Starting phenix.real_space_refine on Mon Mar 11 16:27:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/03_2024/7ukg_26580.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/03_2024/7ukg_26580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/03_2024/7ukg_26580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/03_2024/7ukg_26580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/03_2024/7ukg_26580.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/03_2024/7ukg_26580.pdb" } resolution = 2.24 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= -0.003 sd= 0.062 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 K 4 8.98 5 S 60 5.16 5 C 5704 2.51 5 N 1424 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8652 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "J" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "K" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "L" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.79, per 1000 atoms: 0.55 Number of scatterers: 8652 At special positions: 0 Unit cell: (99.946, 99.946, 79.296, 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) K 4 19.00 S 60 16.00 O 1460 8.00 N 1424 7.00 C 5704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.7 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 85.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 320 through 347 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.012A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 401 through 424 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.011A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 320 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.011A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 401 through 424 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.012A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 401 through 424 Processing helix chain 'I' and resid 96 through 117 Processing helix chain 'J' and resid 96 through 117 Processing helix chain 'K' and resid 96 through 117 Processing helix chain 'L' and resid 96 through 117 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU A 219 " --> pdb=" O CYS A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU B 219 " --> pdb=" O CYS B 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU C 219 " --> pdb=" O CYS C 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU D 219 " --> pdb=" O CYS D 209 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 2055 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: 2.51 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2616 1.34 - 1.46: 1520 1.46 - 1.57: 4608 1.57 - 1.69: 0 1.69 - 1.80: 92 Bond restraints: 8836 Sorted by residual: bond pdb=" N ARG B 418 " pdb=" CA ARG B 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.81e+00 bond pdb=" N ARG C 418 " pdb=" CA ARG C 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.79e+00 bond pdb=" N ARG A 418 " pdb=" CA ARG A 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.79e+00 bond pdb=" N ARG D 418 " pdb=" CA ARG D 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.76e+00 bond pdb=" CB THR B 316 " pdb=" CG2 THR B 316 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.17e+00 ... (remaining 8831 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.41: 188 106.41 - 113.32: 4988 113.32 - 120.24: 3238 120.24 - 127.15: 3532 127.15 - 134.06: 66 Bond angle restraints: 12012 Sorted by residual: angle pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " pdb=" CG TYR A 188 " ideal model delta sigma weight residual 113.90 118.83 -4.93 1.80e+00 3.09e-01 7.49e+00 angle pdb=" CA TYR B 188 " pdb=" CB TYR B 188 " pdb=" CG TYR B 188 " ideal model delta sigma weight residual 113.90 118.82 -4.92 1.80e+00 3.09e-01 7.46e+00 angle pdb=" CA TYR D 188 " pdb=" CB TYR D 188 " pdb=" CG TYR D 188 " ideal model delta sigma weight residual 113.90 118.78 -4.88 1.80e+00 3.09e-01 7.36e+00 angle pdb=" CA TYR C 188 " pdb=" CB TYR C 188 " pdb=" CG TYR C 188 " ideal model delta sigma weight residual 113.90 118.77 -4.87 1.80e+00 3.09e-01 7.31e+00 angle pdb=" CG ARG D 256 " pdb=" CD ARG D 256 " pdb=" NE ARG D 256 " ideal model delta sigma weight residual 112.00 116.92 -4.92 2.20e+00 2.07e-01 4.99e+00 ... (remaining 12007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 4612 15.49 - 30.98: 468 30.98 - 46.47: 84 46.47 - 61.95: 12 61.95 - 77.44: 8 Dihedral angle restraints: 5184 sinusoidal: 1888 harmonic: 3296 Sorted by residual: dihedral pdb=" CG ARG B 411 " pdb=" CD ARG B 411 " pdb=" NE ARG B 411 " pdb=" CZ ARG B 411 " ideal model delta sinusoidal sigma weight residual -90.00 -133.87 43.87 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG C 411 " pdb=" CD ARG C 411 " pdb=" NE ARG C 411 " pdb=" CZ ARG C 411 " ideal model delta sinusoidal sigma weight residual -90.00 -133.87 43.87 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG D 411 " pdb=" CD ARG D 411 " pdb=" NE ARG D 411 " pdb=" CZ ARG D 411 " ideal model delta sinusoidal sigma weight residual -90.00 -133.86 43.86 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 5181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 714 0.027 - 0.054: 486 0.054 - 0.081: 186 0.081 - 0.108: 50 0.108 - 0.136: 40 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA PHE C 194 " pdb=" N PHE C 194 " pdb=" C PHE C 194 " pdb=" CB PHE C 194 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA PHE A 194 " pdb=" N PHE A 194 " pdb=" C PHE A 194 " pdb=" CB PHE A 194 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA PHE B 194 " pdb=" N PHE B 194 " pdb=" C PHE B 194 " pdb=" CB PHE B 194 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1473 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 417 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLN C 417 " 0.062 2.00e-02 2.50e+03 pdb=" O GLN C 417 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG C 418 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 417 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLN A 417 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN A 417 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 418 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 417 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLN B 417 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN B 417 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 418 " 0.021 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 2177 2.79 - 3.38: 10535 3.38 - 3.97: 16944 3.97 - 4.55: 24020 4.55 - 5.14: 33707 Nonbonded interactions: 87383 Sorted by model distance: nonbonded pdb=" OG1 THR D 166 " pdb=" NE2 GLN D 169 " model vdw 2.208 2.520 nonbonded pdb=" OG1 THR C 166 " pdb=" NE2 GLN C 169 " model vdw 2.209 2.520 nonbonded pdb=" OG1 THR B 166 " pdb=" OE1 GLN B 169 " model vdw 2.327 2.440 nonbonded pdb=" OG1 THR A 166 " pdb=" OE1 GLN A 169 " model vdw 2.328 2.440 nonbonded pdb=" O THR A 369 " pdb=" OG1 THR A 370 " model vdw 2.393 2.440 ... (remaining 87378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 166 through 424) selection = (chain 'B' and resid 166 through 424) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.590 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: 0.010 Extract box with map and model: 23.500 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.100 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.006 0.049 8836 Z= 0.376 Angle : 0.579 5.237 12012 Z= 0.331 Chirality : 0.043 0.136 1476 Planarity : 0.004 0.036 1448 Dihedral : 13.160 77.443 3056 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.95 (0.25), residues: 1112 helix: 2.16 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.32 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.002 0.000 HIS C 306 PHE 0.018 0.002 PHE D 194 TYR 0.021 0.002 TYR B 188 ARG 0.009 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.475 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.2135 time to fit residues: 164.7754 Evaluate side-chains 124 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 169 GLN C 179 HIS D 169 GLN D 179 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8836 Z= 0.188 Angle : 0.459 5.019 12012 Z= 0.254 Chirality : 0.039 0.123 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.545 11.890 1236 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.54 % Allowed : 10.61 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.48 (0.25), residues: 1112 helix: 2.55 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.40 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 362 HIS 0.002 0.001 HIS C 306 PHE 0.016 0.002 PHE D 194 TYR 0.020 0.002 TYR C 188 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 0.990 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 138 average time/residue: 1.0877 time to fit residues: 160.9793 Evaluate side-chains 125 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.0970 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.0270 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8836 Z= 0.132 Angle : 0.417 4.943 12012 Z= 0.229 Chirality : 0.037 0.113 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.394 11.630 1236 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.87 % Allowed : 10.82 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.87 (0.25), residues: 1112 helix: 2.81 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.58 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.003 0.001 HIS A 306 PHE 0.013 0.001 PHE D 194 TYR 0.017 0.001 TYR A 188 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.030 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 140 average time/residue: 1.1053 time to fit residues: 165.8824 Evaluate side-chains 126 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 98 optimal weight: 0.0470 chunk 104 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.0570 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8836 Z= 0.128 Angle : 0.416 4.962 12012 Z= 0.225 Chirality : 0.037 0.112 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.290 10.639 1236 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.43 % Allowed : 11.36 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.12 (0.25), residues: 1112 helix: 2.99 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.69 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 362 HIS 0.003 0.001 HIS B 306 PHE 0.020 0.001 PHE C 289 TYR 0.017 0.001 TYR A 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.009 Fit side-chains REVERT: A 170 ARG cc_start: 0.6150 (mmt180) cc_final: 0.5946 (mmp80) outliers start: 4 outliers final: 0 residues processed: 135 average time/residue: 1.1430 time to fit residues: 164.9691 Evaluate side-chains 127 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.0370 chunk 26 optimal weight: 4.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8836 Z= 0.212 Angle : 0.470 5.029 12012 Z= 0.257 Chirality : 0.039 0.118 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.436 10.844 1236 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.87 % Allowed : 12.55 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.90 (0.25), residues: 1112 helix: 2.83 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.58 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 362 HIS 0.002 0.001 HIS B 306 PHE 0.015 0.002 PHE A 194 TYR 0.023 0.002 TYR A 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 0.873 Fit side-chains REVERT: A 170 ARG cc_start: 0.6161 (mmt180) cc_final: 0.5908 (mmp80) REVERT: C 183 MET cc_start: 0.6449 (OUTLIER) cc_final: 0.5828 (mpp) outliers start: 8 outliers final: 0 residues processed: 141 average time/residue: 1.1262 time to fit residues: 169.8561 Evaluate side-chains 134 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.0020 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8836 Z= 0.180 Angle : 0.453 4.993 12012 Z= 0.246 Chirality : 0.038 0.115 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.409 10.786 1236 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.76 % Allowed : 12.55 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.95 (0.25), residues: 1112 helix: 2.88 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.56 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.003 0.001 HIS A 306 PHE 0.014 0.002 PHE C 194 TYR 0.020 0.002 TYR A 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.960 Fit side-chains REVERT: A 170 ARG cc_start: 0.6187 (mmt180) cc_final: 0.5923 (mmp80) REVERT: B 183 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5834 (mpp) REVERT: D 183 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.5837 (mpp) outliers start: 7 outliers final: 0 residues processed: 138 average time/residue: 1.1828 time to fit residues: 174.5038 Evaluate side-chains 129 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain D residue 183 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8836 Z= 0.204 Angle : 0.472 5.024 12012 Z= 0.256 Chirality : 0.039 0.117 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.454 10.979 1236 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.87 % Allowed : 12.77 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.88 (0.25), residues: 1112 helix: 2.82 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.55 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.002 0.001 HIS D 306 PHE 0.015 0.002 PHE A 194 TYR 0.022 0.002 TYR A 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.013 Fit side-chains REVERT: A 170 ARG cc_start: 0.6169 (mmt180) cc_final: 0.5924 (mmp80) REVERT: A 183 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.5854 (mpp) REVERT: B 183 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.5870 (mpp) REVERT: D 183 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.5871 (mpp) outliers start: 8 outliers final: 1 residues processed: 136 average time/residue: 1.1562 time to fit residues: 167.8827 Evaluate side-chains 130 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain D residue 183 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8836 Z= 0.234 Angle : 0.491 5.055 12012 Z= 0.266 Chirality : 0.040 0.124 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.526 11.569 1236 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.65 % Allowed : 12.88 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.72 (0.25), residues: 1112 helix: 2.72 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.50 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 362 HIS 0.002 0.001 HIS A 306 PHE 0.015 0.002 PHE C 194 TYR 0.022 0.002 TYR A 188 ARG 0.006 0.000 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.980 Fit side-chains REVERT: A 183 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5936 (mpp) REVERT: B 183 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.5981 (mpp) REVERT: C 183 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.5966 (mpp) REVERT: D 183 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.5982 (mpp) outliers start: 6 outliers final: 1 residues processed: 136 average time/residue: 1.2034 time to fit residues: 175.1631 Evaluate side-chains 135 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 183 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 169 GLN B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8836 Z= 0.167 Angle : 0.453 5.063 12012 Z= 0.245 Chirality : 0.038 0.115 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.419 11.424 1236 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.54 % Allowed : 13.20 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.88 (0.25), residues: 1112 helix: 2.85 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.44 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 362 HIS 0.003 0.001 HIS D 306 PHE 0.013 0.001 PHE D 194 TYR 0.018 0.002 TYR A 188 ARG 0.006 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.033 Fit side-chains REVERT: B 183 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.5873 (mpp) outliers start: 5 outliers final: 1 residues processed: 129 average time/residue: 1.1929 time to fit residues: 164.1533 Evaluate side-chains 127 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 8 optimal weight: 0.0870 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.0470 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8836 Z= 0.134 Angle : 0.434 6.058 12012 Z= 0.234 Chirality : 0.037 0.111 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.313 11.532 1236 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.11 % Allowed : 13.53 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.06 (0.25), residues: 1112 helix: 2.97 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.49 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 172 HIS 0.003 0.001 HIS A 306 PHE 0.012 0.001 PHE B 289 TYR 0.016 0.002 TYR A 188 ARG 0.005 0.000 ARG C 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.905 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 1.2269 time to fit residues: 164.5415 Evaluate side-chains 125 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.0870 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.152590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105179 restraints weight = 8989.962| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.62 r_work: 0.3137 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8836 Z= 0.141 Angle : 0.439 5.658 12012 Z= 0.236 Chirality : 0.037 0.111 1476 Planarity : 0.004 0.029 1448 Dihedral : 3.289 11.530 1236 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.11 % Allowed : 13.74 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.09 (0.25), residues: 1112 helix: 3.00 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.46 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.002 0.001 HIS C 306 PHE 0.011 0.001 PHE B 289 TYR 0.017 0.002 TYR A 188 ARG 0.003 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3596.86 seconds wall clock time: 64 minutes 51.76 seconds (3891.76 seconds total)