 (tp-100) outliers start: 9 outliers final: 6 residues processed: 65 average time/residue: 1.5835 time to fit residues: 106.5712 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN H 204 ASN L 79 GLN L 210 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.072672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.054363 restraints weight = 30308.609| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 4.73 r_work: 0.2539 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5128 Z= 0.292 Angle : 0.694 10.728 6959 Z= 0.362 Chirality : 0.045 0.138 750 Planarity : 0.004 0.055 890 Dihedral : 4.996 29.739 704 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 1.63 % Allowed : 15.61 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % 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 (0.35), residues: 646 helix: -0.86 (0.75), residues: 40 sheet: 0.99 (0.31), residues: 289 loop : -0.13 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.002 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.013 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2732.18 seconds wall clock time: 50 minutes 48.40 seconds (3048.40 seconds total)