Starting phenix.real_space_refine on Mon Dec 30 11:06:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1b_16377/12_2024/8c1b_16377.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1b_16377/12_2024/8c1b_16377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c1b_16377/12_2024/8c1b_16377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1b_16377/12_2024/8c1b_16377.map" model { file = "/net/cci-nas-00/data/ceres_data/8c1b_16377/12_2024/8c1b_16377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1b_16377/12_2024/8c1b_16377.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.057 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 27 5.16 5 C 4105 2.51 5 N 1119 2.21 5 O 1318 1.98 5 H 6106 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12675 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 4913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 4913 Classifications: {'peptide': 319} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 296} Chain: "R" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 2646 Classifications: {'peptide': 169} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 162} Chain: "X" Number of atoms: 4913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 4913 Classifications: {'peptide': 319} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 296} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY H 315 " occ=0.00 ... (5 atoms not shown) pdb=" HA3 GLY H 315 " occ=0.00 residue: pdb=" N HIS H 316 " occ=0.00 ... (15 atoms not shown) pdb=" HE2 HIS H 316 " occ=0.00 residue: pdb=" N GLY X 315 " occ=0.00 ... (5 atoms not shown) pdb=" HA3 GLY X 315 " occ=0.00 residue: pdb=" N HIS X 316 " occ=0.00 ... (15 atoms not shown) pdb=" HE2 HIS X 316 " occ=0.00 Time building chain proxies: 7.48, per 1000 atoms: 0.59 Number of scatterers: 12675 At special positions: 0 Unit cell: (96.3713, 122.278, 103.625, 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 27 16.00 O 1318 8.00 N 1119 7.00 C 4105 6.00 H 6106 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS X 325 " distance=2.06 Simple disulfide: pdb=" SG CYS H 251 " - pdb=" SG CYS H 309 " distance=2.04 Simple disulfide: pdb=" SG CYS H 325 " - pdb=" SG CYS X 237 " distance=2.05 Simple disulfide: pdb=" SG CYS H 355 " - pdb=" SG CYS H 415 " distance=2.04 Simple disulfide: pdb=" SG CYS H 461 " - pdb=" SG CYS H 521 " distance=2.04 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 68 " distance=2.04 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 151 " distance=2.04 Simple disulfide: pdb=" SG CYS X 251 " - pdb=" SG CYS X 309 " distance=2.04 Simple disulfide: pdb=" SG CYS X 355 " - pdb=" SG CYS X 415 " distance=2.03 Simple disulfide: pdb=" SG CYS X 461 " - pdb=" SG CYS X 521 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM12645 O5 NAG R 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " " BMA C 3 " - " MAN C 4 " ALPHA1-4 " NAG B 2 " - " MAN B 3 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 1 " - " ASN H 391 " " NAG B 1 " - " ASN R 42 " " NAG C 1 " - " ASN X 391 " " NAG R 501 " - " ASN R 166 " " NAG R 502 " - " ASN R 21 " " NAG R 503 " - " ASN R 135 " Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1524 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 19 sheets defined 9.9% alpha, 48.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'H' and resid 273 through 275 No H-bonds generated for 'chain 'H' and resid 273 through 275' Processing helix chain 'H' and resid 298 through 303 Processing helix chain 'H' and resid 341 through 347 Processing helix chain 'H' and resid 403 through 409 Processing helix chain 'H' and resid 483 through 485 No H-bonds generated for 'chain 'H' and resid 483 through 485' Processing helix chain 'H' and resid 509 through 516 Processing helix chain 'R' and resid 59 through 63 Processing helix chain 'R' and resid 111 through 113 No H-bonds generated for 'chain 'R' and resid 111 through 113' Processing helix chain 'R' and resid 142 through 146 removed outlier: 3.698A pdb=" N SER R 146 " --> pdb=" O VAL R 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 275 No H-bonds generated for 'chain 'X' and resid 273 through 275' Processing helix chain 'X' and resid 298 through 303 Processing helix chain 'X' and resid 341 through 347 Processing helix chain 'X' and resid 403 through 409 Processing helix chain 'X' and resid 483 through 485 No H-bonds generated for 'chain 'X' and resid 483 through 485' Processing helix chain 'X' and resid 510 through 516 Processing sheet with id=AA1, first strand: chain 'H' and resid 277 through 284 removed outlier: 6.381A pdb=" N ALA H 288 " --> pdb=" O GLY H 255 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY H 255 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN H 248 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA X 288 " --> pdb=" O GLY X 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 270 through 271 Processing sheet with id=AA3, first strand: chain 'H' and resid 334 through 337 removed outlier: 4.712A pdb=" N ASP H 359 " --> pdb=" O LEU H 394 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU H 394 " --> pdb=" O ASP H 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 368 through 373 Processing sheet with id=AA5, first strand: chain 'H' and resid 441 through 446 removed outlier: 5.532A pdb=" N PHE H 500 " --> pdb=" O ASN H 465 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 441 through 446 removed outlier: 5.532A pdb=" N PHE H 500 " --> pdb=" O ASN H 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 480 through 481 Processing sheet with id=AA8, first strand: chain 'R' and resid 6 through 10 Processing sheet with id=AA9, first strand: chain 'R' and resid 15 through 17 removed outlier: 6.568A pdb=" N ILE R 16 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 44 through 46 removed outlier: 4.480A pdb=" N TRP R 39 " --> pdb=" O SER R 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 88 through 92 Processing sheet with id=AB3, first strand: chain 'R' and resid 96 through 98 removed outlier: 6.709A pdb=" N VAL R 97 " --> pdb=" O ILE R 170 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR R 148 " --> pdb=" O LYS R 122 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS R 122 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR R 150 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR R 120 " --> pdb=" O TYR R 150 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR R 152 " --> pdb=" O VAL R 118 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL R 118 " --> pdb=" O THR R 152 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS R 128 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS R 122 " --> pdb=" O ALA R 126 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA R 126 " --> pdb=" O LYS R 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 96 through 98 removed outlier: 6.709A pdb=" N VAL R 97 " --> pdb=" O ILE R 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'X' and resid 270 through 271 Processing sheet with id=AB6, first strand: chain 'X' and resid 334 through 337 removed outlier: 3.774A pdb=" N ASP X 359 " --> pdb=" O LEU X 394 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU X 394 " --> pdb=" O ASP X 359 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 368 through 373 Processing sheet with id=AB8, first strand: chain 'X' and resid 441 through 446 removed outlier: 5.418A pdb=" N PHE X 500 " --> pdb=" O ASN X 465 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 441 through 446 removed outlier: 5.418A pdb=" N PHE X 500 " --> pdb=" O ASN X 465 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 480 through 481 292 hydrogen bonds defined for protein. 747 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: 4.83 Time building geometry restraints manager: 3.91 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: 6106 1.04 - 1.24: 798 1.24 - 1.44: 2168 1.44 - 1.64: 3731 1.64 - 1.84: 34 Bond restraints: 12837 Sorted by residual: bond pdb=" N ASP X 224 " pdb=" H1 ASP X 224 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASP H 224 " pdb=" H1 ASP H 224 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C1 NAG R 501 " pdb=" O5 NAG R 501 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" CA VAL R 22 " pdb=" CB VAL R 22 " ideal model delta sigma weight residual 1.540 1.590 -0.050 1.36e-02 5.41e+03 1.35e+01 bond pdb=" C1 NAG R 502 " pdb=" O5 NAG R 502 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 ... (remaining 12832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 22002 2.49 - 4.97: 891 4.97 - 7.46: 139 7.46 - 9.95: 15 9.95 - 12.43: 4 Bond angle restraints: 23051 Sorted by residual: angle pdb=" C ASN R 166 " pdb=" CA ASN R 166 " pdb=" CB ASN R 166 " ideal model delta sigma weight residual 109.84 121.81 -11.97 1.63e+00 3.76e-01 5.39e+01 angle pdb=" CA GLN R 157 " pdb=" CB GLN R 157 " pdb=" CG GLN R 157 " ideal model delta sigma weight residual 114.10 126.53 -12.43 2.00e+00 2.50e-01 3.87e+01 angle pdb=" N VAL R 22 " pdb=" CA VAL R 22 " pdb=" CB VAL R 22 " ideal model delta sigma weight residual 111.23 119.92 -8.69 1.65e+00 3.67e-01 2.77e+01 angle pdb=" C GLU H 319 " pdb=" CA GLU H 319 " pdb=" CB GLU H 319 " ideal model delta sigma weight residual 110.62 101.26 9.36 1.86e+00 2.89e-01 2.53e+01 angle pdb=" C GLY R 64 " pdb=" N GLU R 65 " pdb=" CA GLU R 65 " ideal model delta sigma weight residual 120.82 127.56 -6.74 1.41e+00 5.03e-01 2.29e+01 ... (remaining 23046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 5853 22.05 - 44.10: 402 44.10 - 66.15: 84 66.15 - 88.20: 27 88.20 - 110.26: 10 Dihedral angle restraints: 6376 sinusoidal: 3601 harmonic: 2775 Sorted by residual: dihedral pdb=" CB CYS H 325 " pdb=" SG CYS H 325 " pdb=" SG CYS X 237 " pdb=" CB CYS X 237 " ideal model delta sinusoidal sigma weight residual -86.00 -167.92 81.92 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS H 237 " pdb=" SG CYS H 237 " pdb=" SG CYS X 325 " pdb=" CB CYS X 325 " ideal model delta sinusoidal sigma weight residual 93.00 166.28 -73.28 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" C ASN R 166 " pdb=" N ASN R 166 " pdb=" CA ASN R 166 " pdb=" CB ASN R 166 " ideal model delta harmonic sigma weight residual -122.60 -139.35 16.75 0 2.50e+00 1.60e-01 4.49e+01 ... (remaining 6373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 980 0.115 - 0.229: 85 0.229 - 0.344: 6 0.344 - 0.458: 1 0.458 - 0.572: 1 Chirality restraints: 1073 Sorted by residual: chirality pdb=" CA ASN R 166 " pdb=" N ASN R 166 " pdb=" C ASN R 166 " pdb=" CB ASN R 166 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.19e+00 chirality pdb=" CG LEU R 90 " pdb=" CB LEU R 90 " pdb=" CD1 LEU R 90 " pdb=" CD2 LEU R 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA GLN R 157 " pdb=" N GLN R 157 " pdb=" C GLN R 157 " pdb=" CB GLN R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1070 not shown) Planarity restraints: 1911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 166 " -0.005 2.00e-02 2.50e+03 9.57e-02 1.15e+02 pdb=" CG ASN R 166 " -0.119 2.00e-02 2.50e+03 pdb=" OD1 ASN R 166 " 0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN R 166 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG R 501 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 166 " 0.029 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" CG ASN R 166 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN R 166 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN R 166 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR X 257 " 0.084 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO X 258 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO X 258 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO X 258 " 0.067 5.00e-02 4.00e+02 ... (remaining 1908 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 2448 2.29 - 2.87: 26597 2.87 - 3.45: 30408 3.45 - 4.02: 43005 4.02 - 4.60: 63202 Nonbonded interactions: 165660 Sorted by model distance: nonbonded pdb=" HE2 HIS H 477 " pdb=" O LYS H 516 " model vdw 1.713 2.450 nonbonded pdb="HE22 GLN H 234 " pdb=" O SER X 235 " model vdw 1.733 2.450 nonbonded pdb=" O GLY R 124 " pdb="HH22 ARG X 390 " model vdw 1.737 2.450 nonbonded pdb=" HE2 HIS X 477 " pdb=" O LYS X 516 " model vdw 1.746 2.450 nonbonded pdb=" HE ARG X 522 " pdb=" OE1 GLN X 535 " model vdw 1.751 2.450 ... (remaining 165655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 4.280 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: 0.200 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.190 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 0.077 6731 Z= 0.482 Angle : 1.307 12.434 9174 Z= 0.710 Chirality : 0.068 0.572 1073 Planarity : 0.009 0.124 1160 Dihedral : 16.551 110.256 2703 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.24 % Favored : 95.51 % Rotamer: Outliers : 0.28 % Allowed : 9.33 % Favored : 90.39 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 10.00 % 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: -0.06 (0.29), residues: 801 helix: -1.61 (0.63), residues: 56 sheet: 1.02 (0.27), residues: 357 loop : -0.81 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP R 13 HIS 0.013 0.003 HIS H 381 PHE 0.021 0.003 PHE X 318 TYR 0.021 0.003 TYR R 80 ARG 0.015 0.001 ARG R 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 0.3502 time to fit residues: 13.3049 Evaluate side-chains 20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 389 GLN X 419 HIS X 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6731 Z= 0.174 Angle : 0.610 5.803 9174 Z= 0.317 Chirality : 0.043 0.167 1073 Planarity : 0.005 0.066 1160 Dihedral : 10.974 74.392 1193 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.11 % Allowed : 8.91 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.61 (0.29), residues: 801 helix: -1.51 (0.58), residues: 57 sheet: 1.21 (0.26), residues: 377 loop : -0.06 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 513 HIS 0.004 0.001 HIS R 134 PHE 0.007 0.001 PHE X 500 TYR 0.005 0.001 TYR H 307 ARG 0.002 0.000 ARG X 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 272 MET cc_start: 0.5913 (mpp) cc_final: 0.5672 (mpp) outliers start: 8 outliers final: 3 residues processed: 28 average time/residue: 0.2649 time to fit residues: 12.1615 Evaluate side-chains 22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 56 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 381 HIS ** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6731 Z= 0.240 Angle : 0.592 4.521 9174 Z= 0.303 Chirality : 0.041 0.172 1073 Planarity : 0.005 0.048 1160 Dihedral : 7.944 49.052 1193 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.11 % Allowed : 8.77 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.92 (0.29), residues: 801 helix: -1.54 (0.60), residues: 58 sheet: 1.48 (0.26), residues: 347 loop : 0.23 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 513 HIS 0.005 0.001 HIS X 316 PHE 0.009 0.001 PHE X 346 TYR 0.008 0.001 TYR R 149 ARG 0.006 0.000 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 28 average time/residue: 0.3096 time to fit residues: 13.6815 Evaluate side-chains 21 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6731 Z= 0.205 Angle : 0.542 5.459 9174 Z= 0.277 Chirality : 0.041 0.146 1073 Planarity : 0.004 0.046 1160 Dihedral : 6.665 48.857 1193 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.97 % Allowed : 9.47 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.97 (0.29), residues: 801 helix: -1.47 (0.62), residues: 58 sheet: 1.46 (0.26), residues: 345 loop : 0.32 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 513 HIS 0.003 0.001 HIS X 316 PHE 0.008 0.001 PHE X 501 TYR 0.013 0.001 TYR X 307 ARG 0.004 0.000 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 23 average time/residue: 0.2554 time to fit residues: 10.2342 Evaluate side-chains 19 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6731 Z= 0.257 Angle : 0.562 4.989 9174 Z= 0.288 Chirality : 0.040 0.137 1073 Planarity : 0.004 0.043 1160 Dihedral : 6.067 50.993 1193 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.97 % Allowed : 9.89 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.86 (0.29), residues: 801 helix: -1.44 (0.62), residues: 57 sheet: 1.27 (0.25), residues: 342 loop : 0.36 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 513 HIS 0.005 0.001 HIS X 316 PHE 0.009 0.001 PHE H 445 TYR 0.006 0.001 TYR X 336 ARG 0.006 0.000 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 25 average time/residue: 0.2470 time to fit residues: 10.6858 Evaluate side-chains 19 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6731 Z= 0.227 Angle : 0.534 4.372 9174 Z= 0.274 Chirality : 0.040 0.139 1073 Planarity : 0.004 0.041 1160 Dihedral : 5.734 49.335 1193 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.97 % Allowed : 10.31 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.75 (0.29), residues: 801 helix: -1.48 (0.63), residues: 57 sheet: 1.16 (0.26), residues: 343 loop : 0.30 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 513 HIS 0.003 0.001 HIS X 316 PHE 0.008 0.001 PHE X 501 TYR 0.011 0.001 TYR X 307 ARG 0.004 0.000 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 24 average time/residue: 0.2410 time to fit residues: 10.1389 Evaluate side-chains 20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Chi-restraints excluded: chain X residue 529 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6731 Z= 0.175 Angle : 0.501 4.498 9174 Z= 0.255 Chirality : 0.040 0.149 1073 Planarity : 0.004 0.041 1160 Dihedral : 5.386 48.171 1193 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.84 % Allowed : 10.31 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.94 (0.30), residues: 801 helix: -1.24 (0.65), residues: 57 sheet: 1.22 (0.26), residues: 350 loop : 0.49 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 513 HIS 0.003 0.001 HIS X 316 PHE 0.006 0.001 PHE X 500 TYR 0.012 0.001 TYR X 307 ARG 0.003 0.000 ARG X 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 21 average time/residue: 0.2412 time to fit residues: 9.0610 Evaluate side-chains 19 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Chi-restraints excluded: chain X residue 529 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6731 Z= 0.276 Angle : 0.557 6.002 9174 Z= 0.286 Chirality : 0.040 0.129 1073 Planarity : 0.004 0.041 1160 Dihedral : 5.587 49.803 1193 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.84 % Allowed : 11.00 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.73 (0.29), residues: 801 helix: -1.35 (0.65), residues: 57 sheet: 1.05 (0.26), residues: 348 loop : 0.37 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 110 HIS 0.005 0.001 HIS X 316 PHE 0.010 0.001 PHE R 84 TYR 0.029 0.002 TYR X 307 ARG 0.007 0.001 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 21 average time/residue: 0.2658 time to fit residues: 9.9430 Evaluate side-chains 20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Chi-restraints excluded: chain X residue 529 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6731 Z= 0.219 Angle : 0.526 4.792 9174 Z= 0.270 Chirality : 0.040 0.148 1073 Planarity : 0.004 0.040 1160 Dihedral : 5.365 48.651 1193 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.70 % Allowed : 11.28 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.81 (0.30), residues: 801 helix: -1.22 (0.66), residues: 57 sheet: 1.09 (0.26), residues: 344 loop : 0.43 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 513 HIS 0.003 0.001 HIS H 525 PHE 0.007 0.001 PHE X 500 TYR 0.012 0.001 TYR X 307 ARG 0.003 0.000 ARG X 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.3400 time to fit residues: 11.2824 Evaluate side-chains 22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Chi-restraints excluded: chain X residue 529 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6731 Z= 0.204 Angle : 0.513 4.767 9174 Z= 0.263 Chirality : 0.040 0.148 1073 Planarity : 0.004 0.041 1160 Dihedral : 5.269 48.050 1193 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.70 % Allowed : 11.28 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.82 (0.30), residues: 801 helix: -1.20 (0.66), residues: 57 sheet: 1.09 (0.26), residues: 344 loop : 0.45 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 513 HIS 0.003 0.001 HIS H 525 PHE 0.007 0.001 PHE X 318 TYR 0.014 0.001 TYR X 307 ARG 0.003 0.000 ARG X 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 ARG cc_start: 0.7063 (ptm160) cc_final: 0.6828 (ptm-80) outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.3287 time to fit residues: 11.1692 Evaluate side-chains 22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Chi-restraints excluded: chain X residue 529 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 389 GLN ** 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 = 0.3959 r_free = 0.3959 target = 0.071899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.057146 restraints weight = 93356.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.059489 restraints weight = 38044.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.060924 restraints weight = 21372.632| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6731 Z= 0.257 Angle : 0.547 4.799 9174 Z= 0.281 Chirality : 0.040 0.134 1073 Planarity : 0.004 0.040 1160 Dihedral : 5.484 49.629 1193 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.97 % Allowed : 11.00 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.59 (0.30), residues: 801 helix: -1.36 (0.65), residues: 57 sheet: 0.94 (0.26), residues: 344 loop : 0.28 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 110 HIS 0.005 0.001 HIS H 525 PHE 0.009 0.001 PHE X 318 TYR 0.013 0.001 TYR X 307 ARG 0.006 0.000 ARG X 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3033.17 seconds wall clock time: 55 minutes 4.64 seconds (3304.64 seconds total)