Starting phenix.real_space_refine on Tue Feb 13 09:37:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/02_2024/8f0h_28757.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/02_2024/8f0h_28757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/02_2024/8f0h_28757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/02_2024/8f0h_28757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/02_2024/8f0h_28757.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/02_2024/8f0h_28757.pdb" } resolution = 3.18 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= 0.010 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 24 5.16 5 C 3134 2.51 5 N 839 2.21 5 O 962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 46": "OE1" <-> "OE2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 55": "OE1" <-> "OE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 4959 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 960 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Conformer: "A" Number of residues, atoms: 123, 958 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 976 Chain: "C" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1528 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "H" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 887 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.85, per 1000 atoms: 0.78 Number of scatterers: 4959 At special positions: 0 Unit cell: (67.1, 110, 92.4, 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 24 16.00 O 962 8.00 N 839 7.00 C 3134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 M 1 " - " NAG M 2 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG M 1 " - " ASN C 343 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 14 sheets defined 8.4% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.729A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.453A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.232A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.678A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.543A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.709A pdb=" N GLY B 50 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR B 60 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 48 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 33 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 37 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.709A pdb=" N GLY B 50 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR B 60 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 48 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 33 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 37 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 94 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.669A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.382A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 47 removed outlier: 5.303A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP D 91 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS D 96 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.956A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.956A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.158A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.599A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 405 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: 1.34 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1594 1.34 - 1.46: 1215 1.46 - 1.58: 2244 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 5084 Sorted by residual: bond pdb=" N ILE L 75 " pdb=" CA ILE L 75 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" N THR L 72 " pdb=" CA THR L 72 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.53e+00 bond pdb=" N PHE L 73 " pdb=" CA PHE L 73 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.21e-02 6.83e+03 5.86e+00 bond pdb=" N THR L 74 " pdb=" CA THR L 74 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.77e+00 bond pdb=" N SER L 77 " pdb=" CA SER L 77 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.28e-02 6.10e+03 5.16e+00 ... (remaining 5079 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.26: 172 107.26 - 113.94: 2724 113.94 - 120.63: 1923 120.63 - 127.31: 2033 127.31 - 133.99: 56 Bond angle restraints: 6908 Sorted by residual: angle pdb=" N PHE C 338 " pdb=" CA PHE C 338 " pdb=" C PHE C 338 " ideal model delta sigma weight residual 114.56 109.83 4.73 1.27e+00 6.20e-01 1.39e+01 angle pdb=" C ASN L 76 " pdb=" CA ASN L 76 " pdb=" CB ASN L 76 " ideal model delta sigma weight residual 117.23 112.26 4.97 1.36e+00 5.41e-01 1.34e+01 angle pdb=" N ILE L 75 " pdb=" CA ILE L 75 " pdb=" C ILE L 75 " ideal model delta sigma weight residual 113.07 108.17 4.90 1.36e+00 5.41e-01 1.30e+01 angle pdb=" CA LEU L 78 " pdb=" C LEU L 78 " pdb=" O LEU L 78 " ideal model delta sigma weight residual 122.37 118.24 4.13 1.15e+00 7.56e-01 1.29e+01 angle pdb=" N VAL B 64 " pdb=" CA VAL B 64 " pdb=" C VAL B 64 " ideal model delta sigma weight residual 106.21 109.83 -3.62 1.07e+00 8.73e-01 1.15e+01 ... (remaining 6903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 2936 23.94 - 47.88: 66 47.88 - 71.83: 6 71.83 - 95.77: 6 95.77 - 119.71: 1 Dihedral angle restraints: 3015 sinusoidal: 1205 harmonic: 1810 Sorted by residual: dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N ASN L 30 " pdb=" CA ASN L 30 " ideal model delta harmonic sigma weight residual 180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C2 FUC M 3 " pdb=" C1 FUC M 3 " pdb=" O5 FUC M 3 " pdb=" C5 FUC M 3 " ideal model delta sinusoidal sigma weight residual 57.68 -62.03 119.71 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C1 FUC M 3 " pdb=" C5 FUC M 3 " pdb=" O5 FUC M 3 " pdb=" C4 FUC M 3 " ideal model delta sinusoidal sigma weight residual 59.12 -34.07 93.19 1 3.00e+01 1.11e-03 1.13e+01 ... (remaining 3012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 575 0.042 - 0.085: 109 0.085 - 0.127: 54 0.127 - 0.169: 2 0.169 - 0.212: 1 Chirality restraints: 741 Sorted by residual: chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 9.14e-01 chirality pdb=" CA LEU L 78 " pdb=" N LEU L 78 " pdb=" C LEU L 78 " pdb=" CB LEU L 78 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 738 not shown) Planarity restraints: 893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO L 96 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO C 521 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 100 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO H 101 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 101 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 101 " 0.017 5.00e-02 4.00e+02 ... (remaining 890 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1089 2.78 - 3.31: 4566 3.31 - 3.84: 8336 3.84 - 4.37: 10055 4.37 - 4.90: 17201 Nonbonded interactions: 41247 Sorted by model distance: nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.350 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.352 2.440 nonbonded pdb=" OG SER C 469 " pdb=" OE1 GLU C 471 " model vdw 2.372 2.440 nonbonded pdb=" O PHE B 29 " pdb=" NH2 ARG B 72 " model vdw 2.378 2.520 ... (remaining 41242 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.890 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: 22.530 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.310 Find NCS groups from input model: 0.140 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.003 0.035 5084 Z= 0.162 Angle : 0.500 5.351 6908 Z= 0.300 Chirality : 0.040 0.212 741 Planarity : 0.004 0.044 892 Dihedral : 10.682 119.710 1851 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.38 % Allowed : 4.71 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.33), residues: 624 helix: -1.83 (1.16), residues: 21 sheet: 0.74 (0.40), residues: 176 loop : -0.84 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 107 HIS 0.001 0.001 HIS D 96 PHE 0.006 0.001 PHE H 67 TYR 0.018 0.001 TYR L 91 ARG 0.002 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8246 (tp40) cc_final: 0.7954 (mm-40) REVERT: C 385 THR cc_start: 0.8740 (t) cc_final: 0.8465 (p) REVERT: D 77 VAL cc_start: 0.6240 (t) cc_final: 0.5985 (p) REVERT: H 59 TYR cc_start: 0.8847 (m-80) cc_final: 0.8626 (m-80) REVERT: L 82 ASP cc_start: 0.7534 (m-30) cc_final: 0.6658 (m-30) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.2224 time to fit residues: 48.2365 Evaluate side-chains 123 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 37 GLN L 30 ASN L 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5084 Z= 0.255 Angle : 0.655 10.368 6908 Z= 0.344 Chirality : 0.044 0.167 741 Planarity : 0.005 0.047 892 Dihedral : 8.273 102.568 760 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.39 % Allowed : 13.94 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.33), residues: 624 helix: -2.89 (0.82), residues: 27 sheet: 0.60 (0.39), residues: 174 loop : -0.83 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS C 519 PHE 0.022 0.001 PHE C 429 TYR 0.021 0.002 TYR B 80 ARG 0.007 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8203 (m-80) cc_final: 0.7939 (m-80) REVERT: D 50 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.5625 (m-30) REVERT: D 73 THR cc_start: 0.8149 (m) cc_final: 0.7774 (p) REVERT: L 2 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8444 (mp) outliers start: 18 outliers final: 12 residues processed: 144 average time/residue: 0.2098 time to fit residues: 37.0508 Evaluate side-chains 134 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN D 6 GLN D 37 GLN H 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5084 Z= 0.319 Angle : 0.677 11.673 6908 Z= 0.352 Chirality : 0.046 0.178 741 Planarity : 0.005 0.048 892 Dihedral : 7.963 92.593 760 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.90 % Allowed : 16.76 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.32), residues: 624 helix: -2.92 (0.81), residues: 27 sheet: 0.45 (0.39), residues: 182 loop : -1.06 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 PHE 0.012 0.002 PHE H 79 TYR 0.023 0.002 TYR B 80 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8114 (m-80) cc_final: 0.7897 (m-80) REVERT: D 50 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6545 (m-30) REVERT: D 52 ASP cc_start: 0.7914 (m-30) cc_final: 0.7682 (m-30) REVERT: D 53 ARG cc_start: 0.8194 (ttm110) cc_final: 0.7941 (ttm110) REVERT: D 73 THR cc_start: 0.8216 (m) cc_final: 0.7889 (p) outliers start: 26 outliers final: 15 residues processed: 130 average time/residue: 0.2688 time to fit residues: 43.3758 Evaluate side-chains 129 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5084 Z= 0.267 Angle : 0.648 12.250 6908 Z= 0.335 Chirality : 0.044 0.154 741 Planarity : 0.005 0.051 892 Dihedral : 7.534 83.598 760 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.27 % Allowed : 16.76 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.32), residues: 624 helix: -2.69 (0.84), residues: 27 sheet: 0.37 (0.39), residues: 175 loop : -1.08 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 34 HIS 0.003 0.001 HIS C 519 PHE 0.010 0.001 PHE H 79 TYR 0.024 0.002 TYR B 80 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8562 (p0) cc_final: 0.8254 (p0) REVERT: B 43 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7724 (mmtm) REVERT: B 87 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6867 (mtm180) REVERT: C 386 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8866 (mmtt) REVERT: D 6 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6640 (pt0) REVERT: D 50 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6261 (m-30) REVERT: D 52 ASP cc_start: 0.8054 (m-30) cc_final: 0.7827 (m-30) REVERT: D 53 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7901 (ttm110) outliers start: 28 outliers final: 17 residues processed: 134 average time/residue: 0.2348 time to fit residues: 38.3862 Evaluate side-chains 132 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.0570 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 37 GLN H 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5084 Z= 0.295 Angle : 0.658 13.008 6908 Z= 0.338 Chirality : 0.045 0.181 741 Planarity : 0.005 0.054 892 Dihedral : 7.123 73.092 760 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.90 % Allowed : 17.14 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.32), residues: 624 helix: -2.75 (0.82), residues: 27 sheet: 0.15 (0.37), residues: 184 loop : -1.04 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 PHE 0.010 0.001 PHE H 79 TYR 0.023 0.002 TYR B 80 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7552 (tp-100) REVERT: B 30 ASP cc_start: 0.8551 (p0) cc_final: 0.8351 (p0) REVERT: B 87 ARG cc_start: 0.7237 (mtm-85) cc_final: 0.6946 (mtm180) REVERT: D 50 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6407 (m-30) REVERT: D 52 ASP cc_start: 0.8129 (m-30) cc_final: 0.7878 (m-30) REVERT: D 53 ARG cc_start: 0.8192 (ttm110) cc_final: 0.7929 (ttm110) REVERT: L 78 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7612 (tt) outliers start: 26 outliers final: 17 residues processed: 131 average time/residue: 0.2181 time to fit residues: 34.7798 Evaluate side-chains 134 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.0270 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 57 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN H 3 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5084 Z= 0.194 Angle : 0.622 12.061 6908 Z= 0.318 Chirality : 0.043 0.161 741 Planarity : 0.005 0.052 892 Dihedral : 6.553 59.368 760 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.77 % Allowed : 18.64 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.32), residues: 624 helix: -2.83 (0.79), residues: 27 sheet: 0.35 (0.39), residues: 177 loop : -1.03 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 PHE 0.008 0.001 PHE H 79 TYR 0.023 0.001 TYR B 80 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7582 (tp-100) REVERT: B 76 LYS cc_start: 0.9076 (ptpp) cc_final: 0.8741 (ptpp) REVERT: B 87 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.7068 (mtm180) REVERT: C 478 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8167 (p) REVERT: D 52 ASP cc_start: 0.8071 (m-30) cc_final: 0.7798 (m-30) REVERT: D 53 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7868 (ttm110) REVERT: L 82 ASP cc_start: 0.7334 (m-30) cc_final: 0.6798 (m-30) outliers start: 20 outliers final: 15 residues processed: 129 average time/residue: 0.2311 time to fit residues: 36.3916 Evaluate side-chains 132 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN H 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5084 Z= 0.260 Angle : 0.639 11.722 6908 Z= 0.329 Chirality : 0.044 0.178 741 Planarity : 0.005 0.051 892 Dihedral : 6.085 55.627 760 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.08 % Allowed : 17.51 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.32), residues: 624 helix: -2.83 (0.79), residues: 27 sheet: 0.19 (0.38), residues: 181 loop : -0.98 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 PHE 0.010 0.001 PHE H 79 TYR 0.023 0.002 TYR B 80 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: B 31 ASP cc_start: 0.8184 (m-30) cc_final: 0.7926 (m-30) REVERT: B 76 LYS cc_start: 0.9080 (ptpp) cc_final: 0.8756 (ptpp) REVERT: B 87 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.7107 (mtm180) REVERT: C 386 LYS cc_start: 0.9080 (mmtm) cc_final: 0.8866 (mmtt) REVERT: D 50 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6410 (m-30) REVERT: D 52 ASP cc_start: 0.8226 (m-30) cc_final: 0.7879 (m-30) REVERT: D 53 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7838 (ttm110) outliers start: 27 outliers final: 21 residues processed: 131 average time/residue: 0.2151 time to fit residues: 34.2519 Evaluate side-chains 139 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5084 Z= 0.320 Angle : 0.665 11.143 6908 Z= 0.345 Chirality : 0.045 0.188 741 Planarity : 0.005 0.054 892 Dihedral : 5.718 55.666 760 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.14 % Allowed : 18.46 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.32), residues: 624 helix: -2.82 (0.80), residues: 27 sheet: 0.16 (0.38), residues: 179 loop : -0.99 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS H 104 PHE 0.011 0.001 PHE H 79 TYR 0.026 0.002 TYR B 80 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: B 31 ASP cc_start: 0.8167 (m-30) cc_final: 0.7891 (m-30) REVERT: B 76 LYS cc_start: 0.9077 (ptpp) cc_final: 0.8745 (ptpp) REVERT: B 87 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7141 (mtm180) REVERT: C 386 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8821 (mmtt) REVERT: D 50 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6519 (m-30) REVERT: D 52 ASP cc_start: 0.8291 (m-30) cc_final: 0.7952 (m-30) REVERT: D 53 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7957 (ttm110) outliers start: 22 outliers final: 20 residues processed: 126 average time/residue: 0.2267 time to fit residues: 35.1048 Evaluate side-chains 135 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 chunk 40 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5084 Z= 0.269 Angle : 0.635 9.935 6908 Z= 0.333 Chirality : 0.045 0.180 741 Planarity : 0.005 0.053 892 Dihedral : 5.415 54.624 760 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.14 % Allowed : 19.21 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.32), residues: 624 helix: -2.78 (0.80), residues: 27 sheet: 0.17 (0.39), residues: 175 loop : -0.99 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 PHE 0.011 0.001 PHE H 27 TYR 0.025 0.002 TYR B 80 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7510 (mp10) cc_final: 0.7300 (mp10) REVERT: B 31 ASP cc_start: 0.8090 (m-30) cc_final: 0.7797 (m-30) REVERT: B 76 LYS cc_start: 0.9061 (ptpp) cc_final: 0.8734 (ptpp) REVERT: B 87 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.6990 (mtm-85) REVERT: C 386 LYS cc_start: 0.9084 (mmtm) cc_final: 0.8801 (mmtt) REVERT: D 50 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6521 (m-30) REVERT: D 52 ASP cc_start: 0.8298 (m-30) cc_final: 0.7980 (m-30) outliers start: 22 outliers final: 19 residues processed: 127 average time/residue: 0.2270 time to fit residues: 35.2790 Evaluate side-chains 136 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5084 Z= 0.282 Angle : 0.661 10.999 6908 Z= 0.347 Chirality : 0.045 0.172 741 Planarity : 0.005 0.051 892 Dihedral : 5.456 55.676 760 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.95 % Allowed : 19.77 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.32), residues: 624 helix: -2.79 (0.79), residues: 27 sheet: 0.10 (0.39), residues: 175 loop : -0.95 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.002 0.001 HIS H 104 PHE 0.011 0.001 PHE H 27 TYR 0.026 0.002 TYR B 80 ARG 0.009 0.001 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.632 Fit side-chains REVERT: B 31 ASP cc_start: 0.8071 (m-30) cc_final: 0.7769 (m-30) REVERT: B 76 LYS cc_start: 0.9068 (ptpp) cc_final: 0.8734 (ptpp) REVERT: B 87 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.7118 (mtm-85) REVERT: C 386 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8839 (mmtt) REVERT: D 50 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6506 (m-30) REVERT: D 52 ASP cc_start: 0.8296 (m-30) cc_final: 0.7982 (m-30) REVERT: D 99 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7015 (t80) REVERT: L 78 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8000 (tt) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 0.2262 time to fit residues: 33.7891 Evaluate side-chains 133 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 0.0170 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076972 restraints weight = 10210.646| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.08 r_work: 0.2989 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5084 Z= 0.240 Angle : 0.633 8.848 6908 Z= 0.332 Chirality : 0.044 0.166 741 Planarity : 0.005 0.051 892 Dihedral : 5.397 55.197 760 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.95 % Allowed : 19.96 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.32), residues: 624 helix: -2.79 (0.79), residues: 27 sheet: 0.18 (0.39), residues: 175 loop : -0.92 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.002 0.001 HIS H 104 PHE 0.012 0.001 PHE H 27 TYR 0.025 0.002 TYR B 80 ARG 0.009 0.001 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1901.68 seconds wall clock time: 34 minutes 56.92 seconds (2096.92 seconds total)