Starting phenix.real_space_refine on Tue Feb 13 15:56:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/02_2024/7wp8_32678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/02_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_32678/02_2024/7wp8_32678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/02_2024/7wp8_32678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/02_2024/7wp8_32678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp8_32678/02_2024/7wp8_32678.pdb" } 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 Residue "C ARG 18": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ARG 408": "NH1" <-> "NH2" Residue "F GLU 465": "OE1" <-> "OE2" Residue "F ARG 466": "NH1" <-> "NH2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.08, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.73 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: 1.62 Time building geometry restraints manager: 2.67 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: 99.13 - 106.21: 180 106.21 - 113.28: 3562 113.28 - 120.36: 2585 120.36 - 127.44: 3064 127.44 - 134.52: 84 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 2.440 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 2.440 nonbonded pdb=" OG SER C 43 " pdb=" O GLY D 111 " model vdw 2.283 2.440 nonbonded pdb=" O THR H 112 " pdb=" OG1 THR H 112 " model vdw 2.296 2.440 ... (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 ========== 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: 3.160 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: 13.230 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.510 Find NCS groups from input model: 0.230 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.210 ------------------------------------------------------------------------------- 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 : 0.759 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: 0.2239 time to fit residues: 62.1728 Evaluate side-chains 165 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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: 7.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 74 optimal weight: 4.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 89 GLN D 39 GLN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1950 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= 0.205 Angle : 0.633 6.379 9475 Z= 0.334 Chirality : 0.045 0.177 1007 Planarity : 0.005 0.071 1212 Dihedral : 6.456 82.331 1012 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.19 % Allowed : 14.62 % 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: -3.63 (0.26), residues: 847 helix: -4.74 (0.70), residues: 8 sheet: -1.82 (0.29), residues: 310 loop : -2.89 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 36 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE F 456 TYR 0.025 0.002 TYR E 32 ARG 0.007 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: 16 poor density : 179 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8485 (mmm) cc_final: 0.8220 (mmt) REVERT: E 13 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7385 (mtp85) REVERT: G 35 GLN cc_start: 0.7989 (mp10) cc_final: 0.7660 (mp10) REVERT: G 55 TYR cc_start: 0.7851 (p90) cc_final: 0.7566 (p90) REVERT: G 78 THR cc_start: 0.9104 (p) cc_final: 0.8878 (p) REVERT: H 29 PHE cc_start: 0.7922 (t80) cc_final: 0.7619 (t80) REVERT: L 32 MET cc_start: 0.7794 (mtp) cc_final: 0.7588 (mtp) REVERT: L 37 GLN cc_start: 0.6464 (tm130) cc_final: 0.5955 (tm-30) REVERT: L 102 LYS cc_start: 0.8467 (mmmm) cc_final: 0.8124 (mtmm) outliers start: 16 outliers final: 11 residues processed: 185 average time/residue: 0.2374 time to fit residues: 55.7650 Evaluate side-chains 174 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 ASP 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 H residue 101 HIS 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: 0.7980 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN D 43 GLN ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6977 Z= 0.215 Angle : 0.615 6.409 9475 Z= 0.321 Chirality : 0.045 0.202 1007 Planarity : 0.004 0.047 1212 Dihedral : 6.308 80.160 1012 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.28 % Allowed : 15.16 % Favored : 81.56 % 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: -3.53 (0.26), residues: 847 helix: -4.81 (0.63), residues: 8 sheet: -1.69 (0.30), residues: 296 loop : -2.84 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 36 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE F 456 TYR 0.015 0.001 TYR D 104 ARG 0.004 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: 24 poor density : 166 time to evaluate : 0.797 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: C 4 MET cc_start: 0.8492 (mmm) cc_final: 0.8232 (mmt) REVERT: C 89 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: E 13 ARG cc_start: 0.8071 (mmt180) cc_final: 0.7406 (mtp85) REVERT: E 111 GLN cc_start: 0.8685 (mp10) cc_final: 0.8378 (mp10) REVERT: G 33 TYR cc_start: 0.7118 (m-10) cc_final: 0.6903 (m-10) REVERT: G 35 GLN cc_start: 0.7993 (mp10) cc_final: 0.7642 (mp10) REVERT: G 55 TYR cc_start: 0.7788 (p90) cc_final: 0.7508 (p90) REVERT: G 78 THR cc_start: 0.9102 (p) cc_final: 0.8889 (p) REVERT: H 29 PHE cc_start: 0.8021 (t80) cc_final: 0.7707 (t80) REVERT: L 37 GLN cc_start: 0.6540 (tm130) cc_final: 0.6079 (tm-30) REVERT: L 102 LYS cc_start: 0.8515 (mmmm) cc_final: 0.8144 (mtmt) outliers start: 24 outliers final: 19 residues processed: 173 average time/residue: 0.2189 time to fit residues: 48.3628 Evaluate side-chains 178 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 60 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 30 THR 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 H residue 112 THR Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 0.1980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6977 Z= 0.175 Angle : 0.583 8.075 9475 Z= 0.304 Chirality : 0.043 0.159 1007 Planarity : 0.004 0.044 1212 Dihedral : 6.032 77.341 1012 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.87 % Allowed : 15.85 % Favored : 81.28 % 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 (0.26), residues: 847 helix: -4.61 (0.79), residues: 8 sheet: -1.42 (0.31), residues: 297 loop : -2.77 (0.23), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 36 HIS 0.003 0.001 HIS H 101 PHE 0.011 0.001 PHE L 97 TYR 0.017 0.001 TYR G 55 ARG 0.004 0.000 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 192 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 0.781 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: symmetry clash REVERT: C 4 MET cc_start: 0.8433 (mmm) cc_final: 0.8171 (mmt) REVERT: D 29 PHE cc_start: 0.8521 (t80) cc_final: 0.8303 (t80) REVERT: E 13 ARG cc_start: 0.8064 (mmt180) cc_final: 0.7400 (mtp85) REVERT: E 111 GLN cc_start: 0.8674 (mp10) cc_final: 0.8354 (mp10) REVERT: G 13 MET cc_start: 0.7028 (tpt) cc_final: 0.5976 (tpt) REVERT: G 35 GLN cc_start: 0.8008 (mp10) cc_final: 0.7684 (mp10) REVERT: G 78 THR cc_start: 0.9117 (p) cc_final: 0.8906 (p) REVERT: H 29 PHE cc_start: 0.8039 (t80) cc_final: 0.7728 (t80) REVERT: L 37 GLN cc_start: 0.6474 (tm130) cc_final: 0.6036 (tm-30) REVERT: L 102 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8108 (mtmm) outliers start: 21 outliers final: 16 residues processed: 179 average time/residue: 0.2209 time to fit residues: 50.6229 Evaluate side-chains 175 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 GLN 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 F residue 489 TYR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 30 THR 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 112 THR 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: 2.9990 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6977 Z= 0.271 Angle : 0.628 8.007 9475 Z= 0.328 Chirality : 0.045 0.173 1007 Planarity : 0.004 0.049 1212 Dihedral : 6.393 78.717 1012 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 3.96 % Allowed : 15.71 % Favored : 80.33 % 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: -3.27 (0.27), residues: 847 helix: -5.00 (0.44), residues: 14 sheet: -1.57 (0.29), residues: 321 loop : -2.59 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 36 HIS 0.005 0.001 HIS H 101 PHE 0.017 0.002 PHE D 107 TYR 0.013 0.001 TYR F 489 ARG 0.003 0.000 ARG D 99 *********************** 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 192 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8567 (mmm) cc_final: 0.8272 (mmt) REVERT: D 29 PHE cc_start: 0.8529 (t80) cc_final: 0.8318 (t80) REVERT: E 13 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7509 (mtp85) REVERT: E 103 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6968 (mm-30) REVERT: F 454 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8374 (ttm110) REVERT: G 35 GLN cc_start: 0.8047 (mp10) cc_final: 0.7703 (mp10) REVERT: G 55 TYR cc_start: 0.8014 (p90) cc_final: 0.7786 (p90) REVERT: H 29 PHE cc_start: 0.8122 (t80) cc_final: 0.7831 (t80) REVERT: L 17 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7534 (mm-30) REVERT: L 37 GLN cc_start: 0.6637 (tm130) cc_final: 0.6182 (tm-30) REVERT: L 102 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8111 (mtmm) outliers start: 29 outliers final: 26 residues processed: 174 average time/residue: 0.2226 time to fit residues: 49.1570 Evaluate side-chains 182 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 89 GLN 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 E residue 87 THR Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 481 ASN 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 H residue 30 THR Chi-restraints excluded: chain H residue 69 THR 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 H residue 112 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.0170 chunk 46 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3024 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= 0.188 Angle : 0.597 6.628 9475 Z= 0.311 Chirality : 0.044 0.247 1007 Planarity : 0.004 0.045 1212 Dihedral : 6.172 76.195 1012 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.14 % Allowed : 17.90 % Favored : 78.96 % 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: -3.08 (0.27), residues: 847 helix: -4.94 (0.49), residues: 14 sheet: -1.39 (0.29), residues: 334 loop : -2.52 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 36 HIS 0.003 0.001 HIS H 101 PHE 0.018 0.001 PHE G 104 TYR 0.013 0.001 TYR D 104 ARG 0.004 0.000 ARG D 99 *********************** 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 181 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 0.823 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: C 4 MET cc_start: 0.8517 (mmm) cc_final: 0.8243 (mmt) REVERT: C 89 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: D 29 PHE cc_start: 0.8482 (t80) cc_final: 0.8278 (t80) REVERT: E 13 ARG cc_start: 0.8082 (mmt180) cc_final: 0.7495 (mtp85) REVERT: F 454 ARG cc_start: 0.8631 (tpp80) cc_final: 0.8096 (ttp80) REVERT: G 4 MET cc_start: 0.8112 (tpp) cc_final: 0.7745 (mmt) REVERT: G 35 GLN cc_start: 0.8038 (mp10) cc_final: 0.7668 (mp10) REVERT: G 55 TYR cc_start: 0.7886 (p90) cc_final: 0.7604 (p90) REVERT: H 29 PHE cc_start: 0.8141 (t80) cc_final: 0.7834 (t80) REVERT: L 37 GLN cc_start: 0.6579 (tm130) cc_final: 0.6131 (tm-30) REVERT: L 102 LYS cc_start: 0.8461 (mmmm) cc_final: 0.8079 (mtmm) outliers start: 23 outliers final: 20 residues processed: 169 average time/residue: 0.2236 time to fit residues: 48.1756 Evaluate side-chains 175 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 89 GLN 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 22 CYS Chi-restraints excluded: chain E residue 42 GLU 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 430 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 30 THR 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 H residue 112 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: 6.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6977 Z= 0.185 Angle : 0.596 6.816 9475 Z= 0.310 Chirality : 0.044 0.257 1007 Planarity : 0.004 0.042 1212 Dihedral : 6.045 74.919 1012 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.83 % Allowed : 17.62 % Favored : 78.55 % 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: -2.97 (0.27), residues: 847 helix: -4.39 (0.98), residues: 8 sheet: -1.26 (0.29), residues: 334 loop : -2.54 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 36 HIS 0.003 0.001 HIS H 35 PHE 0.022 0.001 PHE C 71 TYR 0.013 0.001 TYR G 55 ARG 0.003 0.000 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 189 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 0.808 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: C 4 MET cc_start: 0.8497 (mmm) cc_final: 0.8287 (mmt) REVERT: E 13 ARG cc_start: 0.8078 (mmt180) cc_final: 0.7471 (mtp85) REVERT: E 73 ASP cc_start: 0.7134 (t0) cc_final: 0.6582 (p0) REVERT: F 454 ARG cc_start: 0.8649 (tpp80) cc_final: 0.8034 (ttp80) REVERT: G 4 MET cc_start: 0.8106 (tpp) cc_final: 0.7860 (mmt) REVERT: G 35 GLN cc_start: 0.8032 (mp10) cc_final: 0.7657 (mp10) REVERT: G 55 TYR cc_start: 0.7826 (p90) cc_final: 0.7489 (p90) REVERT: H 29 PHE cc_start: 0.8141 (t80) cc_final: 0.7857 (t80) REVERT: L 37 GLN cc_start: 0.6559 (tm130) cc_final: 0.6108 (tm-30) REVERT: L 102 LYS cc_start: 0.8450 (mmmm) cc_final: 0.8057 (mtmm) outliers start: 28 outliers final: 24 residues processed: 175 average time/residue: 0.2125 time to fit residues: 47.7892 Evaluate side-chains 176 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 60 ASP 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 22 CYS Chi-restraints excluded: chain E residue 42 GLU 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 430 THR Chi-restraints excluded: chain F residue 481 ASN 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 H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE 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 H residue 112 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: 3.9990 chunk 15 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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: 0.7831 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6977 Z= 0.222 Angle : 0.614 7.369 9475 Z= 0.321 Chirality : 0.045 0.277 1007 Planarity : 0.004 0.041 1212 Dihedral : 6.154 75.434 1012 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.55 % Allowed : 18.17 % Favored : 78.28 % 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 (0.56), residues: 14 sheet: -1.25 (0.30), residues: 328 loop : -2.47 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 36 HIS 0.005 0.001 HIS H 101 PHE 0.017 0.001 PHE H 107 TYR 0.016 0.001 TYR G 55 ARG 0.003 0.000 ARG D 99 *********************** 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 186 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 0.843 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: 0.8467 (mmm) cc_final: 0.8192 (mmt) REVERT: D 55 ASP cc_start: 0.8201 (p0) cc_final: 0.7669 (t0) REVERT: E 13 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7519 (mtp85) REVERT: G 35 GLN cc_start: 0.8044 (mp10) cc_final: 0.7649 (mp10) REVERT: G 55 TYR cc_start: 0.7819 (p90) cc_final: 0.7610 (p90) REVERT: H 29 PHE cc_start: 0.8180 (t80) cc_final: 0.7883 (t80) REVERT: L 37 GLN cc_start: 0.6562 (tm130) cc_final: 0.6058 (tm-30) REVERT: L 102 LYS cc_start: 0.8453 (mmmm) cc_final: 0.8034 (mtmm) outliers start: 26 outliers final: 25 residues processed: 171 average time/residue: 0.2099 time to fit residues: 46.1475 Evaluate side-chains 178 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 60 ASP 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 22 CYS Chi-restraints excluded: chain E residue 42 GLU 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 430 THR Chi-restraints excluded: chain F residue 481 ASN 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 H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE 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 H residue 112 THR Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.6980 chunk 44 optimal weight: 0.0060 chunk 32 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.2396 ------------------------------------------------------------------------------- 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 ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 6977 Z= 0.158 Angle : 0.600 7.731 9475 Z= 0.308 Chirality : 0.044 0.274 1007 Planarity : 0.004 0.039 1212 Dihedral : 5.701 70.699 1012 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.19 % Allowed : 18.85 % Favored : 78.96 % 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: -2.78 (0.27), residues: 847 helix: -4.14 (1.19), residues: 8 sheet: -1.04 (0.30), residues: 324 loop : -2.46 (0.24), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 36 HIS 0.003 0.001 HIS L 33 PHE 0.017 0.001 PHE F 464 TYR 0.017 0.001 TYR G 55 ARG 0.003 0.000 ARG D 99 *********************** 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 184 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 0.805 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: C 4 MET cc_start: 0.8399 (mmm) cc_final: 0.8085 (mmt) REVERT: D 55 ASP cc_start: 0.8098 (p0) cc_final: 0.7495 (t0) REVERT: E 13 ARG cc_start: 0.8044 (mmt180) cc_final: 0.7488 (mtp85) REVERT: F 454 ARG cc_start: 0.8620 (tpp80) cc_final: 0.8031 (tpp80) REVERT: G 35 GLN cc_start: 0.8083 (mp10) cc_final: 0.7711 (mp10) REVERT: H 29 PHE cc_start: 0.8188 (t80) cc_final: 0.7905 (t80) REVERT: H 56 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7361 (t) REVERT: H 63 LYS cc_start: 0.8417 (mttp) cc_final: 0.7989 (ttmm) REVERT: L 37 GLN cc_start: 0.6499 (tm130) cc_final: 0.5990 (tm-30) outliers start: 16 outliers final: 14 residues processed: 177 average time/residue: 0.2224 time to fit residues: 51.1395 Evaluate side-chains 175 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 42 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 481 ASN 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 51 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6977 Z= 0.221 Angle : 0.651 11.873 9475 Z= 0.332 Chirality : 0.046 0.292 1007 Planarity : 0.004 0.061 1212 Dihedral : 6.007 72.498 1012 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 1.91 % Allowed : 20.36 % 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: -2.74 (0.28), residues: 847 helix: -4.60 (0.78), residues: 8 sheet: -0.89 (0.31), residues: 317 loop : -2.51 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 36 HIS 0.004 0.001 HIS H 101 PHE 0.015 0.002 PHE G 104 TYR 0.051 0.002 TYR G 55 ARG 0.004 0.000 ARG F 457 ********************** 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 168 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 0.773 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: 0.8496 (mmm) cc_final: 0.8185 (mmt) REVERT: D 55 ASP cc_start: 0.8221 (p0) cc_final: 0.7589 (t0) REVERT: E 13 ARG cc_start: 0.8059 (mmt180) cc_final: 0.7495 (mtp85) REVERT: E 73 ASP cc_start: 0.7113 (t0) cc_final: 0.6822 (p0) REVERT: G 35 GLN cc_start: 0.8043 (mp10) cc_final: 0.7662 (mp10) REVERT: H 29 PHE cc_start: 0.8227 (t80) cc_final: 0.7926 (t80) REVERT: H 63 LYS cc_start: 0.8422 (mttp) cc_final: 0.7999 (ttmm) REVERT: L 37 GLN cc_start: 0.6498 (tm-30) cc_final: 0.6001 (tm-30) outliers start: 14 outliers final: 14 residues processed: 162 average time/residue: 0.2159 time to fit residues: 45.0565 Evaluate side-chains 168 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 42 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 481 ASN 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 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107823 restraints weight = 12360.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110430 restraints weight = 7905.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112197 restraints weight = 5897.672| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6977 Z= 0.181 Angle : 0.628 8.072 9475 Z= 0.318 Chirality : 0.045 0.283 1007 Planarity : 0.004 0.052 1212 Dihedral : 5.856 70.995 1012 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.05 % Allowed : 20.36 % 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: -2.73 (0.28), residues: 847 helix: -4.59 (0.79), residues: 8 sheet: -0.84 (0.31), residues: 307 loop : -2.50 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 36 HIS 0.003 0.001 HIS H 35 PHE 0.024 0.001 PHE D 64 TYR 0.051 0.001 TYR G 55 ARG 0.002 0.000 ARG D 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.07 seconds wall clock time: 37 minutes 31.60 seconds (2251.60 seconds total)