Starting phenix.real_space_refine on Mon Sep 23 16:32:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/09_2024/6y5l_10701.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/09_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_10701/09_2024/6y5l_10701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/09_2024/6y5l_10701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/09_2024/6y5l_10701.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5l_10701/09_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. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 3 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: "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 Restraints were copied for chains: C, E, D, F Time building chain proxies: 3.70, per 1000 atoms: 0.96 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False 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: 1.04 Conformation dependent library (CDL) restraints added in 410.5 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: 0.39 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: 0.97 Time building geometry restraints manager: 1.20 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: 0.00 - 1.37: 4959 1.37 - 2.73: 272 2.73 - 4.10: 37 4.10 - 5.46: 0 5.46 - 6.83: 3 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: 2208 17.34 - 34.67: 204 34.67 - 52.01: 48 52.01 - 69.35: 6 69.35 - 86.69: 3 Dihedral angle restraints: 2469 sinusoidal: 1071 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 2466 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: 2.03 - 2.61: 53 2.61 - 3.18: 3632 3.18 - 3.75: 5771 3.75 - 4.33: 7219 4.33 - 4.90: 12244 Nonbonded interactions: 28919 Sorted by model distance: nonbonded pdb=" SG CYS E 281 " pdb=" SG CYS E 305 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS C 281 " pdb=" SG CYS C 305 " model vdw 2.033 3.760 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 ... (remaining 28914 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: 4.270 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.640 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- 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= 0.222 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 : 2.032 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 : 0.540 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: 0.1870 time to fit residues: 44.5014 Evaluate side-chains 163 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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: 0.7338 moved from start: 0.3128 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= 0.279 Angle : 0.681 4.865 5271 Z= 0.370 Chirality : 0.046 0.153 627 Planarity : 0.006 0.041 684 Dihedral : 5.106 37.124 561 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.53 % Allowed : 19.77 % Favored : 77.70 % 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: -0.37 (0.38), residues: 459 helix: 2.52 (0.26), residues: 261 sheet: -4.23 (0.47), residues: 30 loop : -4.33 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 92 HIS 0.010 0.002 HIS B 106 PHE 0.015 0.002 PHE B 70 TYR 0.014 0.003 TYR E 308 ARG 0.006 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 180 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 0.499 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: 0.7392 (mmmt) cc_final: 0.6990 (mtpp) REVERT: B 51 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8744 (ptpp) REVERT: B 58 LYS cc_start: 0.8892 (mttp) cc_final: 0.8657 (mmtp) REVERT: B 64 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7235 (t-90) REVERT: B 110 LEU cc_start: 0.8873 (mt) cc_final: 0.8479 (mt) REVERT: B 112 ASP cc_start: 0.8615 (p0) cc_final: 0.8413 (p0) REVERT: B 121 LYS cc_start: 0.9209 (mtpt) cc_final: 0.8996 (tmtt) REVERT: C 307 LYS cc_start: 0.7240 (mmmt) cc_final: 0.6872 (mtpp) REVERT: E 320 MET cc_start: 0.6833 (ttm) cc_final: 0.6472 (ttm) REVERT: D 51 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8650 (ptpp) REVERT: D 58 LYS cc_start: 0.8917 (mttt) cc_final: 0.8668 (mttm) REVERT: F 54 ARG cc_start: 0.8466 (mtp85) cc_final: 0.8165 (ttm110) REVERT: F 64 HIS cc_start: 0.7945 (m-70) cc_final: 0.7501 (m-70) REVERT: F 121 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8958 (tptp) outliers start: 11 outliers final: 3 residues processed: 170 average time/residue: 0.1955 time to fit residues: 38.9927 Evaluate side-chains 158 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 20 VAL 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: 0.0870 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 32 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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 C 322 ASN E 295 GLN E 296 ASN E 322 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3900 Z= 0.212 Angle : 0.727 11.493 5271 Z= 0.394 Chirality : 0.045 0.154 627 Planarity : 0.005 0.046 684 Dihedral : 4.876 36.298 561 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.91 % Allowed : 20.92 % Favored : 75.17 % 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: 3.27 (0.28), residues: 261 sheet: -4.19 (0.46), residues: 30 loop : -3.95 (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 0.009 0.001 PHE D 70 TYR 0.009 0.002 TYR C 302 ARG 0.005 0.001 ARG B 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 180 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 0.486 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: 0.7260 (mmmt) cc_final: 0.6760 (mtpp) REVERT: B 64 HIS cc_start: 0.7981 (m-70) cc_final: 0.7273 (t-90) REVERT: C 307 LYS cc_start: 0.7303 (mmmt) cc_final: 0.6961 (mtpp) REVERT: E 320 MET cc_start: 0.6741 (ttm) cc_final: 0.6427 (ttm) REVERT: D 58 LYS cc_start: 0.8911 (mttt) cc_final: 0.8601 (mttm) REVERT: D 116 ASN cc_start: 0.8708 (m110) cc_final: 0.7943 (t0) REVERT: D 121 LYS cc_start: 0.8950 (tptp) cc_final: 0.8746 (tptp) REVERT: F 51 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8814 (ptpp) REVERT: F 54 ARG cc_start: 0.8284 (mtp85) cc_final: 0.8025 (ttm110) REVERT: F 58 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8704 (mmtt) REVERT: F 64 HIS cc_start: 0.8038 (m-70) cc_final: 0.7706 (m170) outliers start: 17 outliers final: 10 residues processed: 172 average time/residue: 0.1901 time to fit residues: 38.6189 Evaluate side-chains 155 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 0.0020 chunk 19 optimal weight: 0.0670 chunk 27 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 chunk 21 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 overall best weight: 0.0862 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 296 ASN E 311 GLN ** D 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: 0.7267 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3900 Z= 0.172 Angle : 0.744 11.746 5271 Z= 0.397 Chirality : 0.043 0.172 627 Planarity : 0.005 0.047 684 Dihedral : 4.728 35.798 561 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.53 % Allowed : 25.06 % Favored : 72.41 % 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: 0.74 (0.40), residues: 459 helix: 3.32 (0.29), residues: 261 sheet: -3.85 (0.49), residues: 30 loop : -3.62 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP F 92 HIS 0.010 0.003 HIS D 106 PHE 0.005 0.001 PHE B 63 TYR 0.007 0.001 TYR B 94 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 171 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 0.490 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 290 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7829 (m-40) REVERT: A 307 LYS cc_start: 0.7195 (mmmt) cc_final: 0.6748 (mtpp) REVERT: B 64 HIS cc_start: 0.7920 (m-70) cc_final: 0.7287 (t-90) REVERT: C 307 LYS cc_start: 0.7324 (mmmt) cc_final: 0.6999 (mtpp) REVERT: D 58 LYS cc_start: 0.8929 (mttt) cc_final: 0.8605 (mttm) REVERT: D 110 LEU cc_start: 0.9002 (mt) cc_final: 0.8764 (mt) REVERT: D 116 ASN cc_start: 0.8666 (m110) cc_final: 0.7752 (t0) REVERT: D 120 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8246 (mm-30) REVERT: F 58 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8812 (mmtp) REVERT: F 64 HIS cc_start: 0.7954 (m-70) cc_final: 0.7397 (t-170) outliers start: 11 outliers final: 4 residues processed: 165 average time/residue: 0.2027 time to fit residues: 39.2594 Evaluate side-chains 149 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN 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: 4.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN E 295 GLN E 296 ASN E 322 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3900 Z= 0.311 Angle : 0.832 13.328 5271 Z= 0.440 Chirality : 0.049 0.187 627 Planarity : 0.005 0.050 684 Dihedral : 4.922 36.185 561 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.37 % Allowed : 26.21 % Favored : 69.43 % 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: 3.05 (0.28), residues: 261 sheet: -3.72 (0.55), residues: 30 loop : -3.72 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.010 0.004 HIS D 106 PHE 0.008 0.001 PHE F 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: 19 poor density : 155 time to evaluate : 0.512 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 41 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 307 LYS cc_start: 0.7298 (mmmt) cc_final: 0.6805 (mtpp) REVERT: B 58 LYS cc_start: 0.8935 (mmtp) cc_final: 0.8618 (mmtp) REVERT: B 64 HIS cc_start: 0.7900 (m-70) cc_final: 0.7319 (t-90) REVERT: C 307 LYS cc_start: 0.7165 (mmmt) cc_final: 0.6776 (mtpp) REVERT: D 58 LYS cc_start: 0.8928 (mttt) cc_final: 0.8654 (mttm) REVERT: F 64 HIS cc_start: 0.7928 (m-70) cc_final: 0.7441 (t-170) REVERT: F 110 LEU cc_start: 0.9023 (mm) cc_final: 0.8756 (mm) outliers start: 19 outliers final: 16 residues processed: 164 average time/residue: 0.1868 time to fit residues: 36.1364 Evaluate side-chains 155 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 B residue 115 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 281 CYS 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 Chi-restraints excluded: chain F residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 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 322 ASN E 296 ASN ** D 47 GLN ** 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: 0.7365 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3900 Z= 0.313 Angle : 0.900 13.764 5271 Z= 0.471 Chirality : 0.049 0.170 627 Planarity : 0.005 0.046 684 Dihedral : 5.048 36.804 561 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.14 % Allowed : 28.51 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.40), residues: 459 helix: 2.89 (0.28), residues: 261 sheet: -3.40 (0.65), residues: 30 loop : -3.61 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 92 HIS 0.012 0.004 HIS B 106 PHE 0.007 0.001 PHE F 70 TYR 0.014 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 171 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 0.435 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: 0.7367 (mmmt) cc_final: 0.6859 (mtpp) REVERT: B 64 HIS cc_start: 0.7810 (m-70) cc_final: 0.7239 (t-170) REVERT: B 121 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8631 (tptp) REVERT: C 307 LYS cc_start: 0.7283 (mmmt) cc_final: 0.6899 (mtpp) REVERT: D 58 LYS cc_start: 0.8968 (mttt) cc_final: 0.8682 (mttm) REVERT: F 58 LYS cc_start: 0.8945 (mttm) cc_final: 0.8648 (mmtp) REVERT: F 64 HIS cc_start: 0.7908 (m-70) cc_final: 0.7479 (t70) outliers start: 18 outliers final: 15 residues processed: 162 average time/residue: 0.1847 time to fit residues: 35.2752 Evaluate side-chains 160 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 281 CYS Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 25 LEU 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 Chi-restraints excluded: chain F residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.0670 chunk 36 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 27 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** 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: 0.7320 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3900 Z= 0.224 Angle : 0.898 15.705 5271 Z= 0.473 Chirality : 0.048 0.181 627 Planarity : 0.005 0.047 684 Dihedral : 4.883 36.917 561 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.45 % Allowed : 31.95 % 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: 0.28 (0.39), residues: 459 helix: 2.59 (0.29), residues: 261 sheet: -3.64 (0.59), residues: 36 loop : -3.17 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 92 HIS 0.013 0.004 HIS B 106 PHE 0.004 0.001 PHE F 70 TYR 0.008 0.002 TYR A 302 ARG 0.009 0.001 ARG B 124 *********************** 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 167 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.481 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: 0.7456 (mmmt) cc_final: 0.6972 (mtpp) REVERT: A 320 MET cc_start: 0.6768 (mtp) cc_final: 0.5953 (ttm) REVERT: A 322 ASN cc_start: 0.7261 (t0) cc_final: 0.6441 (t0) REVERT: B 58 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8614 (mmtp) REVERT: C 307 LYS cc_start: 0.7305 (mmmt) cc_final: 0.6893 (mtpp) REVERT: D 54 ARG cc_start: 0.8147 (ttm110) cc_final: 0.7687 (ptp90) REVERT: D 64 HIS cc_start: 0.7974 (m-70) cc_final: 0.7279 (t-90) REVERT: F 37 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7494 (t70) REVERT: F 58 LYS cc_start: 0.8976 (mttm) cc_final: 0.8626 (mmtp) outliers start: 15 outliers final: 11 residues processed: 158 average time/residue: 0.1923 time to fit residues: 35.6097 Evaluate side-chains 152 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 296 ASN Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 37 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** 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: 0.7355 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3900 Z= 0.292 Angle : 0.992 15.856 5271 Z= 0.517 Chirality : 0.052 0.192 627 Planarity : 0.006 0.041 684 Dihedral : 5.046 36.607 561 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.06 % Allowed : 30.80 % 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: 0.29 (0.40), residues: 459 helix: 2.54 (0.29), residues: 261 sheet: -3.43 (0.64), residues: 36 loop : -3.11 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.014 0.004 HIS B 106 PHE 0.007 0.001 PHE D 63 TYR 0.013 0.003 TYR A 302 ARG 0.009 0.001 ARG B 124 *********************** 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 164 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.503 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: 0.7563 (tm-30) cc_final: 0.7174 (tm-30) REVERT: A 307 LYS cc_start: 0.7543 (mmmt) cc_final: 0.7041 (mtpp) REVERT: B 58 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8606 (mmtp) REVERT: C 307 LYS cc_start: 0.7326 (mmmt) cc_final: 0.6938 (mtpp) REVERT: D 58 LYS cc_start: 0.8960 (mttt) cc_final: 0.8707 (mttm) REVERT: D 64 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.7353 (t-90) REVERT: F 37 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7343 (t70) REVERT: F 58 LYS cc_start: 0.8984 (mttm) cc_final: 0.8596 (mmtp) REVERT: F 117 LYS cc_start: 0.9180 (mtmt) cc_final: 0.8956 (mtmm) outliers start: 22 outliers final: 13 residues processed: 153 average time/residue: 0.2186 time to fit residues: 39.7071 Evaluate side-chains 152 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 281 CYS 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 E residue 322 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 37 ASP Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.0270 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** 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: 0.7335 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3900 Z= 0.254 Angle : 1.026 16.319 5271 Z= 0.542 Chirality : 0.052 0.256 627 Planarity : 0.006 0.038 684 Dihedral : 5.164 36.560 561 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.91 % Allowed : 32.87 % Favored : 63.22 % 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: 0.21 (0.40), residues: 459 helix: 2.39 (0.30), residues: 261 sheet: -3.34 (0.66), residues: 36 loop : -3.04 (0.43), residues: 162 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 0.006 0.001 PHE D 63 TYR 0.010 0.002 TYR A 302 ARG 0.010 0.001 ARG B 124 *********************** 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 165 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.495 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: 0.7557 (mmmt) cc_final: 0.7060 (mtpp) REVERT: B 112 ASP cc_start: 0.8855 (p0) cc_final: 0.8611 (p0) REVERT: C 307 LYS cc_start: 0.7283 (mmmt) cc_final: 0.6856 (mtpp) REVERT: E 302 TYR cc_start: 0.3927 (t80) cc_final: 0.2424 (m-80) REVERT: E 315 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7738 (tppt) REVERT: D 58 LYS cc_start: 0.8944 (mttt) cc_final: 0.8693 (mttm) REVERT: D 64 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7418 (t-90) REVERT: D 121 LYS cc_start: 0.8918 (tptp) cc_final: 0.8625 (tptp) REVERT: F 37 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7531 (t70) REVERT: F 121 LYS cc_start: 0.8689 (tptp) cc_final: 0.8483 (tptp) outliers start: 17 outliers final: 10 residues processed: 153 average time/residue: 0.1979 time to fit residues: 35.7106 Evaluate side-chains 156 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 B residue 115 MET 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 307 LYS Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain F residue 37 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 overall best weight: 0.1152 ------------------------------------------------------------------------------- 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 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3900 Z= 0.232 Angle : 1.025 17.401 5271 Z= 0.553 Chirality : 0.050 0.206 627 Planarity : 0.005 0.040 684 Dihedral : 5.247 36.492 561 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.53 % Allowed : 34.02 % Favored : 63.45 % 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: 0.31 (0.40), residues: 459 helix: 2.37 (0.31), residues: 261 sheet: -3.30 (0.65), residues: 36 loop : -2.78 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 92 HIS 0.015 0.004 HIS B 106 PHE 0.004 0.001 PHE D 63 TYR 0.007 0.001 TYR F 94 ARG 0.011 0.001 ARG B 124 ********************** 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 155 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.430 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: 0.7428 (mmmt) cc_final: 0.6957 (mtpp) REVERT: B 112 ASP cc_start: 0.8744 (p0) cc_final: 0.8448 (p0) REVERT: C 307 LYS cc_start: 0.7192 (mmmt) cc_final: 0.6779 (mtpp) REVERT: E 302 TYR cc_start: 0.3792 (t80) cc_final: 0.2323 (m-80) REVERT: E 315 LYS cc_start: 0.8034 (mmtm) cc_final: 0.7604 (tppt) REVERT: D 58 LYS cc_start: 0.8947 (mttt) cc_final: 0.8709 (mttm) REVERT: D 64 HIS cc_start: 0.7959 (m-70) cc_final: 0.7417 (t-90) REVERT: D 117 LYS cc_start: 0.9143 (mtmt) cc_final: 0.8872 (ptpp) REVERT: D 121 LYS cc_start: 0.8930 (tptp) cc_final: 0.8634 (tptp) REVERT: F 37 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7698 (t70) REVERT: F 38 LEU cc_start: 0.9322 (pt) cc_final: 0.9119 (pt) outliers start: 11 outliers final: 8 residues processed: 148 average time/residue: 0.1901 time to fit residues: 33.1730 Evaluate side-chains 153 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 115 MET 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 41 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain F residue 37 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.0010 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 28 optimal weight: 0.1980 chunk 27 optimal weight: 0.3980 overall best weight: 0.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN C 322 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.137023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095934 restraints weight = 6784.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.098937 restraints weight = 4308.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100631 restraints weight = 3352.656| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3900 Z= 0.244 Angle : 1.061 18.612 5271 Z= 0.568 Chirality : 0.051 0.196 627 Planarity : 0.005 0.040 684 Dihedral : 5.790 41.418 561 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.76 % Allowed : 33.56 % Favored : 63.68 % 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: 0.42 (0.40), residues: 459 helix: 2.44 (0.30), residues: 261 sheet: -3.32 (0.66), residues: 36 loop : -2.67 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.015 0.003 HIS B 106 PHE 0.004 0.001 PHE D 63 TYR 0.008 0.002 TYR C 302 ARG 0.010 0.001 ARG B 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1521.49 seconds wall clock time: 36 minutes 16.67 seconds (2176.67 seconds total)