Starting phenix.real_space_refine on Tue Feb 13 06:52:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/02_2024/6y5l_10701.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/02_2024/6y5l_10701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/02_2024/6y5l_10701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/02_2024/6y5l_10701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/02_2024/6y5l_10701.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/02_2024/6y5l_10701.pdb" } resolution = 3.6 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= 0.004 sd= 0.140 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2403 2.51 5 N 654 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 31": "OD1" <-> "OD2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 31": "OD1" <-> "OD2" Residue "C TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 531 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain breaks: 1 Chain: "B" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 740 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 531 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain breaks: 1 Chain: "E" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 531 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain breaks: 1 Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 740 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "F" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 740 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.60, per 1000 atoms: 0.67 Number of scatterers: 3855 At special positions: 0 Unit cell: (68.481, 71.742, 147.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 786 8.00 N 654 7.00 C 2403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 38 " " NAG C 401 " - " ASN C 38 " " NAG E 401 " - " ASN E 38 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 770.9 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 55.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 38 through 125 Processing helix chain 'D' and resid 38 through 125 Processing helix chain 'F' and resid 38 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AA5, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AA6, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AA7, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AA9, first strand: chain 'E' and resid 294 through 295 273 hydrogen bonds defined for protein. 792 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: 0.94 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1270 1.34 - 1.46: 370 1.46 - 1.57: 2242 1.57 - 1.69: 0 1.69 - 1.80: 18 Bond restraints: 3900 Sorted by residual: bond pdb=" C1 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C1 NAG E 401 " pdb=" O5 NAG E 401 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" C5 NAG E 401 " pdb=" O5 NAG E 401 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.27e+00 bond pdb=" C5 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 3895 not shown) Histogram of bond angle deviations from ideal: 100.91 - 107.53: 114 107.53 - 114.15: 2324 114.15 - 120.77: 1633 120.77 - 127.39: 1179 127.39 - 134.01: 21 Bond angle restraints: 5271 Sorted by residual: angle pdb=" N ILE E 29 " pdb=" CA ILE E 29 " pdb=" C ILE E 29 " ideal model delta sigma weight residual 112.96 110.20 2.76 1.00e+00 1.00e+00 7.60e+00 angle pdb=" N ILE C 29 " pdb=" CA ILE C 29 " pdb=" C ILE C 29 " ideal model delta sigma weight residual 112.96 110.22 2.74 1.00e+00 1.00e+00 7.50e+00 angle pdb=" N ILE A 29 " pdb=" CA ILE A 29 " pdb=" C ILE A 29 " ideal model delta sigma weight residual 112.96 110.23 2.73 1.00e+00 1.00e+00 7.47e+00 angle pdb=" N ALA E 317 " pdb=" CA ALA E 317 " pdb=" C ALA E 317 " ideal model delta sigma weight residual 110.42 114.10 -3.68 1.46e+00 4.69e-01 6.35e+00 angle pdb=" N ALA A 317 " pdb=" CA ALA A 317 " pdb=" C ALA A 317 " ideal model delta sigma weight residual 110.42 114.05 -3.63 1.46e+00 4.69e-01 6.18e+00 ... (remaining 5266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2214 17.34 - 34.67: 204 34.67 - 52.01: 48 52.01 - 69.35: 6 69.35 - 86.69: 3 Dihedral angle restraints: 2475 sinusoidal: 1077 harmonic: 1398 Sorted by residual: dihedral pdb=" CA PRO C 306 " pdb=" C PRO C 306 " pdb=" N LYS C 307 " pdb=" CA LYS C 307 " ideal model delta harmonic sigma weight residual -180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PRO A 306 " pdb=" C PRO A 306 " pdb=" N LYS A 307 " pdb=" CA LYS A 307 " ideal model delta harmonic sigma weight residual -180.00 -163.76 -16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PRO E 306 " pdb=" C PRO E 306 " pdb=" N LYS E 307 " pdb=" CA LYS E 307 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 343 0.028 - 0.057: 154 0.057 - 0.085: 64 0.085 - 0.113: 40 0.113 - 0.141: 26 Chirality restraints: 627 Sorted by residual: chirality pdb=" CA ASP F 46 " pdb=" N ASP F 46 " pdb=" C ASP F 46 " pdb=" CB ASP F 46 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ASP B 46 " pdb=" N ASP B 46 " pdb=" C ASP B 46 " pdb=" CB ASP B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ASP D 46 " pdb=" N ASP D 46 " pdb=" C ASP D 46 " pdb=" CB ASP D 46 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 624 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 46 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" CG ASP B 46 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP B 46 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 46 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 46 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" CG ASP F 46 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP F 46 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 46 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 46 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" CG ASP D 46 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP D 46 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP D 46 " 0.016 2.00e-02 2.50e+03 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 163 2.71 - 3.26: 4084 3.26 - 3.80: 5948 3.80 - 4.35: 6904 4.35 - 4.90: 11814 Nonbonded interactions: 28913 Sorted by model distance: nonbonded pdb=" NZ LYS A 27 " pdb=" OE2 GLU B 97 " model vdw 2.161 2.520 nonbonded pdb=" NZ LYS E 27 " pdb=" OE2 GLU F 97 " model vdw 2.259 2.520 nonbonded pdb=" NZ LYS C 27 " pdb=" OE2 GLU D 97 " model vdw 2.388 2.520 nonbonded pdb=" O LEU D 38 " pdb=" OG1 THR D 41 " model vdw 2.400 2.440 nonbonded pdb=" O LEU B 38 " pdb=" OG1 THR B 41 " model vdw 2.400 2.440 ... (remaining 28908 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 2.600 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: 12.670 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.580 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 : 0.004 0.032 3900 Z= 0.216 Angle : 0.701 6.830 5271 Z= 0.401 Chirality : 0.048 0.141 627 Planarity : 0.006 0.051 684 Dihedral : 14.311 86.685 1548 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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: -2.14 (0.34), residues: 459 helix: 0.80 (0.25), residues: 261 sheet: -4.11 (0.66), residues: 30 loop : -4.75 (0.34), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 92 HIS 0.005 0.002 HIS F 64 PHE 0.023 0.003 PHE D 63 TYR 0.022 0.003 TYR E 308 ARG 0.002 0.000 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7178 (mtpp) REVERT: B 51 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8788 (ptpp) REVERT: B 54 ARG cc_start: 0.8310 (mtp85) cc_final: 0.7903 (ttm110) REVERT: B 110 LEU cc_start: 0.9037 (mt) cc_final: 0.8639 (mt) REVERT: B 121 LYS cc_start: 0.9238 (mtpt) cc_final: 0.9020 (tmtt) REVERT: C 307 LYS cc_start: 0.7251 (mmmt) cc_final: 0.6919 (mtpp) REVERT: E 307 LYS cc_start: 0.7392 (mmmt) cc_final: 0.7108 (mtpp) REVERT: E 320 MET cc_start: 0.6638 (ttm) cc_final: 0.5879 (ttm) REVERT: D 51 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8650 (ptpp) REVERT: D 54 ARG cc_start: 0.8365 (mtp85) cc_final: 0.8128 (ttm110) REVERT: D 58 LYS cc_start: 0.8887 (mttt) cc_final: 0.8652 (mttm) REVERT: D 110 LEU cc_start: 0.9188 (mt) cc_final: 0.8738 (mt) REVERT: F 54 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8197 (ttm110) REVERT: F 64 HIS cc_start: 0.7756 (m-70) cc_final: 0.7452 (m-70) REVERT: F 112 ASP cc_start: 0.8912 (p0) cc_final: 0.8608 (p0) REVERT: F 121 LYS cc_start: 0.9208 (mtpt) cc_final: 0.8890 (tptp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1930 time to fit residues: 45.9320 Evaluate side-chains 163 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.0270 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 60 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 322 ASN D 53 ASN D 60 ASN D 78 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3900 Z= 0.286 Angle : 0.672 4.894 5271 Z= 0.360 Chirality : 0.046 0.156 627 Planarity : 0.006 0.041 684 Dihedral : 5.215 37.051 561 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.06 % Allowed : 15.86 % Favored : 79.08 % 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: -0.47 (0.38), residues: 459 helix: 2.46 (0.26), residues: 261 sheet: -4.31 (0.44), residues: 30 loop : -4.41 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 92 HIS 0.010 0.002 HIS B 106 PHE 0.014 0.002 PHE B 70 TYR 0.015 0.003 TYR C 302 ARG 0.003 0.001 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7472 (mmmt) cc_final: 0.7058 (mtpp) REVERT: A 320 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.5579 (ttm) REVERT: B 51 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8748 (ptpp) REVERT: B 64 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7249 (t-90) REVERT: B 110 LEU cc_start: 0.8972 (mt) cc_final: 0.8610 (mt) REVERT: B 121 LYS cc_start: 0.9234 (mtpt) cc_final: 0.9025 (tmtt) REVERT: C 41 GLU cc_start: 0.7909 (tp30) cc_final: 0.7539 (tp30) REVERT: C 307 LYS cc_start: 0.7244 (mmmt) cc_final: 0.6868 (mtpp) REVERT: E 22 ASN cc_start: 0.7078 (m-40) cc_final: 0.6480 (t0) REVERT: E 320 MET cc_start: 0.6776 (ttm) cc_final: 0.6397 (ttm) REVERT: D 54 ARG cc_start: 0.8298 (mtp85) cc_final: 0.8091 (ttm110) REVERT: D 58 LYS cc_start: 0.8909 (mttt) cc_final: 0.8654 (mttm) REVERT: F 64 HIS cc_start: 0.7953 (m-70) cc_final: 0.7569 (m170) outliers start: 22 outliers final: 14 residues processed: 173 average time/residue: 0.1893 time to fit residues: 38.5138 Evaluate side-chains 173 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 322 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3900 Z= 0.209 Angle : 0.696 10.943 5271 Z= 0.371 Chirality : 0.043 0.147 627 Planarity : 0.005 0.047 684 Dihedral : 4.920 36.227 561 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.60 % Allowed : 17.24 % Favored : 78.16 % 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: 0.60 (0.41), residues: 459 helix: 3.47 (0.27), residues: 261 sheet: -4.21 (0.47), residues: 30 loop : -4.13 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 92 HIS 0.012 0.003 HIS B 106 PHE 0.009 0.001 PHE D 70 TYR 0.009 0.002 TYR C 302 ARG 0.004 0.001 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7309 (mmmt) cc_final: 0.6812 (mtpp) REVERT: B 58 LYS cc_start: 0.9060 (mttt) cc_final: 0.8784 (mmtp) REVERT: B 64 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7150 (t-90) REVERT: B 110 LEU cc_start: 0.8822 (mt) cc_final: 0.8609 (mt) REVERT: C 41 GLU cc_start: 0.7908 (tp30) cc_final: 0.7587 (tp30) REVERT: C 307 LYS cc_start: 0.7331 (mmmt) cc_final: 0.7023 (mtpp) REVERT: E 22 ASN cc_start: 0.6887 (m-40) cc_final: 0.6515 (t0) REVERT: E 320 MET cc_start: 0.6806 (ttm) cc_final: 0.6460 (ttm) REVERT: D 51 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8823 (ptpp) REVERT: D 58 LYS cc_start: 0.8932 (mttt) cc_final: 0.8665 (mttm) REVERT: D 114 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8879 (mt-10) REVERT: D 116 ASN cc_start: 0.8737 (m110) cc_final: 0.8128 (t0) REVERT: D 121 LYS cc_start: 0.8952 (tptp) cc_final: 0.8719 (tptp) REVERT: F 58 LYS cc_start: 0.8961 (mttt) cc_final: 0.8689 (mmtp) REVERT: F 64 HIS cc_start: 0.7950 (m-70) cc_final: 0.7171 (t-170) outliers start: 20 outliers final: 18 residues processed: 170 average time/residue: 0.1825 time to fit residues: 36.8622 Evaluate side-chains 164 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN C 322 ASN E 322 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3900 Z= 0.317 Angle : 0.823 12.598 5271 Z= 0.426 Chirality : 0.047 0.161 627 Planarity : 0.006 0.048 684 Dihedral : 5.074 36.198 561 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.52 % Allowed : 22.99 % Favored : 71.49 % 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: 0.58 (0.40), residues: 459 helix: 3.38 (0.27), residues: 261 sheet: -3.98 (0.53), residues: 30 loop : -4.06 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 92 HIS 0.012 0.003 HIS B 106 PHE 0.009 0.001 PHE B 70 TYR 0.017 0.003 TYR C 302 ARG 0.003 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7317 (mmmt) cc_final: 0.6936 (mtpp) REVERT: A 320 MET cc_start: 0.6834 (ttm) cc_final: 0.6422 (ttp) REVERT: B 58 LYS cc_start: 0.9072 (mttt) cc_final: 0.8753 (mmtp) REVERT: B 64 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7242 (t-90) REVERT: B 110 LEU cc_start: 0.8869 (mt) cc_final: 0.8648 (mt) REVERT: C 41 GLU cc_start: 0.7933 (tp30) cc_final: 0.7515 (tp30) REVERT: C 307 LYS cc_start: 0.7318 (mmmt) cc_final: 0.6919 (mtpp) REVERT: E 22 ASN cc_start: 0.7043 (m-40) cc_final: 0.6654 (t0) REVERT: E 320 MET cc_start: 0.7003 (ttm) cc_final: 0.6618 (ttm) REVERT: D 54 ARG cc_start: 0.8274 (ttm110) cc_final: 0.8061 (ttm110) REVERT: D 58 LYS cc_start: 0.8938 (mttt) cc_final: 0.8639 (mttm) REVERT: D 121 LYS cc_start: 0.8842 (tptp) cc_final: 0.8595 (tptp) REVERT: F 54 ARG cc_start: 0.8303 (ttm110) cc_final: 0.8061 (ttm110) REVERT: F 64 HIS cc_start: 0.7912 (m-70) cc_final: 0.7617 (m170) outliers start: 24 outliers final: 19 residues processed: 168 average time/residue: 0.1799 time to fit residues: 35.9057 Evaluate side-chains 165 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3900 Z= 0.361 Angle : 0.878 12.143 5271 Z= 0.458 Chirality : 0.050 0.175 627 Planarity : 0.006 0.048 684 Dihedral : 5.239 37.112 561 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.75 % Allowed : 25.52 % Favored : 68.74 % 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: 0.41 (0.40), residues: 459 helix: 3.12 (0.27), residues: 261 sheet: -3.64 (0.59), residues: 30 loop : -3.99 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 92 HIS 0.011 0.003 HIS B 106 PHE 0.008 0.001 PHE B 70 TYR 0.017 0.004 TYR C 302 ARG 0.004 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7420 (mmmt) cc_final: 0.7049 (mtpp) REVERT: A 320 MET cc_start: 0.7273 (ttm) cc_final: 0.7014 (ttm) REVERT: B 58 LYS cc_start: 0.9025 (mttt) cc_final: 0.8715 (mmtp) REVERT: B 64 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7269 (t-170) REVERT: B 120 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8357 (mm-30) REVERT: C 307 LYS cc_start: 0.7295 (mmmt) cc_final: 0.6891 (mtpp) REVERT: E 22 ASN cc_start: 0.7163 (m-40) cc_final: 0.6781 (t0) REVERT: E 320 MET cc_start: 0.7214 (ttm) cc_final: 0.6885 (ttm) REVERT: D 37 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.7785 (t70) REVERT: D 58 LYS cc_start: 0.8962 (mttt) cc_final: 0.8676 (mttm) REVERT: D 115 MET cc_start: 0.8054 (tpt) cc_final: 0.7748 (tpt) REVERT: F 54 ARG cc_start: 0.8352 (ttm110) cc_final: 0.8034 (ttm110) REVERT: F 64 HIS cc_start: 0.8000 (m-70) cc_final: 0.7636 (t70) outliers start: 25 outliers final: 20 residues processed: 168 average time/residue: 0.1751 time to fit residues: 35.0235 Evaluate side-chains 169 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3900 Z= 0.269 Angle : 0.858 12.876 5271 Z= 0.440 Chirality : 0.047 0.155 627 Planarity : 0.006 0.048 684 Dihedral : 5.013 37.233 561 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.29 % Allowed : 27.82 % Favored : 66.90 % 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: 0.51 (0.40), residues: 459 helix: 3.13 (0.28), residues: 261 sheet: -3.50 (0.64), residues: 30 loop : -3.83 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 92 HIS 0.011 0.003 HIS B 106 PHE 0.005 0.001 PHE F 70 TYR 0.012 0.002 TYR C 302 ARG 0.004 0.001 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7325 (mmmt) cc_final: 0.6793 (mtpp) REVERT: A 320 MET cc_start: 0.6956 (ttm) cc_final: 0.6334 (ttp) REVERT: B 56 ILE cc_start: 0.9217 (pt) cc_final: 0.8935 (pt) REVERT: B 64 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7147 (t-170) REVERT: B 115 MET cc_start: 0.7827 (ttt) cc_final: 0.7505 (mtt) REVERT: B 120 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8547 (mm-30) REVERT: C 307 LYS cc_start: 0.7327 (mmmt) cc_final: 0.6877 (mtpp) REVERT: E 22 ASN cc_start: 0.7062 (m-40) cc_final: 0.6747 (t0) REVERT: E 41 GLU cc_start: 0.8001 (tp30) cc_final: 0.7786 (tp30) REVERT: D 58 LYS cc_start: 0.8960 (mttt) cc_final: 0.8690 (mttm) REVERT: D 64 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7260 (t-90) REVERT: D 115 MET cc_start: 0.8079 (tpt) cc_final: 0.7825 (tpt) REVERT: F 54 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7941 (ttm110) REVERT: F 58 LYS cc_start: 0.8994 (mttt) cc_final: 0.8635 (mttm) outliers start: 23 outliers final: 17 residues processed: 165 average time/residue: 0.1790 time to fit residues: 35.2241 Evaluate side-chains 161 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3900 Z= 0.285 Angle : 0.879 14.612 5271 Z= 0.453 Chirality : 0.049 0.158 627 Planarity : 0.006 0.049 684 Dihedral : 5.058 36.874 561 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.98 % Allowed : 28.74 % Favored : 65.29 % 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: 0.33 (0.40), residues: 459 helix: 2.91 (0.28), residues: 261 sheet: -3.42 (0.68), residues: 30 loop : -3.80 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.014 0.004 HIS D 106 PHE 0.005 0.001 PHE D 70 TYR 0.015 0.003 TYR E 302 ARG 0.004 0.001 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7335 (mmmt) cc_final: 0.6804 (mtpp) REVERT: A 320 MET cc_start: 0.7217 (ttm) cc_final: 0.6930 (ttp) REVERT: B 58 LYS cc_start: 0.9014 (mttt) cc_final: 0.8582 (mmtp) REVERT: B 64 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7200 (t-90) REVERT: B 120 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8557 (mm-30) REVERT: C 307 LYS cc_start: 0.7301 (mmmt) cc_final: 0.6844 (mtpp) REVERT: E 22 ASN cc_start: 0.7053 (m-40) cc_final: 0.6770 (t0) REVERT: D 37 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.7779 (t70) REVERT: D 58 LYS cc_start: 0.8945 (mttt) cc_final: 0.8691 (mttm) REVERT: D 64 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7277 (t-90) REVERT: D 115 MET cc_start: 0.8070 (tpt) cc_final: 0.7813 (tpt) REVERT: F 54 ARG cc_start: 0.8334 (ttm110) cc_final: 0.7936 (ttm110) REVERT: F 58 LYS cc_start: 0.8998 (mttt) cc_final: 0.8615 (mttm) outliers start: 26 outliers final: 19 residues processed: 169 average time/residue: 0.1747 time to fit residues: 35.1450 Evaluate side-chains 169 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3900 Z= 0.285 Angle : 0.935 15.462 5271 Z= 0.480 Chirality : 0.049 0.187 627 Planarity : 0.006 0.049 684 Dihedral : 5.076 36.900 561 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.75 % Allowed : 29.66 % Favored : 64.60 % 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: 0.13 (0.40), residues: 459 helix: 2.62 (0.29), residues: 261 sheet: -3.35 (0.71), residues: 30 loop : -3.68 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.015 0.004 HIS B 106 PHE 0.005 0.001 PHE F 70 TYR 0.014 0.003 TYR C 302 ARG 0.005 0.001 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7401 (mmmt) cc_final: 0.6917 (mtpp) REVERT: A 320 MET cc_start: 0.7162 (ttm) cc_final: 0.6889 (ttp) REVERT: B 58 LYS cc_start: 0.9043 (mttt) cc_final: 0.8514 (mmtp) REVERT: B 64 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7065 (t-90) REVERT: B 120 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8557 (mm-30) REVERT: C 307 LYS cc_start: 0.7461 (mmmt) cc_final: 0.6984 (mtpp) REVERT: E 22 ASN cc_start: 0.7026 (m-40) cc_final: 0.6723 (t0) REVERT: E 41 GLU cc_start: 0.8107 (tp30) cc_final: 0.7855 (tp30) REVERT: E 302 TYR cc_start: 0.3596 (t80) cc_final: 0.2177 (m-80) REVERT: D 37 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.7830 (t70) REVERT: D 58 LYS cc_start: 0.8956 (mttt) cc_final: 0.8706 (mttm) REVERT: D 64 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7314 (t-90) REVERT: D 115 MET cc_start: 0.8045 (tpt) cc_final: 0.7836 (tpt) REVERT: D 121 LYS cc_start: 0.8830 (tptp) cc_final: 0.8535 (tptp) REVERT: F 37 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.7736 (t70) REVERT: F 54 ARG cc_start: 0.8364 (ttm110) cc_final: 0.8078 (ttm110) REVERT: F 58 LYS cc_start: 0.8996 (mttt) cc_final: 0.8625 (mttm) outliers start: 25 outliers final: 19 residues processed: 164 average time/residue: 0.1829 time to fit residues: 35.7819 Evaluate side-chains 171 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 35 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3900 Z= 0.280 Angle : 0.955 16.106 5271 Z= 0.495 Chirality : 0.050 0.176 627 Planarity : 0.006 0.049 684 Dihedral : 5.103 37.138 561 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 5.75 % Allowed : 29.66 % Favored : 64.60 % 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: 0.15 (0.40), residues: 459 helix: 2.58 (0.29), residues: 261 sheet: -3.28 (0.73), residues: 30 loop : -3.56 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.018 0.003 HIS B 106 PHE 0.007 0.001 PHE B 63 TYR 0.013 0.003 TYR A 302 ARG 0.005 0.001 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7556 (mmmt) cc_final: 0.7047 (mtpp) REVERT: B 58 LYS cc_start: 0.9061 (mttt) cc_final: 0.8524 (mmtp) REVERT: B 64 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.7170 (t-90) REVERT: B 120 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8627 (mm-30) REVERT: C 307 LYS cc_start: 0.7396 (mmmt) cc_final: 0.6920 (mtpp) REVERT: E 302 TYR cc_start: 0.3606 (t80) cc_final: 0.2142 (m-80) REVERT: D 58 LYS cc_start: 0.8956 (mttt) cc_final: 0.8697 (mttm) REVERT: D 64 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7341 (t-90) REVERT: D 115 MET cc_start: 0.8038 (tpt) cc_final: 0.7833 (tpt) REVERT: D 121 LYS cc_start: 0.8892 (tptp) cc_final: 0.8604 (tptp) REVERT: F 37 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8043 (t70) REVERT: F 54 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8015 (ttm110) REVERT: F 58 LYS cc_start: 0.8974 (mttt) cc_final: 0.8757 (mttt) outliers start: 25 outliers final: 20 residues processed: 163 average time/residue: 0.1750 time to fit residues: 33.9079 Evaluate side-chains 165 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN C 322 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3900 Z= 0.263 Angle : 1.004 16.779 5271 Z= 0.515 Chirality : 0.050 0.235 627 Planarity : 0.005 0.046 684 Dihedral : 5.098 37.189 561 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.83 % Allowed : 31.03 % Favored : 64.14 % 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: 0.23 (0.40), residues: 459 helix: 2.56 (0.30), residues: 261 sheet: -3.19 (0.74), residues: 30 loop : -3.40 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.017 0.002 HIS B 106 PHE 0.004 0.001 PHE A 294 TYR 0.010 0.002 TYR A 302 ARG 0.005 0.001 ARG D 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7064 (mtpp) REVERT: B 58 LYS cc_start: 0.9073 (mttt) cc_final: 0.8522 (mmtp) REVERT: B 64 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7238 (t-90) REVERT: C 307 LYS cc_start: 0.7311 (mmmt) cc_final: 0.6917 (mtpp) REVERT: E 290 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8100 (m-40) REVERT: E 302 TYR cc_start: 0.3549 (t80) cc_final: 0.2035 (m-80) REVERT: D 37 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: D 58 LYS cc_start: 0.8950 (mttt) cc_final: 0.8649 (mttm) REVERT: D 64 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7394 (t-90) REVERT: D 121 LYS cc_start: 0.8911 (tptp) cc_final: 0.8616 (tptp) REVERT: F 54 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8008 (ttm110) REVERT: F 58 LYS cc_start: 0.8993 (mttt) cc_final: 0.8753 (mttt) outliers start: 21 outliers final: 16 residues processed: 156 average time/residue: 0.1828 time to fit residues: 33.9817 Evaluate side-chains 164 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 28 optimal weight: 0.0870 chunk 27 optimal weight: 0.5980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN C 322 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.133630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094085 restraints weight = 6718.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096769 restraints weight = 4418.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098337 restraints weight = 3505.656| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3900 Z= 0.267 Angle : 1.013 16.855 5271 Z= 0.519 Chirality : 0.049 0.202 627 Planarity : 0.006 0.043 684 Dihedral : 5.172 37.390 561 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.37 % Allowed : 32.64 % Favored : 62.99 % 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: 0.27 (0.41), residues: 459 helix: 2.54 (0.30), residues: 261 sheet: -3.09 (0.76), residues: 30 loop : -3.29 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.017 0.003 HIS B 106 PHE 0.005 0.001 PHE B 63 TYR 0.010 0.002 TYR E 302 ARG 0.005 0.001 ARG D 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1456.19 seconds wall clock time: 26 minutes 56.13 seconds (1616.13 seconds total)