Starting phenix.real_space_refine on Wed Mar 5 22:28:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5l_10701/03_2025/6y5l_10701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5l_10701/03_2025/6y5l_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/cci-nas-00/data/ceres_data/6y5l_10701/03_2025/6y5l_10701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5l_10701/03_2025/6y5l_10701.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5l_10701/03_2025/6y5l_10701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5l_10701/03_2025/6y5l_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-5624/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: 2.74, per 1000 atoms: 0.71 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 - 3.00 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: 0.86 Conformation dependent library (CDL) restraints added in 402.5 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: 0.31 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: 0.86 Time building geometry restraints manager: 1.03 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: 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.490 Find NCS groups from input model: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.402 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: 0.1839 time to fit residues: 43.8508 Evaluate side-chains 163 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.131442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090443 restraints weight = 6889.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092887 restraints weight = 4570.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.094357 restraints weight = 3642.944| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 37.041 561 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 to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.457 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: 0.7824 (mmmt) cc_final: 0.7418 (mtpp) REVERT: A 320 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5547 (ttm) REVERT: B 51 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8854 (ptpp) REVERT: B 58 LYS cc_start: 0.9116 (mttp) cc_final: 0.8864 (mmtp) REVERT: B 64 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7468 (t-90) REVERT: B 110 LEU cc_start: 0.8956 (mt) cc_final: 0.8566 (mt) REVERT: B 112 ASP cc_start: 0.8748 (p0) cc_final: 0.8538 (p0) REVERT: B 121 LYS cc_start: 0.9318 (mtpt) cc_final: 0.9018 (tmtt) REVERT: C 41 GLU cc_start: 0.7950 (tp30) cc_final: 0.7704 (tp30) REVERT: C 307 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7208 (mtpp) REVERT: E 22 ASN cc_start: 0.7063 (m-40) cc_final: 0.6462 (t0) REVERT: E 320 MET cc_start: 0.6775 (ttm) cc_final: 0.6475 (ttm) REVERT: D 51 LYS cc_start: 0.9287 (mmtt) cc_final: 0.8859 (ptpt) REVERT: D 54 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8321 (ttp-110) REVERT: D 58 LYS cc_start: 0.9148 (mttt) cc_final: 0.8791 (mttm) REVERT: D 110 LEU cc_start: 0.9131 (mt) cc_final: 0.8928 (mt) REVERT: F 51 LYS cc_start: 0.9380 (mmtt) cc_final: 0.9005 (ptpt) REVERT: F 54 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8425 (ttm110) REVERT: F 58 LYS cc_start: 0.9169 (mttt) cc_final: 0.8889 (mmtt) REVERT: F 64 HIS cc_start: 0.8274 (m-70) cc_final: 0.7827 (m-70) REVERT: F 121 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8980 (tptp) outliers start: 13 outliers final: 5 residues processed: 171 average time/residue: 0.1944 time to fit residues: 39.2223 Evaluate side-chains 161 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 0.0010 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.2784 ------------------------------------------------------------------------------- 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 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.133672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099609 restraints weight = 6929.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.100024 restraints weight = 6329.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.101066 restraints weight = 4749.009| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3798 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= 0.197 Angle : 0.718 11.843 5271 Z= 0.388 Chirality : 0.044 0.145 627 Planarity : 0.006 0.047 684 Dihedral : 4.909 36.269 561 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.22 % Allowed : 19.54 % Favored : 77.24 % 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: 0.45 (0.40), residues: 459 helix: 3.26 (0.28), residues: 261 sheet: -4.19 (0.46), residues: 30 loop : -4.05 (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 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 177 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.426 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: 0.7481 (mmmt) cc_final: 0.7026 (mtpp) REVERT: B 64 HIS cc_start: 0.8212 (m-70) cc_final: 0.7435 (t-90) REVERT: B 121 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8981 (tmtt) REVERT: C 290 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7931 (m-40) REVERT: C 307 LYS cc_start: 0.7473 (mmmt) cc_final: 0.7192 (mtpp) REVERT: E 22 ASN cc_start: 0.6847 (m-40) cc_final: 0.6457 (t0) REVERT: E 320 MET cc_start: 0.6626 (ttm) cc_final: 0.6326 (ttm) REVERT: D 58 LYS cc_start: 0.9004 (mttt) cc_final: 0.8702 (mttm) REVERT: D 110 LEU cc_start: 0.9011 (mt) cc_final: 0.8743 (mt) REVERT: D 116 ASN cc_start: 0.8802 (m110) cc_final: 0.8013 (t0) REVERT: D 121 LYS cc_start: 0.8957 (tptp) cc_final: 0.8752 (tptp) REVERT: F 58 LYS cc_start: 0.9011 (mttt) cc_final: 0.8740 (mmtt) REVERT: F 64 HIS cc_start: 0.8278 (m-70) cc_final: 0.7969 (m170) outliers start: 14 outliers final: 7 residues processed: 172 average time/residue: 0.1806 time to fit residues: 36.8200 Evaluate side-chains 153 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 D residue 91 LEU 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 20 optimal weight: 0.0030 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.0070 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.2608 ------------------------------------------------------------------------------- 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 295 GLN 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 53 ASN F 106 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.133176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099626 restraints weight = 6786.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.100045 restraints weight = 6183.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.101036 restraints weight = 5017.021| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4418 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= 0.200 Angle : 0.772 12.179 5271 Z= 0.411 Chirality : 0.046 0.206 627 Planarity : 0.005 0.048 684 Dihedral : 4.795 35.754 561 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.68 % Allowed : 24.14 % Favored : 72.18 % 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: 0.61 (0.40), residues: 459 helix: 3.29 (0.28), residues: 261 sheet: -3.91 (0.50), residues: 30 loop : -3.84 (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 to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.415 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: A 307 LYS cc_start: 0.7454 (mmmt) cc_final: 0.7009 (mtpp) REVERT: B 64 HIS cc_start: 0.8025 (m-70) cc_final: 0.7388 (t-90) REVERT: C 290 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.8082 (m-40) REVERT: C 307 LYS cc_start: 0.7496 (mmmt) cc_final: 0.7194 (mtpp) REVERT: E 22 ASN cc_start: 0.7026 (m-40) cc_final: 0.6725 (t0) REVERT: E 290 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7929 (m-40) REVERT: E 320 MET cc_start: 0.6751 (ttm) cc_final: 0.6460 (ttm) REVERT: D 51 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8967 (ptpp) REVERT: D 54 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7970 (ttm110) REVERT: D 58 LYS cc_start: 0.8897 (mttt) cc_final: 0.8634 (mttm) REVERT: D 116 ASN cc_start: 0.8643 (m110) cc_final: 0.7715 (t0) REVERT: D 120 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8143 (mm-30) REVERT: F 51 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8915 (ptpp) REVERT: F 54 ARG cc_start: 0.8336 (ttm110) cc_final: 0.8113 (ttm110) REVERT: F 58 LYS cc_start: 0.8913 (mttt) cc_final: 0.8660 (mmtp) REVERT: F 64 HIS cc_start: 0.8072 (m-70) cc_final: 0.7460 (t-170) outliers start: 16 outliers final: 8 residues processed: 162 average time/residue: 0.1806 time to fit residues: 34.5799 Evaluate side-chains 155 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 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 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 51 LYS Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 51 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 0 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.136046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.103439 restraints weight = 6899.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104371 restraints weight = 5814.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.105540 restraints weight = 4468.226| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4698 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= 0.220 Angle : 0.802 13.467 5271 Z= 0.427 Chirality : 0.046 0.199 627 Planarity : 0.005 0.048 684 Dihedral : 4.770 35.890 561 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.45 % Allowed : 26.21 % Favored : 70.34 % 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: 3.05 (0.29), residues: 261 sheet: -3.78 (0.53), residues: 30 loop : -3.80 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 92 HIS 0.009 0.003 HIS D 106 PHE 0.006 0.001 PHE B 70 TYR 0.010 0.002 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 172 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.416 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: 0.7476 (mmmt) cc_final: 0.7013 (mtpp) REVERT: A 320 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6668 (ttp) REVERT: B 58 LYS cc_start: 0.8896 (mmtp) cc_final: 0.8606 (mmtp) REVERT: B 64 HIS cc_start: 0.8011 (m-70) cc_final: 0.7380 (t-90) REVERT: B 124 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8264 (ttp80) REVERT: C 307 LYS cc_start: 0.7538 (mmmt) cc_final: 0.7246 (mtpp) REVERT: E 22 ASN cc_start: 0.7050 (m-40) cc_final: 0.6777 (t0) REVERT: E 320 MET cc_start: 0.6960 (ttm) cc_final: 0.6613 (ttm) REVERT: D 51 LYS cc_start: 0.9241 (ptpt) cc_final: 0.8978 (ptpp) REVERT: D 58 LYS cc_start: 0.8901 (mttt) cc_final: 0.8643 (mttm) REVERT: F 51 LYS cc_start: 0.9026 (ptpt) cc_final: 0.8775 (ptpp) REVERT: F 64 HIS cc_start: 0.7964 (m-70) cc_final: 0.7424 (t-170) REVERT: F 114 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8306 (mt-10) outliers start: 15 outliers final: 10 residues processed: 164 average time/residue: 0.1838 time to fit residues: 35.6474 Evaluate side-chains 157 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain C residue 20 VAL 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 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN C 322 ASN 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.134726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094137 restraints weight = 6871.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096729 restraints weight = 4573.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098240 restraints weight = 3648.796| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4969 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= 0.278 Angle : 0.864 14.198 5271 Z= 0.459 Chirality : 0.048 0.178 627 Planarity : 0.006 0.049 684 Dihedral : 4.966 36.323 561 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.68 % Allowed : 26.67 % Favored : 69.66 % 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: 2.85 (0.28), residues: 261 sheet: -3.57 (0.59), residues: 30 loop : -3.75 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.011 0.003 HIS D 106 PHE 0.007 0.001 PHE F 70 TYR 0.014 0.003 TYR A 302 ARG 0.006 0.001 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.440 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 41 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7085 (tm-30) REVERT: A 307 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7287 (mtpp) REVERT: B 64 HIS cc_start: 0.8184 (m-70) cc_final: 0.7503 (t-170) REVERT: B 121 LYS cc_start: 0.8841 (tmtt) cc_final: 0.8584 (tptp) REVERT: C 290 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8196 (m-40) REVERT: C 307 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7274 (mtpp) REVERT: E 22 ASN cc_start: 0.7024 (m-40) cc_final: 0.6734 (t0) REVERT: E 320 MET cc_start: 0.7063 (ttm) cc_final: 0.6770 (ttm) REVERT: D 51 LYS cc_start: 0.9447 (ptpt) cc_final: 0.9192 (ptpp) REVERT: D 58 LYS cc_start: 0.9049 (mttt) cc_final: 0.8742 (mttm) REVERT: F 51 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9083 (ptpp) REVERT: F 64 HIS cc_start: 0.8078 (m-70) cc_final: 0.7525 (t-170) REVERT: F 67 GLU cc_start: 0.7667 (pp20) cc_final: 0.7426 (pp20) outliers start: 16 outliers final: 10 residues processed: 164 average time/residue: 0.1869 time to fit residues: 36.0961 Evaluate side-chains 162 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 51 LYS Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 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 = 0.4085 r_free = 0.4085 target = 0.132187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099931 restraints weight = 6837.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.100120 restraints weight = 5359.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101291 restraints weight = 4814.302| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5253 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= 0.327 Angle : 0.914 13.320 5271 Z= 0.488 Chirality : 0.050 0.166 627 Planarity : 0.006 0.045 684 Dihedral : 5.052 36.468 561 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.37 % Allowed : 29.43 % Favored : 66.21 % 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: 0.19 (0.39), residues: 459 helix: 2.63 (0.28), residues: 261 sheet: -3.68 (0.56), residues: 36 loop : -3.44 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 92 HIS 0.013 0.004 HIS D 106 PHE 0.008 0.001 PHE F 70 TYR 0.017 0.003 TYR C 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 174 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.449 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: A 41 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 307 LYS cc_start: 0.7674 (mmmt) cc_final: 0.7197 (mtpp) REVERT: B 58 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8552 (mmtp) REVERT: B 64 HIS cc_start: 0.7749 (m-70) cc_final: 0.7201 (t-170) REVERT: B 120 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8239 (mm-30) REVERT: B 121 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8570 (tptp) REVERT: C 307 LYS cc_start: 0.7505 (mmmt) cc_final: 0.7111 (mtpp) REVERT: E 22 ASN cc_start: 0.7246 (m-40) cc_final: 0.6971 (t0) REVERT: D 54 ARG cc_start: 0.8191 (ttm110) cc_final: 0.7959 (ttm110) REVERT: D 58 LYS cc_start: 0.8798 (mttt) cc_final: 0.8592 (mttm) REVERT: F 37 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7968 (t70) REVERT: F 58 LYS cc_start: 0.8866 (mttt) cc_final: 0.8535 (mttm) REVERT: F 64 HIS cc_start: 0.7801 (m-70) cc_final: 0.7288 (t-170) REVERT: F 110 LEU cc_start: 0.8823 (mm) cc_final: 0.8588 (mp) REVERT: F 120 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8306 (mm-30) outliers start: 19 outliers final: 12 residues processed: 164 average time/residue: 0.1808 time to fit residues: 35.0398 Evaluate side-chains 158 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 107 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 7 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.134016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094442 restraints weight = 6826.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097226 restraints weight = 4460.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.098852 restraints weight = 3500.034| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5452 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= 0.239 Angle : 0.932 15.886 5271 Z= 0.494 Chirality : 0.050 0.224 627 Planarity : 0.006 0.044 684 Dihedral : 5.012 36.161 561 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.60 % Allowed : 31.49 % Favored : 63.91 % 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: 0.30 (0.39), residues: 459 helix: 2.59 (0.29), residues: 261 sheet: -3.49 (0.61), residues: 36 loop : -3.18 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.012 0.003 HIS B 106 PHE 0.006 0.001 PHE B 70 TYR 0.011 0.002 TYR C 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 176 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 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: A 41 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 307 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7431 (mtpp) REVERT: A 320 MET cc_start: 0.7099 (ttm) cc_final: 0.6706 (ttp) REVERT: B 58 LYS cc_start: 0.9093 (mmtp) cc_final: 0.8655 (mmtp) REVERT: B 120 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8552 (mm-30) REVERT: B 121 LYS cc_start: 0.8911 (tmtt) cc_final: 0.8678 (tptp) REVERT: C 307 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7308 (mtpp) REVERT: E 290 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8072 (m-40) REVERT: E 302 TYR cc_start: 0.4169 (t80) cc_final: 0.2748 (m-80) REVERT: D 51 LYS cc_start: 0.9443 (ptpt) cc_final: 0.9194 (ptpp) REVERT: D 54 ARG cc_start: 0.8657 (ttm110) cc_final: 0.8387 (ttm110) REVERT: D 58 LYS cc_start: 0.9056 (mttt) cc_final: 0.8739 (mttm) REVERT: D 64 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7442 (t-90) REVERT: D 115 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7511 (mtm) REVERT: F 37 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8196 (t70) REVERT: F 51 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9166 (ptpp) REVERT: F 54 ARG cc_start: 0.8700 (ttm110) cc_final: 0.8350 (ptp-110) REVERT: F 64 HIS cc_start: 0.8031 (m-70) cc_final: 0.7520 (t-170) REVERT: F 121 LYS cc_start: 0.8723 (tptp) cc_final: 0.8511 (tptp) outliers start: 20 outliers final: 12 residues processed: 164 average time/residue: 0.1947 time to fit residues: 37.6415 Evaluate side-chains 166 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 43 VAL 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 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 51 LYS 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 3 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** 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 = 0.4090 r_free = 0.4090 target = 0.132336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092546 restraints weight = 6742.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095063 restraints weight = 4591.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.096524 restraints weight = 3682.309| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3900 Z= 0.345 Angle : 1.034 15.304 5271 Z= 0.552 Chirality : 0.054 0.250 627 Planarity : 0.006 0.043 684 Dihedral : 5.343 36.582 561 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.06 % Allowed : 31.95 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.39), residues: 459 helix: 2.39 (0.29), residues: 261 sheet: -3.43 (0.65), residues: 36 loop : -3.09 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 92 HIS 0.016 0.005 HIS D 106 PHE 0.007 0.001 PHE D 70 TYR 0.016 0.003 TYR C 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 176 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.445 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: A 302 TYR cc_start: 0.3786 (t80) cc_final: 0.2457 (m-80) REVERT: A 307 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7631 (mtpp) REVERT: B 120 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8491 (mm-30) REVERT: B 121 LYS cc_start: 0.8946 (tmtt) cc_final: 0.8699 (tptp) REVERT: C 307 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7362 (mtpp) REVERT: E 302 TYR cc_start: 0.3838 (t80) cc_final: 0.2485 (m-80) REVERT: D 51 LYS cc_start: 0.9480 (ptpt) cc_final: 0.9168 (ptpp) REVERT: D 54 ARG cc_start: 0.8699 (ttm110) cc_final: 0.8397 (ttm110) REVERT: D 58 LYS cc_start: 0.9074 (mttt) cc_final: 0.8762 (mttm) REVERT: D 64 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7512 (t-90) REVERT: D 121 LYS cc_start: 0.8977 (tptp) cc_final: 0.8690 (tptp) REVERT: F 37 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8170 (t70) REVERT: F 54 ARG cc_start: 0.8726 (ttm110) cc_final: 0.8366 (ptp-110) REVERT: F 64 HIS cc_start: 0.8071 (m-70) cc_final: 0.7617 (t-170) REVERT: F 121 LYS cc_start: 0.8711 (tptp) cc_final: 0.8491 (tptp) outliers start: 22 outliers final: 11 residues processed: 163 average time/residue: 0.1924 time to fit residues: 36.9993 Evaluate side-chains 163 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 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 307 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.0470 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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 C 296 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.134701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094436 restraints weight = 6823.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097107 restraints weight = 4519.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.098709 restraints weight = 3577.513| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3900 Z= 0.264 Angle : 1.059 17.078 5271 Z= 0.559 Chirality : 0.053 0.231 627 Planarity : 0.006 0.043 684 Dihedral : 5.572 36.712 561 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.14 % Allowed : 33.33 % Favored : 62.53 % 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: 0.18 (0.40), residues: 459 helix: 2.30 (0.30), residues: 261 sheet: -3.33 (0.66), residues: 36 loop : -2.91 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.016 0.004 HIS B 106 PHE 0.004 0.001 PHE F 70 TYR 0.009 0.002 TYR C 302 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 174 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7446 (mtpp) REVERT: A 320 MET cc_start: 0.7382 (ttm) cc_final: 0.7041 (ttp) REVERT: B 120 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8509 (mm-30) REVERT: C 290 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8208 (m-40) REVERT: C 307 LYS cc_start: 0.7713 (mmmt) cc_final: 0.7286 (mtpp) REVERT: C 320 MET cc_start: 0.6694 (ttm) cc_final: 0.6126 (ttp) REVERT: E 290 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8150 (m-40) REVERT: E 302 TYR cc_start: 0.3879 (t80) cc_final: 0.2446 (m-80) REVERT: E 315 LYS cc_start: 0.8179 (mmtm) cc_final: 0.7838 (tppt) REVERT: D 51 LYS cc_start: 0.9469 (ptpt) cc_final: 0.9126 (ptpp) REVERT: D 54 ARG cc_start: 0.8752 (ttm110) cc_final: 0.8462 (ttm110) REVERT: D 58 LYS cc_start: 0.9076 (mttt) cc_final: 0.8769 (mttm) REVERT: D 64 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7542 (t-90) REVERT: D 121 LYS cc_start: 0.8938 (tptp) cc_final: 0.8661 (tptp) REVERT: F 37 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7872 (t70) REVERT: F 54 ARG cc_start: 0.8731 (ttm110) cc_final: 0.8369 (ptp-110) REVERT: F 117 LYS cc_start: 0.9236 (mtmt) cc_final: 0.9023 (mtmm) REVERT: F 121 LYS cc_start: 0.8675 (tptp) cc_final: 0.8445 (tptp) outliers start: 18 outliers final: 10 residues processed: 162 average time/residue: 0.2099 time to fit residues: 40.2058 Evaluate side-chains 164 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 16 optimal weight: 0.3980 chunk 9 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.134056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093999 restraints weight = 6648.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096549 restraints weight = 4462.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.098117 restraints weight = 3560.306| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3900 Z= 0.302 Angle : 1.141 17.953 5271 Z= 0.597 Chirality : 0.056 0.216 627 Planarity : 0.006 0.041 684 Dihedral : 6.051 36.390 561 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.91 % Allowed : 33.56 % Favored : 62.53 % 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: 0.20 (0.40), residues: 459 helix: 2.28 (0.30), residues: 261 sheet: -3.31 (0.70), residues: 36 loop : -2.83 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.016 0.004 HIS B 106 PHE 0.006 0.001 PHE E 294 TYR 0.012 0.003 TYR C 302 ARG 0.011 0.001 ARG B 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.30 seconds wall clock time: 36 minutes 18.84 seconds (2178.84 seconds total)