Starting phenix.real_space_refine on Fri Aug 2 17:15:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/08_2024/6y5l_10701.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/08_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_10701/08_2024/6y5l_10701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/08_2024/6y5l_10701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/08_2024/6y5l_10701.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/08_2024/6y5l_10701.cif" } 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-5409/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: 3.80, per 1000 atoms: 0.99 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 613.1 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: 0.32 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: 0.89 Time building geometry restraints manager: 1.58 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 3.120 nonbonded pdb=" NZ LYS E 27 " pdb=" OE2 GLU F 97 " model vdw 2.259 3.120 nonbonded pdb=" NZ LYS C 27 " pdb=" OE2 GLU D 97 " model vdw 2.388 3.120 nonbonded pdb=" O LEU D 38 " pdb=" OG1 THR D 41 " model vdw 2.400 3.040 nonbonded pdb=" O LEU B 38 " pdb=" OG1 THR B 41 " model vdw 2.400 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.980 ------------------------------------------------------------------------------- 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 : 0.465 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: 0.1838 time to fit residues: 43.7804 Evaluate side-chains 163 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 0.4980 chunk 34 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 322 ASN B 60 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 322 ASN E 296 ASN E 322 ASN D 60 ASN D 78 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 60 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3900 Z= 0.274 Angle : 0.682 4.689 5271 Z= 0.370 Chirality : 0.047 0.153 627 Planarity : 0.006 0.041 684 Dihedral : 5.172 37.043 561 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.99 % Allowed : 19.08 % Favored : 77.93 % 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: -0.35 (0.38), residues: 459 helix: 2.57 (0.26), residues: 261 sheet: -4.22 (0.46), residues: 30 loop : -4.37 (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 0.015 0.002 PHE D 70 TYR 0.014 0.003 TYR C 302 ARG 0.004 0.001 ARG F 123 *********************** 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 183 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 0.419 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: A 307 LYS cc_start: 0.7439 (mmmt) cc_final: 0.7047 (mtpp) REVERT: A 320 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.5502 (ttm) REVERT: B 51 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8734 (ptpp) REVERT: B 58 LYS cc_start: 0.8890 (mttp) cc_final: 0.8657 (mmtp) REVERT: B 64 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7236 (t-90) REVERT: B 110 LEU cc_start: 0.8875 (mt) cc_final: 0.8488 (mt) REVERT: B 112 ASP cc_start: 0.8613 (p0) cc_final: 0.8406 (p0) REVERT: B 121 LYS cc_start: 0.9220 (mtpt) cc_final: 0.9008 (tmtt) REVERT: C 41 GLU cc_start: 0.7955 (tp30) cc_final: 0.7715 (tp30) REVERT: C 307 LYS cc_start: 0.7153 (mmmt) cc_final: 0.6805 (mtpp) REVERT: E 22 ASN cc_start: 0.7077 (m-40) cc_final: 0.6481 (t0) REVERT: E 320 MET cc_start: 0.6821 (ttm) cc_final: 0.6454 (ttm) REVERT: D 51 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8776 (ptpt) REVERT: D 58 LYS cc_start: 0.8918 (mttt) cc_final: 0.8675 (mttm) REVERT: F 51 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8914 (ptpt) REVERT: F 54 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8242 (ttm110) REVERT: F 64 HIS cc_start: 0.7947 (m-70) cc_final: 0.7501 (m-70) REVERT: F 121 LYS cc_start: 0.9183 (mtpt) cc_final: 0.8969 (tptp) outliers start: 13 outliers final: 5 residues processed: 171 average time/residue: 0.1938 time to fit residues: 39.1936 Evaluate side-chains 161 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS 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: 0.5980 chunk 27 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 296 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 295 GLN E 296 ASN E 322 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 0.038 3900 Z= 0.204 Angle : 0.733 11.578 5271 Z= 0.397 Chirality : 0.045 0.158 627 Planarity : 0.006 0.047 684 Dihedral : 4.939 36.330 561 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.45 % Allowed : 20.23 % Favored : 76.32 % 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: 0.46 (0.40), residues: 459 helix: 3.28 (0.28), residues: 261 sheet: -4.20 (0.46), residues: 30 loop : -4.07 (0.38), 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 0.008 0.001 PHE D 70 TYR 0.008 0.002 TYR C 302 ARG 0.005 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 179 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 0.454 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: 0.7374 (mmmt) cc_final: 0.6903 (mtpp) REVERT: B 64 HIS cc_start: 0.7971 (m-70) cc_final: 0.7263 (t-90) REVERT: C 307 LYS cc_start: 0.7342 (mmmt) cc_final: 0.7056 (mtpp) REVERT: E 22 ASN cc_start: 0.6872 (m-40) cc_final: 0.6477 (t0) REVERT: E 320 MET cc_start: 0.6734 (ttm) cc_final: 0.6401 (ttm) REVERT: D 54 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8071 (ttm110) REVERT: D 58 LYS cc_start: 0.8930 (mttt) cc_final: 0.8699 (mttt) REVERT: D 116 ASN cc_start: 0.8707 (m110) cc_final: 0.7931 (t0) REVERT: D 121 LYS cc_start: 0.8937 (tptp) cc_final: 0.8732 (tptp) REVERT: F 51 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8797 (ptpt) REVERT: F 54 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7980 (ttm110) REVERT: F 58 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8657 (mmtt) REVERT: F 64 HIS cc_start: 0.8027 (m-70) cc_final: 0.7712 (m170) outliers start: 15 outliers final: 10 residues processed: 172 average time/residue: 0.1840 time to fit residues: 37.3915 Evaluate side-chains 156 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.0570 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 322 ASN B 105 GLN C 322 ASN E 296 ASN E 311 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3900 Z= 0.198 Angle : 0.764 11.394 5271 Z= 0.408 Chirality : 0.045 0.179 627 Planarity : 0.005 0.048 684 Dihedral : 4.852 35.838 561 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.45 % Allowed : 24.60 % Favored : 71.95 % 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: 0.55 (0.40), residues: 459 helix: 3.25 (0.28), residues: 261 sheet: -3.92 (0.50), residues: 30 loop : -3.88 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 92 HIS 0.010 0.003 HIS B 106 PHE 0.007 0.001 PHE B 70 TYR 0.008 0.002 TYR C 302 ARG 0.006 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 172 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 0.448 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: 0.7259 (mmmt) cc_final: 0.6789 (mtpp) REVERT: B 64 HIS cc_start: 0.7951 (m-70) cc_final: 0.7320 (t-90) REVERT: C 290 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7973 (m-40) REVERT: C 307 LYS cc_start: 0.7323 (mmmt) cc_final: 0.7023 (mtpp) REVERT: E 22 ASN cc_start: 0.6951 (m-40) cc_final: 0.6623 (t0) REVERT: E 290 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7917 (m-40) REVERT: E 320 MET cc_start: 0.6637 (ttm) cc_final: 0.6365 (ttm) REVERT: D 58 LYS cc_start: 0.8935 (mttt) cc_final: 0.8636 (mttm) REVERT: D 116 ASN cc_start: 0.8694 (m110) cc_final: 0.7750 (t0) REVERT: D 120 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8248 (mm-30) REVERT: F 47 GLN cc_start: 0.8765 (pp30) cc_final: 0.8532 (pp30) REVERT: F 51 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8860 (mtmm) REVERT: F 58 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8820 (mmtp) REVERT: F 64 HIS cc_start: 0.8010 (m-70) cc_final: 0.7397 (t-170) outliers start: 15 outliers final: 8 residues processed: 164 average time/residue: 0.1806 time to fit residues: 34.9865 Evaluate side-chains 156 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 91 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.0050 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN C 322 ASN E 295 GLN E 311 GLN E 322 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4641 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= 0.301 Angle : 0.824 12.764 5271 Z= 0.437 Chirality : 0.049 0.188 627 Planarity : 0.006 0.050 684 Dihedral : 4.951 36.205 561 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.91 % Allowed : 25.98 % Favored : 70.11 % 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: 0.39 (0.40), residues: 459 helix: 3.05 (0.28), residues: 261 sheet: -3.79 (0.55), residues: 30 loop : -3.86 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 92 HIS 0.012 0.003 HIS D 106 PHE 0.008 0.001 PHE B 70 TYR 0.016 0.003 TYR C 302 ARG 0.007 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 174 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 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: A 41 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7196 (tm-30) REVERT: A 307 LYS cc_start: 0.7267 (mmmt) cc_final: 0.6735 (mtpp) REVERT: A 320 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6834 (ttp) REVERT: B 58 LYS cc_start: 0.8918 (mmtp) cc_final: 0.8610 (mmtp) REVERT: B 64 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7233 (t-90) REVERT: C 290 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8114 (m-40) REVERT: C 307 LYS cc_start: 0.7406 (mmmt) cc_final: 0.7074 (mtpp) REVERT: E 22 ASN cc_start: 0.7039 (m-40) cc_final: 0.6703 (t0) REVERT: E 320 MET cc_start: 0.6842 (ttm) cc_final: 0.6495 (ttm) REVERT: D 58 LYS cc_start: 0.8930 (mttt) cc_final: 0.8665 (mttm) REVERT: F 64 HIS cc_start: 0.7937 (m-70) cc_final: 0.7433 (t-170) REVERT: F 114 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8559 (mt-10) outliers start: 17 outliers final: 10 residues processed: 164 average time/residue: 0.1815 time to fit residues: 35.1955 Evaluate side-chains 156 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 A residue 320 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL 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 F residue 91 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 322 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3900 Z= 0.307 Angle : 0.900 13.927 5271 Z= 0.481 Chirality : 0.050 0.182 627 Planarity : 0.006 0.048 684 Dihedral : 5.026 36.750 561 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.14 % Allowed : 27.59 % Favored : 68.28 % 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: 0.32 (0.39), residues: 459 helix: 2.85 (0.28), residues: 261 sheet: -3.45 (0.63), residues: 30 loop : -3.70 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 92 HIS 0.013 0.003 HIS D 106 PHE 0.007 0.001 PHE B 70 TYR 0.016 0.003 TYR C 302 ARG 0.008 0.001 ARG B 124 *********************** 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 175 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 0.507 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: 0.7292 (mmmt) cc_final: 0.6752 (mtpp) REVERT: B 64 HIS cc_start: 0.7985 (m-70) cc_final: 0.7395 (t-90) REVERT: B 121 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8647 (tptp) REVERT: C 307 LYS cc_start: 0.7320 (mmmt) cc_final: 0.6926 (mtpp) REVERT: E 22 ASN cc_start: 0.7014 (m-40) cc_final: 0.6696 (t0) REVERT: E 320 MET cc_start: 0.7116 (ttm) cc_final: 0.6818 (ttm) REVERT: D 58 LYS cc_start: 0.8953 (mttt) cc_final: 0.8686 (mttm) REVERT: F 58 LYS cc_start: 0.8946 (mttm) cc_final: 0.8657 (mmtp) REVERT: F 64 HIS cc_start: 0.7911 (m-70) cc_final: 0.7469 (t70) outliers start: 18 outliers final: 12 residues processed: 165 average time/residue: 0.1885 time to fit residues: 36.8116 Evaluate side-chains 161 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain C residue 20 VAL 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 F residue 53 ASN Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.1742 > 50: distance: 28 - 53: 28.734 distance: 31 - 50: 12.245 distance: 37 - 42: 16.596 distance: 42 - 43: 4.569 distance: 43 - 46: 6.966 distance: 44 - 45: 12.167 distance: 44 - 50: 12.299 distance: 46 - 47: 8.065 distance: 47 - 48: 4.905 distance: 47 - 49: 6.599 distance: 50 - 51: 13.470 distance: 51 - 52: 19.664 distance: 52 - 53: 23.873 distance: 52 - 54: 16.675 distance: 54 - 55: 32.688 distance: 55 - 56: 13.231 distance: 55 - 58: 56.327 distance: 56 - 57: 3.951 distance: 56 - 60: 54.651 distance: 58 - 59: 23.883 distance: 60 - 61: 14.841 distance: 61 - 62: 21.423 distance: 62 - 63: 6.354 distance: 62 - 68: 17.846 distance: 64 - 65: 28.357 distance: 64 - 66: 24.618 distance: 65 - 67: 51.814 distance: 68 - 69: 32.881 distance: 68 - 74: 42.242 distance: 69 - 70: 16.044 distance: 69 - 72: 25.257 distance: 70 - 71: 15.437 distance: 70 - 75: 24.204 distance: 72 - 73: 29.007 distance: 73 - 74: 25.226 distance: 75 - 76: 5.501 distance: 76 - 77: 32.648 distance: 76 - 79: 18.462 distance: 77 - 78: 8.904 distance: 77 - 83: 8.391 distance: 79 - 80: 16.511 distance: 80 - 81: 20.967 distance: 80 - 82: 13.239 distance: 83 - 84: 21.310 distance: 84 - 85: 20.360 distance: 84 - 87: 30.200 distance: 85 - 86: 34.576 distance: 85 - 91: 11.345 distance: 87 - 88: 14.705 distance: 88 - 89: 15.791 distance: 88 - 90: 6.451 distance: 91 - 92: 21.261 distance: 92 - 93: 28.860 distance: 92 - 95: 46.751 distance: 93 - 94: 3.020 distance: 93 - 100: 18.412 distance: 95 - 96: 13.195 distance: 96 - 97: 15.693 distance: 97 - 98: 37.607 distance: 98 - 99: 52.481 distance: 100 - 101: 16.932 distance: 100 - 106: 16.806 distance: 101 - 104: 9.746 distance: 102 - 107: 38.721 distance: 104 - 105: 19.147 distance: 105 - 106: 15.870 distance: 107 - 108: 19.000 distance: 108 - 109: 5.662 distance: 108 - 111: 39.358 distance: 109 - 110: 12.742 distance: 109 - 118: 27.935 distance: 111 - 112: 7.109 distance: 112 - 113: 16.055 distance: 112 - 114: 14.771 distance: 113 - 115: 17.694 distance: 114 - 116: 16.438 distance: 115 - 117: 16.962 distance: 116 - 117: 31.359 distance: 118 - 137: 3.104