Starting phenix.real_space_refine on Thu Mar 14 23:58:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn2_25209/03_2024/7sn2_25209_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn2_25209/03_2024/7sn2_25209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn2_25209/03_2024/7sn2_25209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn2_25209/03_2024/7sn2_25209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn2_25209/03_2024/7sn2_25209_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn2_25209/03_2024/7sn2_25209_neut_trim.pdb" } resolution = 4.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 3284 2.51 5 N 868 2.21 5 O 1016 1.98 5 H 4904 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 165": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10092 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3477 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 13, 'TRANS': 209} Chain: "H" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3236 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3251 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 89 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.77, per 1000 atoms: 0.57 Number of scatterers: 10092 At special positions: 0 Unit cell: (85.8, 113.85, 99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1016 8.00 N 868 7.00 C 3284 6.00 H 4904 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-2 " MAN C 4 " - " NAG C 5 " " MAN C 6 " - " NAG C 7 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 331 " " NAG C 1 " - " ASN A 343 " Time building additional restraints: 10.06 Conformation dependent library (CDL) restraints added in 1.7 seconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 11.4% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 322 through 326 removed outlier: 4.062A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 326 " --> pdb=" O THR A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.084A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.690A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.562A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 187 through 192 removed outlier: 4.389A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.580A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 4.211A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.914A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 120 through 122 removed outlier: 5.924A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 120 through 122 removed outlier: 5.924A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.457A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.507A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.746A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 145 through 149 178 hydrogen bonds defined for protein. 426 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: 3.52 Time building geometry restraints manager: 10.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 4900 1.04 - 1.24: 685 1.24 - 1.44: 1708 1.44 - 1.64: 2905 1.64 - 1.85: 22 Bond restraints: 10220 Sorted by residual: bond pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " ideal model delta sigma weight residual 1.530 1.569 -0.039 1.58e-02 4.01e+03 6.05e+00 bond pdb=" C2 MAN C 6 " pdb=" O2 MAN C 6 " ideal model delta sigma weight residual 1.407 1.454 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" CB THR A 385 " pdb=" CG2 THR A 385 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.88e+00 bond pdb=" CA ALA A 435 " pdb=" C ALA A 435 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.31e-02 5.83e+03 4.69e+00 bond pdb=" C6 BMA C 3 " pdb=" O6 BMA C 3 " ideal model delta sigma weight residual 1.411 1.453 -0.042 2.00e-02 2.50e+03 4.37e+00 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 87.44 - 97.00: 3 97.00 - 106.56: 437 106.56 - 116.12: 12332 116.12 - 125.68: 5378 125.68 - 135.24: 158 Bond angle restraints: 18308 Sorted by residual: angle pdb=" N LYS A 529 " pdb=" CA LYS A 529 " pdb=" C LYS A 529 " ideal model delta sigma weight residual 111.02 120.97 -9.95 1.22e+00 6.72e-01 6.65e+01 angle pdb=" N ASN A 437 " pdb=" CA ASN A 437 " pdb=" CB ASN A 437 " ideal model delta sigma weight residual 109.97 98.40 11.57 1.47e+00 4.63e-01 6.20e+01 angle pdb=" HB2 ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB3 ASN A 437 " ideal model delta sigma weight residual 110.00 89.16 20.84 3.00e+00 1.11e-01 4.82e+01 angle pdb=" CG ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB2 ASN A 437 " ideal model delta sigma weight residual 108.00 87.44 20.56 3.00e+00 1.11e-01 4.70e+01 angle pdb=" CA ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB2 ASN A 437 " ideal model delta sigma weight residual 109.00 88.49 20.51 3.00e+00 1.11e-01 4.67e+01 ... (remaining 18303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.01: 4717 25.01 - 50.02: 278 50.02 - 75.03: 48 75.03 - 100.04: 17 100.04 - 125.05: 9 Dihedral angle restraints: 5069 sinusoidal: 2787 harmonic: 2282 Sorted by residual: dihedral pdb=" CA SER A 530 " pdb=" C SER A 530 " pdb=" N THR A 531 " pdb=" CA THR A 531 " ideal model delta harmonic sigma weight residual 180.00 136.70 43.30 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 17.59 75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CA VAL A 395 " pdb=" C VAL A 395 " pdb=" N TYR A 396 " pdb=" CA TYR A 396 " ideal model delta harmonic sigma weight residual -180.00 -143.39 -36.61 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 5066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 756 0.118 - 0.237: 61 0.237 - 0.355: 8 0.355 - 0.474: 1 0.474 - 0.592: 1 Chirality restraints: 827 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.34e+02 chirality pdb=" C1 NAG C 7 " pdb=" O2 MAN C 6 " pdb=" C2 NAG C 7 " pdb=" O5 NAG C 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.05e+02 chirality pdb=" C1 NAG C 5 " pdb=" O2 MAN C 4 " pdb=" C2 NAG C 5 " pdb=" O5 NAG C 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 2.01e+02 ... (remaining 824 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 91 " 0.527 9.50e-02 1.11e+02 1.76e-01 3.40e+01 pdb=" NE ARG L 91 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG L 91 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG L 91 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 91 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG L 91 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG L 91 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG L 91 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG L 91 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 99 " 0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ARG H 99 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG H 99 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP H 100 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 94 " -0.371 9.50e-02 1.11e+02 1.24e-01 1.67e+01 pdb=" NE ARG H 94 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG H 94 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 94 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 94 " -0.010 2.00e-02 2.50e+03 pdb="HH11 ARG H 94 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG H 94 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG H 94 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 94 " -0.001 2.00e-02 2.50e+03 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 195 2.11 - 2.73: 16965 2.73 - 3.35: 27854 3.35 - 3.98: 35537 3.98 - 4.60: 53717 Nonbonded interactions: 134268 Sorted by model distance: nonbonded pdb=" O ALA A 372 " pdb="HH22 ARG H 100D" model vdw 1.482 1.850 nonbonded pdb="HD21 ASN A 370 " pdb=" HH TYR H 58 " model vdw 1.545 2.100 nonbonded pdb="HH22 ARG A 328 " pdb=" O LYS A 528 " model vdw 1.611 1.850 nonbonded pdb=" H SER H 156 " pdb=" OD1 ASN H 197 " model vdw 1.680 1.850 nonbonded pdb=" H LYS A 462 " pdb=" OE2 GLU A 465 " model vdw 1.686 1.850 ... (remaining 134263 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: 0.700 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: 0.180 Extract box with map and model: 3.500 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 39.260 Find NCS groups from input model: 0.220 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.007 0.073 5316 Z= 0.466 Angle : 1.308 12.656 7236 Z= 0.712 Chirality : 0.073 0.592 827 Planarity : 0.013 0.236 916 Dihedral : 17.661 125.050 2052 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.78 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -1.92 (0.32), residues: 642 helix: -2.74 (0.79), residues: 32 sheet: -0.58 (0.35), residues: 222 loop : -1.61 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 436 HIS 0.009 0.003 HIS H 35 PHE 0.047 0.004 PHE A 329 TYR 0.052 0.004 TYR A 508 ARG 0.010 0.001 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.785 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7930 (m-30) cc_final: 0.7578 (m-30) REVERT: A 428 ASP cc_start: 0.8175 (t70) cc_final: 0.7963 (t70) REVERT: H 34 MET cc_start: 0.7390 (mmt) cc_final: 0.7137 (mmt) REVERT: H 46 GLU cc_start: 0.7527 (tt0) cc_final: 0.6900 (pt0) REVERT: L 13 LEU cc_start: 0.7664 (tp) cc_final: 0.7422 (tp) REVERT: L 189 HIS cc_start: 0.6327 (t-90) cc_final: 0.5910 (t70) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3675 time to fit residues: 65.8772 Evaluate side-chains 117 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5316 Z= 0.229 Angle : 0.748 8.307 7236 Z= 0.391 Chirality : 0.049 0.429 827 Planarity : 0.007 0.101 916 Dihedral : 14.327 106.617 917 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.79 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.32), residues: 642 helix: -3.33 (0.58), residues: 38 sheet: -0.07 (0.35), residues: 221 loop : -1.46 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 100C HIS 0.005 0.002 HIS L 189 PHE 0.025 0.002 PHE A 329 TYR 0.022 0.002 TYR A 396 ARG 0.004 0.001 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.761 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7866 (m-30) cc_final: 0.7534 (m-30) REVERT: H 34 MET cc_start: 0.7347 (mmt) cc_final: 0.7116 (mmt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3566 time to fit residues: 61.7959 Evaluate side-chains 115 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 48 optimal weight: 0.0010 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 58 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5316 Z= 0.215 Angle : 0.696 7.563 7236 Z= 0.358 Chirality : 0.048 0.354 827 Planarity : 0.007 0.101 916 Dihedral : 12.819 104.354 917 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.54 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.33), residues: 642 helix: -3.22 (0.57), residues: 38 sheet: -0.09 (0.34), residues: 223 loop : -1.37 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 100C HIS 0.004 0.001 HIS H 35 PHE 0.024 0.001 PHE A 329 TYR 0.016 0.001 TYR A 396 ARG 0.004 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.779 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7889 (m-30) cc_final: 0.7545 (m-30) REVERT: L 174 SER cc_start: 0.9387 (t) cc_final: 0.9156 (t) REVERT: L 185 ASP cc_start: 0.7800 (m-30) cc_final: 0.7462 (m-30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.3844 time to fit residues: 64.9923 Evaluate side-chains 110 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5316 Z= 0.220 Angle : 0.659 6.396 7236 Z= 0.339 Chirality : 0.047 0.346 827 Planarity : 0.006 0.082 916 Dihedral : 11.616 102.559 917 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.94 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.33), residues: 642 helix: -3.18 (0.60), residues: 38 sheet: -0.09 (0.34), residues: 223 loop : -1.31 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 100C HIS 0.004 0.001 HIS H 35 PHE 0.024 0.001 PHE A 329 TYR 0.025 0.002 TYR A 508 ARG 0.005 0.001 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.799 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: 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: symmetry clash REVERT: A 406 GLU cc_start: 0.7509 (tp30) cc_final: 0.7285 (tp30) REVERT: A 427 ASP cc_start: 0.7907 (m-30) cc_final: 0.7568 (m-30) REVERT: L 174 SER cc_start: 0.9375 (t) cc_final: 0.9127 (t) REVERT: L 185 ASP cc_start: 0.7916 (m-30) cc_final: 0.7616 (m-30) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.3917 time to fit residues: 63.4769 Evaluate side-chains 109 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5316 Z= 0.220 Angle : 0.658 6.263 7236 Z= 0.337 Chirality : 0.046 0.332 827 Planarity : 0.006 0.091 916 Dihedral : 10.854 101.197 917 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.48 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.33), residues: 642 helix: -3.07 (0.61), residues: 38 sheet: -0.04 (0.35), residues: 223 loop : -1.29 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 100C HIS 0.003 0.001 HIS L 189 PHE 0.023 0.001 PHE A 329 TYR 0.019 0.001 TYR A 396 ARG 0.003 0.000 ARG H 100D *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.858 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7921 (m-30) cc_final: 0.7600 (m-30) REVERT: H 34 MET cc_start: 0.7275 (mmt) cc_final: 0.6947 (mmt) REVERT: H 123 PRO cc_start: 0.9165 (Cg_exo) cc_final: 0.8755 (Cg_endo) REVERT: L 174 SER cc_start: 0.9364 (t) cc_final: 0.9109 (t) REVERT: L 185 ASP cc_start: 0.8131 (m-30) cc_final: 0.7837 (m-30) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3526 time to fit residues: 55.9388 Evaluate side-chains 108 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5316 Z= 0.190 Angle : 0.631 6.153 7236 Z= 0.324 Chirality : 0.046 0.322 827 Planarity : 0.006 0.074 916 Dihedral : 10.359 99.164 917 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.63 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.33), residues: 642 helix: -3.01 (0.63), residues: 38 sheet: 0.03 (0.35), residues: 222 loop : -1.30 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 100C HIS 0.003 0.001 HIS L 189 PHE 0.022 0.001 PHE A 329 TYR 0.013 0.001 TYR A 396 ARG 0.006 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.749 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7870 (m-30) cc_final: 0.7545 (m-30) REVERT: A 508 TYR cc_start: 0.7214 (m-80) cc_final: 0.6991 (m-80) REVERT: H 34 MET cc_start: 0.7269 (mmt) cc_final: 0.7041 (mmt) REVERT: H 123 PRO cc_start: 0.9029 (Cg_exo) cc_final: 0.8811 (Cg_endo) REVERT: H 206 LYS cc_start: 0.8417 (tptm) cc_final: 0.8138 (tptp) REVERT: L 174 SER cc_start: 0.9318 (t) cc_final: 0.9042 (t) REVERT: L 185 ASP cc_start: 0.8125 (m-30) cc_final: 0.7844 (m-30) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.3560 time to fit residues: 60.1136 Evaluate side-chains 113 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5316 Z= 0.169 Angle : 0.628 6.321 7236 Z= 0.321 Chirality : 0.046 0.315 827 Planarity : 0.006 0.066 916 Dihedral : 9.799 94.575 917 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.54 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.34), residues: 642 helix: -3.13 (0.64), residues: 38 sheet: 0.10 (0.36), residues: 222 loop : -1.24 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 100C HIS 0.003 0.001 HIS L 189 PHE 0.021 0.001 PHE A 329 TYR 0.009 0.001 TYR H 91 ARG 0.006 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 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: 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: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7896 (m-30) cc_final: 0.7557 (m-30) REVERT: A 508 TYR cc_start: 0.7288 (m-80) cc_final: 0.7069 (m-80) REVERT: H 34 MET cc_start: 0.7268 (mmt) cc_final: 0.6971 (mmt) REVERT: H 206 LYS cc_start: 0.8437 (tptm) cc_final: 0.8136 (tptp) REVERT: L 174 SER cc_start: 0.9272 (t) cc_final: 0.8985 (t) REVERT: L 185 ASP cc_start: 0.8058 (m-30) cc_final: 0.7796 (m-30) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.4032 time to fit residues: 65.7061 Evaluate side-chains 105 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5316 Z= 0.315 Angle : 0.699 8.140 7236 Z= 0.357 Chirality : 0.046 0.327 827 Planarity : 0.007 0.070 916 Dihedral : 9.565 80.571 917 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.50 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.33), residues: 642 helix: -3.17 (0.64), residues: 38 sheet: -0.19 (0.35), residues: 223 loop : -1.47 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 100C HIS 0.002 0.001 HIS A 519 PHE 0.021 0.002 PHE A 329 TYR 0.018 0.002 TYR L 49 ARG 0.007 0.001 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.725 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7882 (m-30) cc_final: 0.7543 (m-30) REVERT: H 34 MET cc_start: 0.7340 (mmt) cc_final: 0.7133 (mmt) REVERT: L 174 SER cc_start: 0.9379 (t) cc_final: 0.9142 (t) REVERT: L 185 ASP cc_start: 0.8092 (m-30) cc_final: 0.7814 (m-30) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3916 time to fit residues: 61.8702 Evaluate side-chains 103 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 0.027 5316 Z= 0.203 Angle : 0.651 7.621 7236 Z= 0.331 Chirality : 0.046 0.282 827 Planarity : 0.007 0.066 916 Dihedral : 9.019 69.867 917 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.33), residues: 642 helix: -3.15 (0.64), residues: 38 sheet: -0.03 (0.35), residues: 222 loop : -1.39 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 100C HIS 0.003 0.001 HIS L 189 PHE 0.022 0.001 PHE A 329 TYR 0.012 0.001 TYR H 176 ARG 0.011 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.838 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7827 (m-30) cc_final: 0.7474 (m-30) REVERT: H 171 GLN cc_start: 0.8352 (pm20) cc_final: 0.8138 (pm20) REVERT: L 174 SER cc_start: 0.9310 (t) cc_final: 0.9036 (t) REVERT: L 185 ASP cc_start: 0.8105 (m-30) cc_final: 0.7835 (m-30) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4151 time to fit residues: 65.6998 Evaluate side-chains 108 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5316 Z= 0.268 Angle : 0.675 7.329 7236 Z= 0.343 Chirality : 0.046 0.299 827 Planarity : 0.006 0.062 916 Dihedral : 8.615 56.810 917 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.33), residues: 642 helix: -3.11 (0.67), residues: 38 sheet: -0.19 (0.35), residues: 223 loop : -1.52 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 100C HIS 0.002 0.001 HIS L 189 PHE 0.021 0.002 PHE A 329 TYR 0.016 0.002 TYR A 508 ARG 0.008 0.001 ARG H 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.872 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7913 (m-30) cc_final: 0.7548 (m-30) REVERT: H 171 GLN cc_start: 0.8370 (pm20) cc_final: 0.8100 (pm20) REVERT: L 174 SER cc_start: 0.9325 (t) cc_final: 0.9070 (t) REVERT: L 185 ASP cc_start: 0.8172 (m-30) cc_final: 0.7898 (m-30) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.4040 time to fit residues: 63.1423 Evaluate side-chains 105 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095612 restraints weight = 37135.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099759 restraints weight = 16605.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102427 restraints weight = 9765.447| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5316 Z= 0.172 Angle : 0.628 6.810 7236 Z= 0.319 Chirality : 0.046 0.268 827 Planarity : 0.006 0.059 916 Dihedral : 8.113 59.928 917 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.33), residues: 642 helix: -3.26 (0.57), residues: 44 sheet: 0.03 (0.36), residues: 222 loop : -1.32 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 100C HIS 0.003 0.001 HIS L 189 PHE 0.021 0.001 PHE A 329 TYR 0.012 0.001 TYR A 508 ARG 0.007 0.001 ARG H 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2997.48 seconds wall clock time: 53 minutes 28.37 seconds (3208.37 seconds total)