Starting phenix.real_space_refine on Tue Sep 24 04:14:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/09_2024/7wp8_32678.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/09_2024/7wp8_32678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/09_2024/7wp8_32678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/09_2024/7wp8_32678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/09_2024/7wp8_32678.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/09_2024/7wp8_32678.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4313 2.51 5 N 1123 2.21 5 O 1330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6797 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "D" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "E" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "F" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1470 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 874 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 930 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 791 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: 6.05, per 1000 atoms: 0.89 Number of scatterers: 6797 At special positions: 0 Unit cell: (89.47, 112.032, 112.032, 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 31 16.00 O 1330 8.00 N 1123 7.00 C 4313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.15 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " " NAG L 201 " - " ASN L 26 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 993.9 milliseconds 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB VAL F 503 " Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 21 sheets defined 3.6% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.850A pdb=" N ARG D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.866A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.703A pdb=" N ASP E 90 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'F' and resid 403 through 410 removed outlier: 3.524A pdb=" N GLU F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.893A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 6 removed outlier: 4.160A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.158A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 47 " --> pdb=" O TRP C 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.697A pdb=" N LEU D 4 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER D 25 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 18 through 19 Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.289A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG D 98 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.289A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.511A pdb=" N THR E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AA9, first strand: chain 'E' and resid 59 through 60 removed outlier: 3.565A pdb=" N HIS E 59 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR E 108 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 357 through 358 removed outlier: 3.737A pdb=" N ASP F 398 " --> pdb=" O VAL F 512 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL F 433 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS F 378 " --> pdb=" O VAL F 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.502A pdb=" N MET G 13 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'G' and resid 50 through 52 Processing sheet with id=AB6, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.783A pdb=" N THR G 59 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.590A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR H 94 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU H 114 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.518A pdb=" N ILE H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY H 98 " --> pdb=" O PHE H 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.727A pdb=" N TYR L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 43 through 47 removed outlier: 6.722A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 321 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: 1.77 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1092 1.25 - 1.39: 1865 1.39 - 1.54: 3785 1.54 - 1.68: 193 1.68 - 1.82: 42 Bond restraints: 6977 Sorted by residual: bond pdb=" CA VAL F 503 " pdb=" C VAL F 503 " ideal model delta sigma weight residual 1.523 1.336 0.188 1.27e-02 6.20e+03 2.18e+02 bond pdb=" C GLN F 498 " pdb=" N PRO F 499 " ideal model delta sigma weight residual 1.337 1.206 0.131 1.11e-02 8.12e+03 1.39e+02 bond pdb=" CA VAL F 503 " pdb=" CB VAL F 503 " ideal model delta sigma weight residual 1.540 1.400 0.141 1.25e-02 6.40e+03 1.26e+02 bond pdb=" CA GLN F 498 " pdb=" C GLN F 498 " ideal model delta sigma weight residual 1.524 1.390 0.134 1.28e-02 6.10e+03 1.09e+02 bond pdb=" C VAL F 503 " pdb=" O VAL F 503 " ideal model delta sigma weight residual 1.237 1.121 0.116 1.17e-02 7.31e+03 9.88e+01 ... (remaining 6972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 9196 2.50 - 5.01: 214 5.01 - 7.51: 44 7.51 - 10.02: 14 10.02 - 12.52: 7 Bond angle restraints: 9475 Sorted by residual: angle pdb=" N VAL F 503 " pdb=" CA VAL F 503 " pdb=" CB VAL F 503 " ideal model delta sigma weight residual 110.54 123.06 -12.52 1.36e+00 5.41e-01 8.48e+01 angle pdb=" CA GLY F 504 " pdb=" C GLY F 504 " pdb=" O GLY F 504 " ideal model delta sigma weight residual 120.75 111.28 9.47 1.03e+00 9.43e-01 8.46e+01 angle pdb=" C GLN F 498 " pdb=" N PRO F 499 " pdb=" CA PRO F 499 " ideal model delta sigma weight residual 119.87 129.27 -9.40 1.04e+00 9.25e-01 8.17e+01 angle pdb=" CA PRO F 499 " pdb=" C PRO F 499 " pdb=" O PRO F 499 " ideal model delta sigma weight residual 118.86 108.34 10.52 1.38e+00 5.25e-01 5.82e+01 angle pdb=" N THR E 113 " pdb=" CA THR E 113 " pdb=" C THR E 113 " ideal model delta sigma weight residual 108.52 120.80 -12.28 1.63e+00 3.76e-01 5.68e+01 ... (remaining 9470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 3692 17.87 - 35.74: 352 35.74 - 53.61: 54 53.61 - 71.48: 9 71.48 - 89.35: 12 Dihedral angle restraints: 4119 sinusoidal: 1633 harmonic: 2486 Sorted by residual: dihedral pdb=" CA TYR G 55 " pdb=" C TYR G 55 " pdb=" N PHE G 56 " pdb=" CA PHE G 56 " ideal model delta harmonic sigma weight residual 180.00 -132.22 -47.78 0 5.00e+00 4.00e-02 9.13e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 0.81 -86.81 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 157.16 -64.16 1 1.00e+01 1.00e-02 5.42e+01 ... (remaining 4116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.531: 1006 0.531 - 1.062: 0 1.062 - 1.593: 0 1.593 - 2.124: 0 2.124 - 2.655: 1 Chirality restraints: 1007 Sorted by residual: chirality pdb=" CA VAL F 503 " pdb=" N VAL F 503 " pdb=" C VAL F 503 " pdb=" CB VAL F 503 " both_signs ideal model delta sigma weight residual False 2.44 -0.21 2.66 2.00e-01 2.50e+01 1.76e+02 chirality pdb=" CA PRO F 499 " pdb=" N PRO F 499 " pdb=" C PRO F 499 " pdb=" CB PRO F 499 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA ASN F 343 " pdb=" N ASN F 343 " pdb=" C ASN F 343 " pdb=" CB ASN F 343 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 1004 not shown) Planarity restraints: 1214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.310 2.00e-02 2.50e+03 2.59e-01 8.41e+02 pdb=" C7 NAG A 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.444 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 201 " -0.201 2.00e-02 2.50e+03 1.65e-01 3.39e+02 pdb=" C7 NAG L 201 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG L 201 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG L 201 " 0.263 2.00e-02 2.50e+03 pdb=" O7 NAG L 201 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.151 2.00e-02 2.50e+03 1.24e-01 1.93e+02 pdb=" C7 NAG A 2 " -0.043 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.113 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.199 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.022 2.00e-02 2.50e+03 ... (remaining 1211 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1556 2.78 - 3.31: 5631 3.31 - 3.84: 11082 3.84 - 4.37: 12156 4.37 - 4.90: 21565 Nonbonded interactions: 51990 Sorted by model distance: nonbonded pdb=" O GLY F 447 " pdb=" OH TYR H 33 " model vdw 2.250 3.040 nonbonded pdb=" CG2 VAL F 503 " pdb=" OE1 GLN F 506 " model vdw 2.269 3.460 nonbonded pdb=" OG SER D 17 " pdb=" O LEU D 83 " model vdw 2.276 3.040 nonbonded pdb=" OG SER C 43 " pdb=" O GLY D 111 " model vdw 2.283 3.040 nonbonded pdb=" O THR H 112 " pdb=" OG1 THR H 112 " model vdw 2.296 3.040 ... (remaining 51985 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.950 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.188 6977 Z= 0.490 Angle : 1.006 12.525 9475 Z= 0.592 Chirality : 0.106 2.655 1007 Planarity : 0.012 0.259 1212 Dihedral : 14.513 89.355 2524 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.97 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.12 (0.25), residues: 847 helix: -4.94 (0.50), residues: 8 sheet: -2.25 (0.29), residues: 284 loop : -3.16 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 33 HIS 0.008 0.002 HIS H 101 PHE 0.017 0.002 PHE G 104 TYR 0.029 0.002 TYR D 104 ARG 0.005 0.001 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8524 (mmm) cc_final: 0.8310 (mmt) REVERT: D 38 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7777 (ttpt) REVERT: E 13 ARG cc_start: 0.7979 (mmt180) cc_final: 0.7344 (mtp85) REVERT: E 65 LYS cc_start: 0.7906 (mttt) cc_final: 0.7596 (mtmt) REVERT: G 13 MET cc_start: 0.7522 (tpt) cc_final: 0.7212 (tpt) REVERT: G 35 GLN cc_start: 0.8008 (mp10) cc_final: 0.7517 (mp10) REVERT: G 78 THR cc_start: 0.9036 (p) cc_final: 0.8800 (p) REVERT: G 85 GLN cc_start: 0.8801 (mm110) cc_final: 0.8512 (mm110) REVERT: H 29 PHE cc_start: 0.7988 (t80) cc_final: 0.7696 (t80) REVERT: H 60 TYR cc_start: 0.8299 (m-80) cc_final: 0.7761 (m-80) REVERT: L 4 LEU cc_start: 0.8584 (mt) cc_final: 0.8254 (mp) REVERT: L 37 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6514 (tm-30) REVERT: L 88 GLN cc_start: 0.8262 (mp10) cc_final: 0.8021 (mp10) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2361 time to fit residues: 65.8857 Evaluate side-chains 165 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 90 GLN D 39 GLN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6977 Z= 0.240 Angle : 0.660 6.482 9475 Z= 0.350 Chirality : 0.046 0.182 1007 Planarity : 0.006 0.074 1212 Dihedral : 6.418 62.581 1012 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 1.91 % Allowed : 14.89 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.26), residues: 847 helix: -4.80 (0.65), residues: 8 sheet: -1.89 (0.28), residues: 319 loop : -2.87 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 36 HIS 0.002 0.001 HIS G 97 PHE 0.015 0.002 PHE F 456 TYR 0.026 0.002 TYR E 32 ARG 0.006 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8512 (mmm) cc_final: 0.8279 (mmt) REVERT: C 8 HIS cc_start: 0.8512 (m90) cc_final: 0.8203 (m90) REVERT: E 13 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7602 (mmt180) REVERT: G 4 MET cc_start: 0.8025 (tpp) cc_final: 0.7173 (mmm) REVERT: G 35 GLN cc_start: 0.8077 (mp10) cc_final: 0.7760 (mp10) REVERT: G 55 TYR cc_start: 0.7907 (p90) cc_final: 0.7637 (p90) REVERT: G 78 THR cc_start: 0.9117 (p) cc_final: 0.8916 (p) REVERT: G 85 GLN cc_start: 0.8837 (mm110) cc_final: 0.8626 (mm110) REVERT: H 29 PHE cc_start: 0.7962 (t80) cc_final: 0.7675 (t80) REVERT: H 81 MET cc_start: 0.5808 (ttt) cc_final: 0.5608 (ttt) REVERT: H 106 ASP cc_start: 0.7271 (m-30) cc_final: 0.6858 (m-30) REVERT: L 37 GLN cc_start: 0.6586 (tm-30) cc_final: 0.6120 (tm-30) REVERT: L 102 LYS cc_start: 0.8551 (mmmm) cc_final: 0.8308 (mtmm) outliers start: 14 outliers final: 9 residues processed: 184 average time/residue: 0.2261 time to fit residues: 52.5539 Evaluate side-chains 169 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 43 GLN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6977 Z= 0.341 Angle : 0.677 6.629 9475 Z= 0.360 Chirality : 0.047 0.205 1007 Planarity : 0.005 0.059 1212 Dihedral : 6.587 57.414 1012 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 2.87 % Allowed : 15.98 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.26), residues: 847 helix: -5.13 (0.34), residues: 14 sheet: -1.72 (0.30), residues: 305 loop : -2.75 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 36 HIS 0.006 0.001 HIS H 101 PHE 0.017 0.002 PHE G 104 TYR 0.017 0.002 TYR G 55 ARG 0.009 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8598 (mmm) cc_final: 0.8266 (mmt) REVERT: C 8 HIS cc_start: 0.8525 (m90) cc_final: 0.8177 (m90) REVERT: C 65 SER cc_start: 0.8964 (m) cc_final: 0.8751 (t) REVERT: D 29 PHE cc_start: 0.8672 (t80) cc_final: 0.8432 (t80) REVERT: E 13 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7465 (mtp85) REVERT: E 37 VAL cc_start: 0.8194 (t) cc_final: 0.7961 (m) REVERT: E 103 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7612 (mm-30) REVERT: G 4 MET cc_start: 0.7995 (tpp) cc_final: 0.7199 (mmm) REVERT: G 13 MET cc_start: 0.7524 (tpt) cc_final: 0.7250 (tpt) REVERT: G 35 GLN cc_start: 0.8043 (mp10) cc_final: 0.7729 (mp10) REVERT: G 55 TYR cc_start: 0.8106 (p90) cc_final: 0.7757 (p90) REVERT: H 106 ASP cc_start: 0.7387 (m-30) cc_final: 0.7142 (m-30) REVERT: L 4 LEU cc_start: 0.8381 (mt) cc_final: 0.7997 (mp) REVERT: L 37 GLN cc_start: 0.6725 (tm130) cc_final: 0.6264 (tm-30) REVERT: L 102 LYS cc_start: 0.8635 (mmmm) cc_final: 0.8301 (mtmm) outliers start: 21 outliers final: 17 residues processed: 174 average time/residue: 0.2118 time to fit residues: 47.3777 Evaluate side-chains 174 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6977 Z= 0.204 Angle : 0.612 6.287 9475 Z= 0.322 Chirality : 0.044 0.151 1007 Planarity : 0.004 0.052 1212 Dihedral : 6.165 48.944 1012 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.87 % Allowed : 16.67 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.27), residues: 847 helix: -5.07 (0.38), residues: 14 sheet: -1.69 (0.29), residues: 314 loop : -2.57 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 36 HIS 0.003 0.001 HIS L 33 PHE 0.018 0.002 PHE H 29 TYR 0.017 0.001 TYR G 55 ARG 0.006 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8483 (mmm) cc_final: 0.8193 (mmt) REVERT: C 8 HIS cc_start: 0.8506 (m90) cc_final: 0.8180 (m90) REVERT: D 29 PHE cc_start: 0.8611 (t80) cc_final: 0.8378 (t80) REVERT: E 13 ARG cc_start: 0.8001 (mmt180) cc_final: 0.7583 (mmt180) REVERT: F 467 ASP cc_start: 0.8776 (t0) cc_final: 0.8570 (t0) REVERT: G 4 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7141 (mmm) REVERT: G 33 TYR cc_start: 0.7179 (m-10) cc_final: 0.6941 (m-10) REVERT: G 35 GLN cc_start: 0.8013 (mp10) cc_final: 0.7747 (mp10) REVERT: G 55 TYR cc_start: 0.7777 (p90) cc_final: 0.7506 (p90) REVERT: G 59 THR cc_start: 0.7998 (p) cc_final: 0.7506 (p) REVERT: H 29 PHE cc_start: 0.8161 (t80) cc_final: 0.7763 (t80) REVERT: L 37 GLN cc_start: 0.6583 (tm130) cc_final: 0.6079 (tm-30) REVERT: L 60 ARG cc_start: 0.5257 (mpp80) cc_final: 0.5000 (mpp80) REVERT: L 102 LYS cc_start: 0.8570 (mmmm) cc_final: 0.8214 (mtmm) outliers start: 21 outliers final: 17 residues processed: 179 average time/residue: 0.1712 time to fit residues: 39.6751 Evaluate side-chains 177 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 43 GLN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 6977 Z= 0.553 Angle : 0.782 7.907 9475 Z= 0.416 Chirality : 0.050 0.201 1007 Planarity : 0.006 0.073 1212 Dihedral : 7.378 59.237 1012 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.87 % Favored : 87.01 % Rotamer: Outliers : 3.42 % Allowed : 17.08 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.26), residues: 847 helix: -5.15 (0.32), residues: 14 sheet: -2.07 (0.28), residues: 334 loop : -2.68 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 36 HIS 0.008 0.002 HIS H 101 PHE 0.019 0.003 PHE D 107 TYR 0.021 0.002 TYR H 27 ARG 0.008 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8694 (mmm) cc_final: 0.8283 (mmt) REVERT: C 8 HIS cc_start: 0.8549 (m90) cc_final: 0.8201 (m90) REVERT: D 29 PHE cc_start: 0.8678 (t80) cc_final: 0.8412 (t80) REVERT: E 13 ARG cc_start: 0.8023 (mmt180) cc_final: 0.7667 (mmt180) REVERT: E 33 TRP cc_start: 0.8251 (m100) cc_final: 0.7725 (m100) REVERT: E 37 VAL cc_start: 0.8273 (t) cc_final: 0.8019 (m) REVERT: G 4 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7358 (mmm) REVERT: G 33 TYR cc_start: 0.7751 (m-10) cc_final: 0.7545 (m-10) REVERT: G 35 GLN cc_start: 0.8057 (mp10) cc_final: 0.7740 (mp10) REVERT: G 55 TYR cc_start: 0.8299 (p90) cc_final: 0.8032 (p90) REVERT: H 67 LYS cc_start: 0.8225 (mttt) cc_final: 0.7824 (tmtt) REVERT: H 101 HIS cc_start: 0.7664 (m90) cc_final: 0.7400 (m90) REVERT: H 106 ASP cc_start: 0.7280 (m-30) cc_final: 0.6647 (m-30) REVERT: L 37 GLN cc_start: 0.6910 (tm130) cc_final: 0.6433 (tm-30) REVERT: L 60 ARG cc_start: 0.5586 (mpp80) cc_final: 0.5144 (mpp80) REVERT: L 102 LYS cc_start: 0.8647 (mmmm) cc_final: 0.8263 (mtmm) outliers start: 25 outliers final: 22 residues processed: 174 average time/residue: 0.2131 time to fit residues: 47.5515 Evaluate side-chains 177 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6977 Z= 0.222 Angle : 0.661 7.592 9475 Z= 0.347 Chirality : 0.046 0.157 1007 Planarity : 0.004 0.061 1212 Dihedral : 6.514 49.371 1012 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.01 % Allowed : 19.26 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.27), residues: 847 helix: -5.04 (0.38), residues: 14 sheet: -1.65 (0.29), residues: 324 loop : -2.57 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 36 HIS 0.004 0.001 HIS L 33 PHE 0.030 0.002 PHE H 107 TYR 0.017 0.001 TYR G 55 ARG 0.006 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8456 (mmm) cc_final: 0.8145 (mmt) REVERT: C 8 HIS cc_start: 0.8497 (m90) cc_final: 0.8149 (m90) REVERT: D 29 PHE cc_start: 0.8592 (t80) cc_final: 0.8362 (t80) REVERT: E 13 ARG cc_start: 0.8009 (mmt180) cc_final: 0.7675 (mmt180) REVERT: E 37 VAL cc_start: 0.8310 (t) cc_final: 0.8053 (m) REVERT: F 467 ASP cc_start: 0.8798 (t0) cc_final: 0.8571 (t0) REVERT: G 4 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7243 (mmm) REVERT: G 35 GLN cc_start: 0.8091 (mp10) cc_final: 0.7746 (mp10) REVERT: G 55 TYR cc_start: 0.7869 (p90) cc_final: 0.7480 (p90) REVERT: G 59 THR cc_start: 0.8007 (p) cc_final: 0.7391 (p) REVERT: G 109 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7667 (ptmt) REVERT: H 29 PHE cc_start: 0.8223 (t80) cc_final: 0.7954 (t80) REVERT: L 37 GLN cc_start: 0.6649 (tm130) cc_final: 0.6192 (tm-30) REVERT: L 102 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8286 (mtmm) outliers start: 22 outliers final: 19 residues processed: 174 average time/residue: 0.2023 time to fit residues: 45.8962 Evaluate side-chains 177 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6977 Z= 0.236 Angle : 0.661 7.235 9475 Z= 0.347 Chirality : 0.046 0.196 1007 Planarity : 0.004 0.058 1212 Dihedral : 6.269 48.921 1012 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.42 % Allowed : 18.85 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.27), residues: 847 helix: -5.02 (0.39), residues: 14 sheet: -1.59 (0.29), residues: 339 loop : -2.48 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 36 HIS 0.002 0.001 HIS H 101 PHE 0.018 0.002 PHE H 107 TYR 0.018 0.001 TYR G 55 ARG 0.009 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8475 (mmm) cc_final: 0.8147 (mmt) REVERT: C 8 HIS cc_start: 0.8476 (m90) cc_final: 0.8145 (m90) REVERT: E 13 ARG cc_start: 0.8010 (mmt180) cc_final: 0.7644 (mmt180) REVERT: E 62 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8332 (tm-30) REVERT: G 4 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7358 (mmm) REVERT: G 35 GLN cc_start: 0.8080 (mp10) cc_final: 0.7755 (mp10) REVERT: G 55 TYR cc_start: 0.7761 (p90) cc_final: 0.7330 (p90) REVERT: G 59 THR cc_start: 0.8068 (p) cc_final: 0.7420 (p) REVERT: G 109 LYS cc_start: 0.7998 (ttpt) cc_final: 0.7701 (ptmt) REVERT: H 29 PHE cc_start: 0.8245 (t80) cc_final: 0.7956 (t80) REVERT: H 63 LYS cc_start: 0.8324 (mttp) cc_final: 0.7943 (ttmm) REVERT: L 37 GLN cc_start: 0.6614 (tm130) cc_final: 0.6215 (tm-30) REVERT: L 102 LYS cc_start: 0.8645 (mmmm) cc_final: 0.8275 (mtmm) outliers start: 25 outliers final: 19 residues processed: 168 average time/residue: 0.2156 time to fit residues: 46.6852 Evaluate side-chains 172 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 50 optimal weight: 0.0270 chunk 53 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 ASN L 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6977 Z= 0.184 Angle : 0.646 7.386 9475 Z= 0.334 Chirality : 0.045 0.144 1007 Planarity : 0.004 0.052 1212 Dihedral : 5.844 44.704 1012 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.73 % Allowed : 20.08 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.27), residues: 847 helix: -4.90 (0.46), residues: 14 sheet: -1.44 (0.29), residues: 338 loop : -2.37 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 36 HIS 0.003 0.001 HIS L 33 PHE 0.038 0.002 PHE D 29 TYR 0.019 0.001 TYR G 55 ARG 0.007 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8369 (mmm) cc_final: 0.8110 (mmt) REVERT: C 8 HIS cc_start: 0.8482 (m90) cc_final: 0.8160 (m90) REVERT: E 13 ARG cc_start: 0.7981 (mmt180) cc_final: 0.7378 (mmm160) REVERT: E 37 VAL cc_start: 0.8503 (t) cc_final: 0.8190 (m) REVERT: E 73 ASP cc_start: 0.7533 (t0) cc_final: 0.6741 (p0) REVERT: G 4 MET cc_start: 0.7923 (tpp) cc_final: 0.7328 (mmm) REVERT: G 21 MET cc_start: 0.7493 (mtp) cc_final: 0.7282 (mtt) REVERT: G 35 GLN cc_start: 0.8115 (mp10) cc_final: 0.7808 (mp10) REVERT: G 59 THR cc_start: 0.7908 (p) cc_final: 0.6981 (p) REVERT: H 29 PHE cc_start: 0.8247 (t80) cc_final: 0.7928 (t80) REVERT: H 63 LYS cc_start: 0.8348 (mttp) cc_final: 0.7949 (ttmm) REVERT: L 4 LEU cc_start: 0.7877 (mt) cc_final: 0.7589 (mp) REVERT: L 37 GLN cc_start: 0.6529 (tm130) cc_final: 0.6125 (tm-30) REVERT: L 102 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8233 (mtmm) outliers start: 20 outliers final: 14 residues processed: 179 average time/residue: 0.2115 time to fit residues: 48.7086 Evaluate side-chains 170 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 0.0570 chunk 66 optimal weight: 0.0070 chunk 69 optimal weight: 7.9990 chunk 73 optimal weight: 0.0030 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.3526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6977 Z= 0.197 Angle : 0.679 10.737 9475 Z= 0.351 Chirality : 0.046 0.194 1007 Planarity : 0.004 0.051 1212 Dihedral : 5.698 43.485 1012 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.19 % Allowed : 19.81 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.27), residues: 847 helix: -4.86 (0.48), residues: 14 sheet: -1.34 (0.29), residues: 325 loop : -2.39 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 36 HIS 0.019 0.002 HIS H 35 PHE 0.030 0.002 PHE D 29 TYR 0.052 0.001 TYR G 55 ARG 0.007 0.001 ARG L 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8383 (mmm) cc_final: 0.8134 (mmt) REVERT: C 8 HIS cc_start: 0.8486 (m90) cc_final: 0.8149 (m90) REVERT: E 13 ARG cc_start: 0.7987 (mmt180) cc_final: 0.7568 (mmt180) REVERT: G 35 GLN cc_start: 0.8157 (mp10) cc_final: 0.7895 (mp10) REVERT: H 29 PHE cc_start: 0.8237 (t80) cc_final: 0.7909 (t80) REVERT: H 63 LYS cc_start: 0.8369 (mttp) cc_final: 0.7979 (ttmm) REVERT: L 37 GLN cc_start: 0.6475 (tm130) cc_final: 0.6106 (tm-30) REVERT: L 102 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8174 (mtmm) outliers start: 16 outliers final: 15 residues processed: 172 average time/residue: 0.2131 time to fit residues: 47.2481 Evaluate side-chains 169 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 101 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6977 Z= 0.300 Angle : 0.707 8.778 9475 Z= 0.367 Chirality : 0.048 0.287 1007 Planarity : 0.004 0.047 1212 Dihedral : 6.174 50.280 1012 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.73 % Allowed : 19.67 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.27), residues: 847 helix: -4.88 (0.46), residues: 14 sheet: -1.41 (0.28), residues: 334 loop : -2.43 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 36 HIS 0.005 0.001 HIS H 101 PHE 0.028 0.002 PHE D 29 TYR 0.064 0.002 TYR G 55 ARG 0.008 0.001 ARG D 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8489 (mmm) cc_final: 0.8180 (mmt) REVERT: C 8 HIS cc_start: 0.8507 (m90) cc_final: 0.8159 (m90) REVERT: E 13 ARG cc_start: 0.7989 (mmt180) cc_final: 0.7685 (mmt180) REVERT: E 37 VAL cc_start: 0.8473 (t) cc_final: 0.8256 (m) REVERT: E 62 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8405 (tm-30) REVERT: G 35 GLN cc_start: 0.8120 (mp10) cc_final: 0.7914 (mp10) REVERT: G 109 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7792 (ptmt) REVERT: H 63 LYS cc_start: 0.8375 (mttp) cc_final: 0.7963 (ttmm) REVERT: L 37 GLN cc_start: 0.6660 (tm-30) cc_final: 0.6279 (tm-30) REVERT: L 102 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8166 (mtmm) outliers start: 20 outliers final: 19 residues processed: 165 average time/residue: 0.2017 time to fit residues: 43.0524 Evaluate side-chains 172 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.0370 chunk 65 optimal weight: 0.0770 chunk 27 optimal weight: 0.0270 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107894 restraints weight = 12414.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.110445 restraints weight = 7951.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.112217 restraints weight = 5996.674| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6977 Z= 0.192 Angle : 0.670 8.068 9475 Z= 0.346 Chirality : 0.045 0.174 1007 Planarity : 0.004 0.042 1212 Dihedral : 5.812 45.233 1012 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.05 % Allowed : 20.63 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.27), residues: 847 helix: -4.75 (0.54), residues: 14 sheet: -1.28 (0.29), residues: 324 loop : -2.39 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 36 HIS 0.010 0.002 HIS H 101 PHE 0.026 0.002 PHE D 29 TYR 0.058 0.001 TYR G 55 ARG 0.007 0.001 ARG L 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1899.72 seconds wall clock time: 38 minutes 30.98 seconds (2310.98 seconds total)