Starting phenix.real_space_refine on Fri Dec 19 11:52:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5l_10701/12_2025/6y5l_10701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5l_10701/12_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 { model { file = "/net/cci-nas-00/data/ceres_data/6y5l_10701/12_2025/6y5l_10701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5l_10701/12_2025/6y5l_10701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5l_10701/12_2025/6y5l_10701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5l_10701/12_2025/6y5l_10701.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/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: 0.79, per 1000 atoms: 0.20 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: 0.23 Conformation dependent library (CDL) restraints added in 100.1 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 55.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 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: 0.72 Time building geometry restraints manager: 0.31 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: 0.01 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: 5.940 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 12.580 ------------------------------------------------------------------------------- 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 3906 Z= 0.174 Angle : 0.704 6.830 5286 Z= 0.402 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG F 54 TYR 0.022 0.003 TYR E 308 PHE 0.023 0.003 PHE D 63 TRP 0.002 0.001 TRP D 92 HIS 0.005 0.002 HIS F 64 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3900) covalent geometry : angle 0.70143 ( 5271) SS BOND : bond 0.00126 ( 3) SS BOND : angle 1.19134 ( 6) hydrogen bonds : bond 0.08119 ( 273) hydrogen bonds : angle 4.50729 ( 792) link_NAG-ASN : bond 0.00245 ( 3) link_NAG-ASN : angle 1.40889 ( 9) *********************** 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 : 0.191 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: 0.0771 time to fit residues: 18.6802 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 : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.131423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091084 restraints weight = 6933.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.093561 restraints weight = 4586.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094988 restraints weight = 3636.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095634 restraints weight = 3205.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095635 restraints weight = 3012.793| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3906 Z= 0.194 Angle : 0.702 4.765 5286 Z= 0.378 Chirality : 0.047 0.152 627 Planarity : 0.006 0.042 684 Dihedral : 5.220 37.195 561 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.45 % Allowed : 18.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.38), residues: 459 helix: 2.50 (0.26), residues: 261 sheet: -4.25 (0.46), residues: 30 loop : -4.38 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 123 TYR 0.014 0.003 TYR C 302 PHE 0.015 0.002 PHE B 70 TRP 0.003 0.001 TRP B 92 HIS 0.010 0.002 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 3900) covalent geometry : angle 0.69321 ( 5271) SS BOND : bond 0.00380 ( 3) SS BOND : angle 1.93526 ( 6) hydrogen bonds : bond 0.03348 ( 273) hydrogen bonds : angle 3.67161 ( 792) link_NAG-ASN : bond 0.00472 ( 3) link_NAG-ASN : angle 2.38862 ( 9) *********************** 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 186 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.172 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: 0.7833 (mmmt) cc_final: 0.7427 (mtpp) REVERT: B 51 LYS cc_start: 0.9245 (mmtt) cc_final: 0.8860 (ptpp) REVERT: B 58 LYS cc_start: 0.9111 (mttp) cc_final: 0.8848 (mmtp) REVERT: B 64 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7470 (t-90) REVERT: B 110 LEU cc_start: 0.8948 (mt) cc_final: 0.8560 (mt) REVERT: B 121 LYS cc_start: 0.9307 (mtpt) cc_final: 0.9012 (tmtt) REVERT: C 41 GLU cc_start: 0.7950 (tp30) cc_final: 0.7665 (tp30) REVERT: C 307 LYS cc_start: 0.7609 (mmmt) cc_final: 0.7263 (mtpp) REVERT: E 320 MET cc_start: 0.6822 (ttm) cc_final: 0.6535 (ttm) REVERT: D 51 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8821 (ptpt) REVERT: D 54 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8316 (ttm110) REVERT: D 58 LYS cc_start: 0.9126 (mttt) cc_final: 0.8755 (mttm) REVERT: F 54 ARG cc_start: 0.8829 (mtp85) cc_final: 0.8318 (ttm110) REVERT: F 58 LYS cc_start: 0.9161 (mttt) cc_final: 0.8844 (mmtt) REVERT: F 64 HIS cc_start: 0.8253 (m-70) cc_final: 0.7804 (m-70) REVERT: F 121 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8966 (tptp) outliers start: 15 outliers final: 8 residues processed: 172 average time/residue: 0.0878 time to fit residues: 17.8789 Evaluate side-chains 165 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 118 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 26 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.2938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.133055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.099192 restraints weight = 6885.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.099568 restraints weight = 6303.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100632 restraints weight = 4742.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102069 restraints weight = 3751.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102547 restraints weight = 3324.261| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3906 Z= 0.144 Angle : 0.718 11.660 5286 Z= 0.388 Chirality : 0.044 0.146 627 Planarity : 0.006 0.047 684 Dihedral : 4.925 36.273 561 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.91 % Allowed : 19.31 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.40), residues: 459 helix: 3.26 (0.28), residues: 261 sheet: -4.20 (0.46), residues: 30 loop : -4.06 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 124 TYR 0.008 0.002 TYR C 302 PHE 0.008 0.001 PHE D 70 TRP 0.002 0.001 TRP B 92 HIS 0.012 0.003 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3900) covalent geometry : angle 0.71073 ( 5271) SS BOND : bond 0.00273 ( 3) SS BOND : angle 1.59227 ( 6) hydrogen bonds : bond 0.03350 ( 273) hydrogen bonds : angle 3.54899 ( 792) link_NAG-ASN : bond 0.00364 ( 3) link_NAG-ASN : angle 2.22486 ( 9) *********************** 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 181 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.173 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: 0.7399 (mmmt) cc_final: 0.6915 (mtpp) REVERT: B 64 HIS cc_start: 0.8187 (m-70) cc_final: 0.7423 (t-90) REVERT: B 110 LEU cc_start: 0.8946 (mt) cc_final: 0.8708 (mt) REVERT: B 112 ASP cc_start: 0.8573 (p0) cc_final: 0.8368 (p0) REVERT: B 121 LYS cc_start: 0.9240 (mtpt) cc_final: 0.8985 (tmtt) REVERT: C 41 GLU cc_start: 0.7890 (tp30) cc_final: 0.7672 (tp30) REVERT: C 307 LYS cc_start: 0.7444 (mmmt) cc_final: 0.7174 (mtpp) REVERT: E 320 MET cc_start: 0.6691 (ttm) cc_final: 0.6377 (ttm) REVERT: D 58 LYS cc_start: 0.9010 (mttt) cc_final: 0.8698 (mttm) REVERT: D 116 ASN cc_start: 0.8811 (m110) cc_final: 0.8007 (t0) REVERT: D 121 LYS cc_start: 0.8960 (tptp) cc_final: 0.8756 (tptp) REVERT: F 51 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8807 (ptpp) REVERT: F 54 ARG cc_start: 0.8287 (mtp85) cc_final: 0.8083 (ttm110) REVERT: F 58 LYS cc_start: 0.9022 (mttt) cc_final: 0.8745 (mmtt) REVERT: F 64 HIS cc_start: 0.8236 (m-70) cc_final: 0.7943 (m170) outliers start: 17 outliers final: 11 residues processed: 173 average time/residue: 0.0844 time to fit residues: 17.4323 Evaluate side-chains 158 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 B residue 118 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 19 optimal weight: 0.1980 chunk 42 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 overall best weight: 0.3586 ------------------------------------------------------------------------------- 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 295 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.131628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090057 restraints weight = 6853.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092443 restraints weight = 4641.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.093640 restraints weight = 3743.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094577 restraints weight = 3358.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094875 restraints weight = 3141.610| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3906 Z= 0.157 Angle : 0.761 12.011 5286 Z= 0.406 Chirality : 0.045 0.203 627 Planarity : 0.005 0.048 684 Dihedral : 4.884 35.878 561 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.37 % Allowed : 23.68 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.40), residues: 459 helix: 3.24 (0.28), residues: 261 sheet: -3.96 (0.51), residues: 30 loop : -3.87 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 124 TYR 0.010 0.002 TYR C 302 PHE 0.008 0.001 PHE B 70 TRP 0.002 0.001 TRP B 92 HIS 0.009 0.003 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3900) covalent geometry : angle 0.75433 ( 5271) SS BOND : bond 0.00298 ( 3) SS BOND : angle 1.56201 ( 6) hydrogen bonds : bond 0.03559 ( 273) hydrogen bonds : angle 3.60560 ( 792) link_NAG-ASN : bond 0.00205 ( 3) link_NAG-ASN : angle 2.19714 ( 9) *********************** 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 176 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.158 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: 0.7702 (mmmt) cc_final: 0.7207 (mtpp) REVERT: B 57 GLU cc_start: 0.9759 (mm-30) cc_final: 0.9501 (mm-30) REVERT: B 58 LYS cc_start: 0.9014 (mmtp) cc_final: 0.8717 (mmtp) REVERT: B 64 HIS cc_start: 0.8072 (OUTLIER) cc_final: 0.7433 (t-90) REVERT: B 110 LEU cc_start: 0.8951 (mt) cc_final: 0.8730 (mt) REVERT: B 121 LYS cc_start: 0.9256 (mtpt) cc_final: 0.9051 (tmtt) REVERT: C 290 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8040 (m-40) REVERT: C 307 LYS cc_start: 0.7763 (mmmt) cc_final: 0.7462 (mtpp) REVERT: E 320 MET cc_start: 0.6822 (ttm) cc_final: 0.6499 (ttm) REVERT: D 51 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8917 (mtmm) REVERT: D 54 ARG cc_start: 0.8616 (ttm110) cc_final: 0.8311 (ttm110) REVERT: D 58 LYS cc_start: 0.9093 (mttt) cc_final: 0.8758 (mttm) REVERT: D 110 LEU cc_start: 0.9048 (mt) cc_final: 0.8831 (mt) REVERT: D 116 ASN cc_start: 0.8750 (m110) cc_final: 0.7746 (t0) REVERT: D 120 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8245 (mm-30) REVERT: D 121 LYS cc_start: 0.8899 (tptp) cc_final: 0.8616 (tptp) REVERT: F 54 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8267 (ttm110) REVERT: F 58 LYS cc_start: 0.9130 (mttt) cc_final: 0.8725 (mmtp) REVERT: F 64 HIS cc_start: 0.8250 (m-70) cc_final: 0.7992 (m170) outliers start: 19 outliers final: 10 residues processed: 164 average time/residue: 0.0824 time to fit residues: 16.0393 Evaluate side-chains 162 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain 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 51 LYS Chi-restraints excluded: chain D residue 64 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 322 ASN ** D 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 = 0.4113 r_free = 0.4113 target = 0.133965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093064 restraints weight = 6829.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095776 restraints weight = 4410.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.097432 restraints weight = 3477.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.098232 restraints weight = 3034.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098289 restraints weight = 2830.766| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3906 Z= 0.186 Angle : 0.796 13.356 5286 Z= 0.428 Chirality : 0.046 0.198 627 Planarity : 0.006 0.048 684 Dihedral : 4.977 36.163 561 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.91 % Allowed : 26.21 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.40), residues: 459 helix: 2.94 (0.28), residues: 261 sheet: -3.69 (0.56), residues: 30 loop : -3.78 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 124 TYR 0.014 0.003 TYR C 302 PHE 0.008 0.001 PHE B 70 TRP 0.003 0.001 TRP B 92 HIS 0.010 0.003 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 3900) covalent geometry : angle 0.78693 ( 5271) SS BOND : bond 0.00395 ( 3) SS BOND : angle 1.65206 ( 6) hydrogen bonds : bond 0.03772 ( 273) hydrogen bonds : angle 3.80597 ( 792) link_NAG-ASN : bond 0.00348 ( 3) link_NAG-ASN : angle 2.77777 ( 9) *********************** 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 175 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.150 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 41 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7135 (tm-30) REVERT: A 307 LYS cc_start: 0.7634 (mmmt) cc_final: 0.7096 (mtpp) REVERT: B 58 LYS cc_start: 0.9150 (mmtp) cc_final: 0.8756 (mmtt) REVERT: B 64 HIS cc_start: 0.8306 (m-70) cc_final: 0.7599 (t-90) REVERT: B 110 LEU cc_start: 0.9014 (mt) cc_final: 0.8799 (mt) REVERT: B 121 LYS cc_start: 0.9271 (mtpt) cc_final: 0.8947 (tptp) REVERT: C 290 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8126 (m-40) REVERT: C 307 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7430 (mtpp) REVERT: E 320 MET cc_start: 0.6986 (ttm) cc_final: 0.6596 (ttm) REVERT: D 47 GLN cc_start: 0.9018 (pp30) cc_final: 0.8810 (pp30) REVERT: D 51 LYS cc_start: 0.9447 (ptpt) cc_final: 0.8993 (mtmm) REVERT: D 54 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8463 (ttm110) REVERT: D 58 LYS cc_start: 0.9127 (mttt) cc_final: 0.8813 (mttm) REVERT: F 54 ARG cc_start: 0.8548 (mtp85) cc_final: 0.8268 (ttm110) REVERT: F 58 LYS cc_start: 0.9209 (mttt) cc_final: 0.8672 (mmtp) REVERT: F 64 HIS cc_start: 0.8278 (m-70) cc_final: 0.7618 (t-170) outliers start: 17 outliers final: 12 residues processed: 166 average time/residue: 0.0870 time to fit residues: 17.0993 Evaluate side-chains 167 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 41 THR Chi-restraints excluded: chain F residue 88 LYS 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 16 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.0020 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.2588 ------------------------------------------------------------------------------- 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 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.135996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095586 restraints weight = 6728.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.098335 restraints weight = 4401.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100000 restraints weight = 3460.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.100903 restraints weight = 3029.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.101175 restraints weight = 2820.118| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3906 Z= 0.152 Angle : 0.835 14.467 5286 Z= 0.443 Chirality : 0.046 0.223 627 Planarity : 0.005 0.047 684 Dihedral : 4.794 36.336 561 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.22 % Allowed : 26.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.40), residues: 459 helix: 2.84 (0.29), residues: 261 sheet: -3.51 (0.61), residues: 30 loop : -3.61 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 124 TYR 0.009 0.002 TYR C 302 PHE 0.004 0.001 PHE F 70 TRP 0.002 0.001 TRP B 92 HIS 0.011 0.003 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3900) covalent geometry : angle 0.82839 ( 5271) SS BOND : bond 0.00125 ( 3) SS BOND : angle 0.86851 ( 6) hydrogen bonds : bond 0.03912 ( 273) hydrogen bonds : angle 3.81358 ( 792) link_NAG-ASN : bond 0.00302 ( 3) link_NAG-ASN : angle 2.66300 ( 9) *********************** 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 172 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.163 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: 0.7597 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 307 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7231 (mtpp) REVERT: A 320 MET cc_start: 0.6582 (ttp) cc_final: 0.6168 (ttm) REVERT: B 58 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8791 (mmtp) REVERT: B 121 LYS cc_start: 0.9218 (mtpt) cc_final: 0.8983 (tmtt) REVERT: C 290 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8162 (m-40) REVERT: C 307 LYS cc_start: 0.7731 (mmmt) cc_final: 0.7378 (mtpp) REVERT: C 315 LYS cc_start: 0.8111 (mmtm) cc_final: 0.7747 (mmtm) REVERT: E 290 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8019 (m-40) REVERT: E 320 MET cc_start: 0.7002 (ttm) cc_final: 0.6719 (ttm) REVERT: D 51 LYS cc_start: 0.9376 (ptpt) cc_final: 0.9108 (ptpp) REVERT: D 54 ARG cc_start: 0.8550 (ttm110) cc_final: 0.8341 (ttm110) REVERT: D 58 LYS cc_start: 0.9106 (mttt) cc_final: 0.8804 (mttm) REVERT: F 58 LYS cc_start: 0.9123 (mttt) cc_final: 0.8601 (mmtp) REVERT: F 64 HIS cc_start: 0.8014 (m-70) cc_final: 0.7465 (t-170) REVERT: F 67 GLU cc_start: 0.7561 (pp20) cc_final: 0.7313 (pp20) outliers start: 14 outliers final: 9 residues processed: 166 average time/residue: 0.0841 time to fit residues: 16.5862 Evaluate side-chains 159 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 41 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 312 ASN C 322 ASN E 296 ASN E 322 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.133271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.093367 restraints weight = 6811.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.095982 restraints weight = 4527.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097563 restraints weight = 3588.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.098320 restraints weight = 3144.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.098859 restraints weight = 2940.303| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3906 Z= 0.205 Angle : 0.901 14.435 5286 Z= 0.480 Chirality : 0.049 0.177 627 Planarity : 0.006 0.046 684 Dihedral : 4.974 36.060 561 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.60 % Allowed : 30.11 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.39), residues: 459 helix: 2.61 (0.28), residues: 261 sheet: -3.62 (0.60), residues: 36 loop : -3.45 (0.41), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 124 TYR 0.015 0.003 TYR C 302 PHE 0.007 0.001 PHE F 70 TRP 0.003 0.001 TRP B 92 HIS 0.013 0.004 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 3900) covalent geometry : angle 0.88895 ( 5271) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.47443 ( 6) hydrogen bonds : bond 0.04229 ( 273) hydrogen bonds : angle 4.09054 ( 792) link_NAG-ASN : bond 0.00322 ( 3) link_NAG-ASN : angle 3.66227 ( 9) *********************** 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 175 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.161 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: 0.7832 (mmmt) cc_final: 0.7339 (mtpp) REVERT: B 58 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8877 (mmtp) REVERT: B 64 HIS cc_start: 0.8053 (m-70) cc_final: 0.7449 (t-170) REVERT: C 290 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8211 (m-40) REVERT: C 307 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7302 (mtpp) REVERT: C 320 MET cc_start: 0.6698 (ttm) cc_final: 0.6397 (ttm) REVERT: E 320 MET cc_start: 0.6954 (ttm) cc_final: 0.6746 (ttm) REVERT: D 47 GLN cc_start: 0.8951 (pp30) cc_final: 0.8695 (pp30) REVERT: D 51 LYS cc_start: 0.9384 (ptpt) cc_final: 0.8967 (mtmm) REVERT: D 58 LYS cc_start: 0.9065 (mttt) cc_final: 0.8761 (mttm) REVERT: F 54 ARG cc_start: 0.8600 (ttm110) cc_final: 0.8261 (ttm110) REVERT: F 58 LYS cc_start: 0.9086 (mttt) cc_final: 0.8849 (mttt) REVERT: F 64 HIS cc_start: 0.7992 (m-70) cc_final: 0.7367 (t-170) REVERT: F 110 LEU cc_start: 0.9019 (mm) cc_final: 0.8740 (mp) outliers start: 20 outliers final: 13 residues processed: 164 average time/residue: 0.0862 time to fit residues: 16.7686 Evaluate side-chains 161 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 C residue 312 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 104 ASN 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 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 21 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN C 296 ASN C 322 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.134167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094370 restraints weight = 6824.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097082 restraints weight = 4494.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098736 restraints weight = 3544.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099436 restraints weight = 3098.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100120 restraints weight = 2903.567| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3906 Z= 0.178 Angle : 0.907 14.374 5286 Z= 0.482 Chirality : 0.049 0.203 627 Planarity : 0.006 0.043 684 Dihedral : 4.986 36.444 561 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.37 % Allowed : 31.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.39), residues: 459 helix: 2.47 (0.29), residues: 261 sheet: -3.44 (0.64), residues: 36 loop : -3.18 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 54 TYR 0.011 0.002 TYR C 302 PHE 0.006 0.001 PHE D 63 TRP 0.003 0.001 TRP B 92 HIS 0.014 0.003 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 3900) covalent geometry : angle 0.89371 ( 5271) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.40209 ( 6) hydrogen bonds : bond 0.04365 ( 273) hydrogen bonds : angle 4.09834 ( 792) link_NAG-ASN : bond 0.00153 ( 3) link_NAG-ASN : angle 3.92974 ( 9) *********************** 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 173 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.156 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: 0.7899 (mmmt) cc_final: 0.7419 (mtpp) REVERT: A 322 ASN cc_start: 0.7401 (t0) cc_final: 0.6490 (t0) REVERT: B 58 LYS cc_start: 0.9092 (mmtp) cc_final: 0.8831 (mmtp) REVERT: C 307 LYS cc_start: 0.7732 (mmmt) cc_final: 0.7305 (mtpp) REVERT: C 315 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7759 (mmtm) REVERT: C 320 MET cc_start: 0.6421 (ttm) cc_final: 0.6096 (ttm) REVERT: E 290 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8041 (m-40) REVERT: E 302 TYR cc_start: 0.4256 (t80) cc_final: 0.2774 (m-80) REVERT: D 51 LYS cc_start: 0.9418 (ptpt) cc_final: 0.9173 (ptpp) REVERT: D 54 ARG cc_start: 0.8645 (ttm110) cc_final: 0.8413 (ttm110) REVERT: D 58 LYS cc_start: 0.9072 (mttt) cc_final: 0.8742 (mttm) REVERT: F 54 ARG cc_start: 0.8586 (ttm110) cc_final: 0.8176 (ttm110) REVERT: F 58 LYS cc_start: 0.9104 (mttt) cc_final: 0.8659 (mttm) REVERT: F 64 HIS cc_start: 0.8016 (m-70) cc_final: 0.7544 (t-170) REVERT: F 67 GLU cc_start: 0.7551 (pp20) cc_final: 0.7295 (pp20) outliers start: 19 outliers final: 11 residues processed: 164 average time/residue: 0.0815 time to fit residues: 15.9348 Evaluate side-chains 158 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 25 LEU Chi-restraints excluded: chain E residue 290 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 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 = 0.4124 r_free = 0.4124 target = 0.134797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094258 restraints weight = 6666.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096896 restraints weight = 4472.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098385 restraints weight = 3557.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.099342 restraints weight = 3141.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099708 restraints weight = 2920.081| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3906 Z= 0.185 Angle : 0.997 16.751 5286 Z= 0.517 Chirality : 0.050 0.197 627 Planarity : 0.005 0.042 684 Dihedral : 5.059 36.739 561 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.14 % Allowed : 32.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.40), residues: 459 helix: 2.29 (0.30), residues: 261 sheet: -3.42 (0.64), residues: 36 loop : -3.02 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 54 TYR 0.011 0.002 TYR C 302 PHE 0.006 0.001 PHE D 63 TRP 0.003 0.001 TRP B 92 HIS 0.015 0.004 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3900) covalent geometry : angle 0.98466 ( 5271) SS BOND : bond 0.00186 ( 3) SS BOND : angle 0.26750 ( 6) hydrogen bonds : bond 0.04440 ( 273) hydrogen bonds : angle 4.26504 ( 792) link_NAG-ASN : bond 0.00160 ( 3) link_NAG-ASN : angle 4.03836 ( 9) *********************** 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 170 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.161 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: 0.7597 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 307 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7417 (mtpp) REVERT: B 54 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8491 (ttm110) REVERT: C 307 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7296 (mtpp) REVERT: E 290 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8047 (m-40) REVERT: E 302 TYR cc_start: 0.3961 (t80) cc_final: 0.2612 (m-80) REVERT: D 51 LYS cc_start: 0.9473 (ptpt) cc_final: 0.8987 (mtmm) REVERT: D 54 ARG cc_start: 0.8669 (ttm110) cc_final: 0.8341 (ttm110) REVERT: D 58 LYS cc_start: 0.9104 (mttt) cc_final: 0.8775 (mttm) REVERT: D 64 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7561 (t-90) REVERT: D 121 LYS cc_start: 0.8704 (tptp) cc_final: 0.8498 (tptp) REVERT: F 54 ARG cc_start: 0.8633 (ttm110) cc_final: 0.8392 (ttm110) REVERT: F 58 LYS cc_start: 0.9100 (mttt) cc_final: 0.8676 (mttm) outliers start: 18 outliers final: 12 residues processed: 159 average time/residue: 0.0877 time to fit residues: 16.4655 Evaluate side-chains 165 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 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 D residue 104 ASN 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: 0.9990 chunk 26 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN ** 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 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 = 0.4136 r_free = 0.4136 target = 0.135468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094776 restraints weight = 6781.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097604 restraints weight = 4457.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.099022 restraints weight = 3517.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100080 restraints weight = 3113.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100419 restraints weight = 2885.611| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3906 Z= 0.182 Angle : 1.028 16.272 5286 Z= 0.536 Chirality : 0.050 0.204 627 Planarity : 0.005 0.039 684 Dihedral : 5.204 36.931 561 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.37 % Allowed : 31.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.40), residues: 459 helix: 2.19 (0.30), residues: 261 sheet: -3.39 (0.64), residues: 36 loop : -2.86 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 54 TYR 0.008 0.002 TYR C 302 PHE 0.005 0.001 PHE D 63 TRP 0.002 0.001 TRP B 92 HIS 0.015 0.004 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 3900) covalent geometry : angle 1.01704 ( 5271) SS BOND : bond 0.00027 ( 3) SS BOND : angle 0.31366 ( 6) hydrogen bonds : bond 0.04586 ( 273) hydrogen bonds : angle 4.28436 ( 792) link_NAG-ASN : bond 0.00385 ( 3) link_NAG-ASN : angle 3.89525 ( 9) ********************** 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 171 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.146 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 41 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7146 (tm-30) REVERT: A 307 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7409 (mtpp) REVERT: B 58 LYS cc_start: 0.9099 (mttt) cc_final: 0.8647 (mmtp) REVERT: C 307 LYS cc_start: 0.7684 (mmmt) cc_final: 0.7251 (mtpp) REVERT: E 302 TYR cc_start: 0.3993 (t80) cc_final: 0.2507 (m-80) REVERT: E 315 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7761 (tppt) REVERT: D 51 LYS cc_start: 0.9472 (ptpt) cc_final: 0.9103 (ptpp) REVERT: D 54 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8395 (ttm110) REVERT: D 58 LYS cc_start: 0.9106 (mttt) cc_final: 0.8779 (mttm) REVERT: D 64 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7584 (t-90) REVERT: D 121 LYS cc_start: 0.8644 (tptp) cc_final: 0.8408 (tptp) REVERT: F 54 ARG cc_start: 0.8679 (ttm110) cc_final: 0.8423 (ttm110) REVERT: F 58 LYS cc_start: 0.9107 (mttt) cc_final: 0.8682 (mttm) REVERT: F 120 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8543 (mm-30) REVERT: F 121 LYS cc_start: 0.8635 (tptp) cc_final: 0.8413 (tptp) outliers start: 19 outliers final: 13 residues processed: 160 average time/residue: 0.0820 time to fit residues: 15.6275 Evaluate side-chains 161 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 E residue 25 LEU Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 104 ASN 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 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 290 ASN C 296 ASN C 312 ASN C 322 ASN E 296 ASN E 322 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.132075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.099913 restraints weight = 6874.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.100880 restraints weight = 5670.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.101873 restraints weight = 4717.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.102590 restraints weight = 3617.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.103231 restraints weight = 3383.309| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 3906 Z= 0.262 Angle : 1.060 15.022 5286 Z= 0.561 Chirality : 0.054 0.195 627 Planarity : 0.006 0.040 684 Dihedral : 5.737 37.832 561 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 3.91 % Allowed : 31.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.39), residues: 459 helix: 2.05 (0.29), residues: 261 sheet: -3.32 (0.66), residues: 36 loop : -2.90 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 54 TYR 0.017 0.004 TYR A 302 PHE 0.008 0.001 PHE E 294 TRP 0.004 0.002 TRP B 92 HIS 0.016 0.004 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 3900) covalent geometry : angle 1.04073 ( 5271) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.12811 ( 6) hydrogen bonds : bond 0.04858 ( 273) hydrogen bonds : angle 4.53771 ( 792) link_NAG-ASN : bond 0.00471 ( 3) link_NAG-ASN : angle 4.98503 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1155.19 seconds wall clock time: 20 minutes 35.61 seconds (1235.61 seconds total)