Starting phenix.real_space_refine on Tue Mar 3 12:07:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5l_10701/03_2026/6y5l_10701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5l_10701/03_2026/6y5l_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_10701/03_2026/6y5l_10701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5l_10701/03_2026/6y5l_10701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5l_10701/03_2026/6y5l_10701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5l_10701/03_2026/6y5l_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-dev-5986/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: 0.68, per 1000 atoms: 0.18 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: 0.30 Conformation dependent library (CDL) restraints added in 119.9 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 55.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 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: 0.49 Time building geometry restraints manager: 0.40 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.900 Find NCS groups from input model: 0.020 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.110 ------------------------------------------------------------------------------- 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 : 0.147 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: 0.5878 (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: 0.9209 (mtpt) cc_final: 0.8890 (tptp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0794 time to fit residues: 19.1555 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 : 0.159 ------------------------------------------------------------------------------- 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 : 0.164 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: 0.8222 (OUTLIER) cc_final: 0.7470 (t-90) REVERT: B 110 LEU cc_start: 0.8948 (mt) cc_final: 0.8559 (mt) REVERT: B 112 ASP cc_start: 0.8731 (p0) cc_final: 0.8531 (p0) 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: 0.7264 (mtpp) REVERT: E 320 MET cc_start: 0.6823 (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: 0.0824 time to fit residues: 16.8326 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 : 0.144 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.132939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099207 restraints weight = 6881.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.099426 restraints weight = 6431.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100691 restraints weight = 4768.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.101863 restraints weight = 3759.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102463 restraints weight = 3392.776| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3906 Z= 0.145 Angle : 0.724 11.800 5286 Z= 0.390 Chirality : 0.045 0.149 627 Planarity : 0.006 0.047 684 Dihedral : 4.966 36.435 561 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.91 % Allowed : 18.85 % 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 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: 3.16 (0.28), residues: 261 sheet: -4.19 (0.46), residues: 30 loop : -4.07 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 0.00318 ( 3900) covalent geometry : angle 0.71660 ( 5271) SS BOND : bond 0.00356 ( 3) SS BOND : angle 1.67025 ( 6) hydrogen bonds : bond 0.03309 ( 273) hydrogen bonds : angle 3.56287 ( 792) link_NAG-ASN : bond 0.00472 ( 3) link_NAG-ASN : angle 2.23439 ( 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 : 0.125 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: 0.7506 (mmmt) cc_final: 0.7035 (mtpp) REVERT: B 64 HIS cc_start: 0.8149 (m-70) cc_final: 0.7403 (t-90) REVERT: B 121 LYS cc_start: 0.9235 (mtpt) cc_final: 0.8990 (tmtt) REVERT: C 22 ASN cc_start: 0.7069 (m-40) cc_final: 0.6862 (t0) REVERT: C 41 GLU cc_start: 0.7892 (tp30) cc_final: 0.7675 (tp30) REVERT: C 307 LYS cc_start: 0.7448 (mmmt) cc_final: 0.7178 (mtpp) REVERT: E 320 MET cc_start: 0.6669 (ttm) cc_final: 0.6365 (ttm) REVERT: D 58 LYS cc_start: 0.9001 (mttt) cc_final: 0.8690 (mttm) REVERT: D 116 ASN cc_start: 0.8800 (m110) cc_final: 0.7991 (t0) REVERT: D 121 LYS cc_start: 0.8923 (tptp) cc_final: 0.8693 (tptp) REVERT: F 51 LYS cc_start: 0.9121 (mmtt) cc_final: 0.8886 (ptpp) REVERT: F 58 LYS cc_start: 0.9008 (mttt) cc_final: 0.8760 (mmtt) REVERT: F 64 HIS cc_start: 0.8192 (m-70) cc_final: 0.7909 (m170) outliers start: 17 outliers final: 10 residues processed: 173 average time/residue: 0.0733 time to fit residues: 15.1724 Evaluate side-chains 160 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 91 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 19 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 322 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 295 GLN E 311 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.130196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.089046 restraints weight = 6848.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.091277 restraints weight = 4718.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092642 restraints weight = 3834.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.093298 restraints weight = 3412.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.093298 restraints weight = 3217.297| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3906 Z= 0.185 Angle : 0.786 11.761 5286 Z= 0.420 Chirality : 0.047 0.190 627 Planarity : 0.006 0.048 684 Dihedral : 5.007 36.034 561 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.14 % Allowed : 25.29 % Favored : 70.57 % 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: 0.48 (0.40), residues: 459 helix: 3.20 (0.27), residues: 261 sheet: -3.97 (0.52), residues: 30 loop : -3.92 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 0.00421 ( 3900) covalent geometry : angle 0.77815 ( 5271) SS BOND : bond 0.00365 ( 3) SS BOND : angle 1.88030 ( 6) hydrogen bonds : bond 0.03630 ( 273) hydrogen bonds : angle 3.69642 ( 792) link_NAG-ASN : bond 0.00141 ( 3) link_NAG-ASN : angle 2.37646 ( 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 172 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.107 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: 0.7715 (mmmt) cc_final: 0.7203 (mtpp) REVERT: B 58 LYS cc_start: 0.9024 (mmtp) cc_final: 0.8712 (mmtp) REVERT: B 64 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7495 (t-90) REVERT: B 121 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8991 (tmtt) REVERT: C 307 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7548 (mtpp) REVERT: E 320 MET cc_start: 0.6979 (ttm) cc_final: 0.6610 (ttm) REVERT: D 54 ARG cc_start: 0.8616 (ttm110) cc_final: 0.8301 (ttm110) REVERT: D 58 LYS cc_start: 0.9082 (mttt) cc_final: 0.8750 (mttm) REVERT: D 121 LYS cc_start: 0.8851 (tptp) cc_final: 0.8598 (tptp) REVERT: F 54 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8251 (ttm110) REVERT: F 58 LYS cc_start: 0.9101 (mttt) cc_final: 0.8725 (mmtp) REVERT: F 64 HIS cc_start: 0.8238 (m-70) cc_final: 0.7975 (m-70) outliers start: 18 outliers final: 13 residues processed: 159 average time/residue: 0.0788 time to fit residues: 14.8758 Evaluate side-chains 162 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 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 51 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 91 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 296 ASN 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 = 0.4121 r_free = 0.4121 target = 0.134569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.101505 restraints weight = 6889.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.102130 restraints weight = 5911.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.103280 restraints weight = 4553.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.104428 restraints weight = 3653.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.105019 restraints weight = 3324.639| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3906 Z= 0.179 Angle : 0.820 13.334 5286 Z= 0.441 Chirality : 0.047 0.200 627 Planarity : 0.005 0.048 684 Dihedral : 4.997 36.253 561 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.68 % Allowed : 26.44 % 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: 0.41 (0.40), residues: 459 helix: 3.03 (0.28), residues: 261 sheet: -3.70 (0.57), residues: 30 loop : -3.81 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 124 TYR 0.012 0.002 TYR C 302 PHE 0.007 0.001 PHE B 70 TRP 0.003 0.001 TRP B 92 HIS 0.010 0.003 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 3900) covalent geometry : angle 0.81075 ( 5271) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.70103 ( 6) hydrogen bonds : bond 0.03770 ( 273) hydrogen bonds : angle 3.78376 ( 792) link_NAG-ASN : bond 0.00279 ( 3) link_NAG-ASN : angle 2.75621 ( 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 176 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7431 (mmmt) cc_final: 0.6973 (mtpp) REVERT: B 58 LYS cc_start: 0.8973 (mmtp) cc_final: 0.8692 (mmtt) REVERT: B 64 HIS cc_start: 0.8115 (m-70) cc_final: 0.7488 (t-90) REVERT: B 121 LYS cc_start: 0.9211 (mtpt) cc_final: 0.9002 (tmtt) REVERT: C 290 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7988 (m-40) REVERT: C 307 LYS cc_start: 0.7570 (mmmt) cc_final: 0.7234 (mtpp) REVERT: E 320 MET cc_start: 0.7029 (ttm) cc_final: 0.6652 (ttm) REVERT: D 51 LYS cc_start: 0.9311 (ptpt) cc_final: 0.8895 (mtmm) REVERT: D 58 LYS cc_start: 0.8958 (mttt) cc_final: 0.8700 (mttm) REVERT: F 54 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8132 (ttm110) REVERT: F 64 HIS cc_start: 0.8125 (m-70) cc_final: 0.7531 (t-170) outliers start: 16 outliers final: 11 residues processed: 168 average time/residue: 0.0779 time to fit residues: 15.6109 Evaluate side-chains 157 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 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 91 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 16 optimal weight: 0.1980 chunk 4 optimal weight: 0.0870 chunk 37 optimal weight: 0.3980 chunk 5 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.1164 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.137902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.097567 restraints weight = 6815.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.100478 restraints weight = 4376.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.102151 restraints weight = 3406.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.103166 restraints weight = 2965.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.103507 restraints weight = 2744.371| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3906 Z= 0.149 Angle : 0.869 15.829 5286 Z= 0.456 Chirality : 0.046 0.195 627 Planarity : 0.005 0.047 684 Dihedral : 4.796 35.972 561 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.68 % Allowed : 27.36 % Favored : 68.97 % 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: 0.31 (0.40), residues: 459 helix: 2.82 (0.29), residues: 261 sheet: -3.49 (0.59), residues: 30 loop : -3.65 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 124 TYR 0.007 0.001 TYR B 94 PHE 0.004 0.001 PHE B 63 TRP 0.002 0.001 TRP F 92 HIS 0.012 0.003 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3900) covalent geometry : angle 0.86320 ( 5271) SS BOND : bond 0.00320 ( 3) SS BOND : angle 0.91348 ( 6) hydrogen bonds : bond 0.03793 ( 273) hydrogen bonds : angle 3.82134 ( 792) link_NAG-ASN : bond 0.00325 ( 3) link_NAG-ASN : angle 2.55159 ( 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 173 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.174 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 290 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7958 (m-40) REVERT: A 307 LYS cc_start: 0.7680 (mmmt) cc_final: 0.7163 (mtpp) REVERT: B 58 LYS cc_start: 0.9068 (mmtp) cc_final: 0.8832 (mmtp) REVERT: B 64 HIS cc_start: 0.8168 (m-70) cc_final: 0.7512 (t-90) REVERT: C 41 GLU cc_start: 0.8128 (tp30) cc_final: 0.7850 (tp30) REVERT: C 290 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8168 (m-40) REVERT: C 307 LYS cc_start: 0.7755 (mmmt) cc_final: 0.7392 (mtpp) REVERT: C 315 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7772 (mmtm) REVERT: E 320 MET cc_start: 0.6954 (ttm) cc_final: 0.6635 (ttm) REVERT: D 51 LYS cc_start: 0.9436 (ptpt) cc_final: 0.9171 (ptpp) REVERT: D 58 LYS cc_start: 0.9103 (mttt) cc_final: 0.8788 (mttm) REVERT: F 58 LYS cc_start: 0.9102 (mttt) cc_final: 0.8653 (mmtp) REVERT: F 64 HIS cc_start: 0.8008 (m-70) cc_final: 0.7446 (t-170) REVERT: F 67 GLU cc_start: 0.7564 (pp20) cc_final: 0.7344 (pp20) outliers start: 16 outliers final: 9 residues processed: 165 average time/residue: 0.0765 time to fit residues: 15.0371 Evaluate side-chains 160 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 296 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 104 ASN 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: 0.0000 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.0050 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.3198 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.136489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103731 restraints weight = 6895.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.104255 restraints weight = 5610.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105538 restraints weight = 4386.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.106717 restraints weight = 3478.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.107398 restraints weight = 3201.601| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3906 Z= 0.165 Angle : 0.870 14.305 5286 Z= 0.461 Chirality : 0.047 0.185 627 Planarity : 0.006 0.047 684 Dihedral : 4.850 35.795 561 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.99 % Allowed : 31.72 % 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: 0.21 (0.40), residues: 459 helix: 2.67 (0.30), residues: 261 sheet: -3.65 (0.56), residues: 36 loop : -3.48 (0.41), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 124 TYR 0.010 0.002 TYR A 302 PHE 0.005 0.001 PHE F 70 TRP 0.003 0.001 TRP B 92 HIS 0.013 0.003 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3900) covalent geometry : angle 0.86029 ( 5271) SS BOND : bond 0.00083 ( 3) SS BOND : angle 1.01019 ( 6) hydrogen bonds : bond 0.04040 ( 273) hydrogen bonds : angle 4.02518 ( 792) link_NAG-ASN : bond 0.00495 ( 3) link_NAG-ASN : angle 3.25139 ( 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 166 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.192 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: 0.7461 (mmmt) cc_final: 0.7016 (mtpp) REVERT: A 320 MET cc_start: 0.6684 (ttm) cc_final: 0.6176 (ttp) REVERT: B 115 MET cc_start: 0.7838 (ttt) cc_final: 0.7550 (mtt) REVERT: B 124 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8290 (ttp80) REVERT: C 290 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8196 (m-40) REVERT: C 307 LYS cc_start: 0.7524 (mmmt) cc_final: 0.7118 (mtpp) REVERT: C 315 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7778 (mmtm) REVERT: E 290 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8098 (m-40) REVERT: D 51 LYS cc_start: 0.9295 (ptpt) cc_final: 0.8938 (mtmm) REVERT: D 54 ARG cc_start: 0.8435 (ttm110) cc_final: 0.8183 (ttm110) REVERT: D 58 LYS cc_start: 0.9017 (mttt) cc_final: 0.8710 (mttm) REVERT: F 58 LYS cc_start: 0.9027 (mttt) cc_final: 0.8598 (mmtp) REVERT: F 64 HIS cc_start: 0.7965 (m-70) cc_final: 0.7288 (t-170) REVERT: F 120 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8587 (mm-30) outliers start: 13 outliers final: 9 residues processed: 158 average time/residue: 0.0805 time to fit residues: 15.1689 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 : 0.149 ------------------------------------------------------------------------------- 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 D residue 104 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN C 312 ASN C 322 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** 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 = 0.4129 r_free = 0.4129 target = 0.135049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094638 restraints weight = 6856.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097355 restraints weight = 4486.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099073 restraints weight = 3531.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.099957 restraints weight = 3080.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.100573 restraints weight = 2867.568| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3906 Z= 0.187 Angle : 0.924 13.908 5286 Z= 0.491 Chirality : 0.049 0.178 627 Planarity : 0.006 0.045 684 Dihedral : 4.978 36.313 561 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.60 % Allowed : 32.87 % 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 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: 0.17 (0.39), residues: 459 helix: 2.55 (0.29), residues: 261 sheet: -3.52 (0.61), residues: 36 loop : -3.37 (0.41), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 124 TYR 0.014 0.002 TYR C 302 PHE 0.006 0.001 PHE D 70 TRP 0.003 0.001 TRP B 92 HIS 0.015 0.004 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 3900) covalent geometry : angle 0.91023 ( 5271) SS BOND : bond 0.00216 ( 3) SS BOND : angle 0.51294 ( 6) hydrogen bonds : bond 0.04175 ( 273) hydrogen bonds : angle 4.17051 ( 792) link_NAG-ASN : bond 0.00274 ( 3) link_NAG-ASN : angle 3.95614 ( 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 169 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 307 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7309 (mtpp) REVERT: B 58 LYS cc_start: 0.9153 (mttt) cc_final: 0.8622 (mmtp) REVERT: B 121 LYS cc_start: 0.9042 (tmtt) cc_final: 0.8808 (tptp) REVERT: B 124 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8268 (ttp80) REVERT: C 290 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8282 (m-40) REVERT: C 307 LYS cc_start: 0.7752 (mmmt) cc_final: 0.7379 (mtpp) REVERT: C 315 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7838 (mmtm) REVERT: E 290 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: D 54 ARG cc_start: 0.8622 (ttm110) cc_final: 0.8356 (ttm110) REVERT: D 58 LYS cc_start: 0.9097 (mttt) cc_final: 0.8763 (mttm) REVERT: D 64 HIS cc_start: 0.8163 (m-70) cc_final: 0.7467 (t-90) REVERT: D 121 LYS cc_start: 0.8948 (tptp) cc_final: 0.8622 (tptp) REVERT: F 58 LYS cc_start: 0.9131 (mttt) cc_final: 0.8646 (mmtp) REVERT: F 64 HIS cc_start: 0.8039 (m-70) cc_final: 0.7545 (t-170) REVERT: F 115 MET cc_start: 0.7788 (ttt) cc_final: 0.7518 (mtm) outliers start: 20 outliers final: 11 residues processed: 157 average time/residue: 0.0792 time to fit residues: 14.8710 Evaluate side-chains 155 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 C residue 312 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 104 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 19 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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** ** 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 = 0.4136 r_free = 0.4136 target = 0.135750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.095793 restraints weight = 6730.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.098511 restraints weight = 4418.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.100136 restraints weight = 3485.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.100822 restraints weight = 3049.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.101513 restraints weight = 2860.361| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3906 Z= 0.178 Angle : 0.963 17.578 5286 Z= 0.511 Chirality : 0.050 0.192 627 Planarity : 0.005 0.045 684 Dihedral : 5.058 36.897 561 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.68 % Allowed : 32.87 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.30), residues: 261 sheet: -3.44 (0.63), residues: 36 loop : -3.18 (0.42), residues: 162 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 0.005 0.001 PHE F 70 TRP 0.003 0.001 TRP B 92 HIS 0.015 0.004 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3900) covalent geometry : angle 0.95124 ( 5271) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.37857 ( 6) hydrogen bonds : bond 0.04406 ( 273) hydrogen bonds : angle 4.18260 ( 792) link_NAG-ASN : bond 0.00370 ( 3) link_NAG-ASN : angle 3.86994 ( 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 171 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.162 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: 0.7771 (mmmt) cc_final: 0.7284 (mtpp) REVERT: B 58 LYS cc_start: 0.9139 (mttt) cc_final: 0.8618 (mmtp) REVERT: B 121 LYS cc_start: 0.9004 (tmtt) cc_final: 0.8620 (tptp) REVERT: B 124 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8236 (ttp80) REVERT: C 307 LYS cc_start: 0.7767 (mmmt) cc_final: 0.7362 (mtpp) REVERT: C 320 MET cc_start: 0.6680 (ttm) cc_final: 0.6391 (ttp) REVERT: E 290 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8032 (m-40) REVERT: E 302 TYR cc_start: 0.3941 (t80) cc_final: 0.2638 (m-80) REVERT: E 315 LYS cc_start: 0.8176 (mmtm) cc_final: 0.7702 (tppt) REVERT: D 51 LYS cc_start: 0.9428 (ptpt) cc_final: 0.9022 (mtmm) REVERT: D 54 ARG cc_start: 0.8619 (ttm110) cc_final: 0.8370 (ttm110) REVERT: D 58 LYS cc_start: 0.9096 (mttt) cc_final: 0.8767 (mttm) REVERT: D 64 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7545 (t-90) REVERT: D 121 LYS cc_start: 0.8894 (tptp) cc_final: 0.8600 (tptp) REVERT: F 58 LYS cc_start: 0.9137 (mttt) cc_final: 0.8698 (mmtp) REVERT: F 64 HIS cc_start: 0.8054 (m-70) cc_final: 0.7606 (t-170) REVERT: F 67 GLU cc_start: 0.7690 (pp20) cc_final: 0.7418 (pp20) REVERT: F 117 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8952 (mtmm) REVERT: F 120 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8481 (mm-30) outliers start: 16 outliers final: 10 residues processed: 161 average time/residue: 0.0785 time to fit residues: 14.9792 Evaluate side-chains 154 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 64 HIS Chi-restraints excluded: chain D residue 66 ILE 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: 0.6980 chunk 26 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN C 312 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 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 = 0.4127 r_free = 0.4127 target = 0.134852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.101381 restraints weight = 6765.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.102659 restraints weight = 5175.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103665 restraints weight = 4451.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104478 restraints weight = 3373.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.105224 restraints weight = 3167.785| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 : 0.004 0.044 3906 Z= 0.199 Angle : 1.027 16.452 5286 Z= 0.547 Chirality : 0.051 0.227 627 Planarity : 0.006 0.044 684 Dihedral : 5.320 37.260 561 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.68 % Allowed : 32.64 % 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: 0.12 (0.39), residues: 459 helix: 2.30 (0.30), residues: 261 sheet: -3.33 (0.65), residues: 36 loop : -3.04 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 124 TYR 0.013 0.002 TYR C 302 PHE 0.005 0.001 PHE F 70 TRP 0.003 0.001 TRP F 92 HIS 0.016 0.004 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 3900) covalent geometry : angle 1.01174 ( 5271) SS BOND : bond 0.00051 ( 3) SS BOND : angle 0.33332 ( 6) hydrogen bonds : bond 0.04512 ( 273) hydrogen bonds : angle 4.30247 ( 792) link_NAG-ASN : bond 0.00472 ( 3) link_NAG-ASN : angle 4.45219 ( 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 164 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.144 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: 0.7662 (mmmt) cc_final: 0.7209 (mtpp) REVERT: B 58 LYS cc_start: 0.9011 (mttt) cc_final: 0.8536 (mmtp) REVERT: B 121 LYS cc_start: 0.9012 (tmtt) cc_final: 0.8754 (tptp) REVERT: C 307 LYS cc_start: 0.7503 (mmmt) cc_final: 0.7108 (mtpp) REVERT: C 320 MET cc_start: 0.6637 (ttm) cc_final: 0.6346 (ttp) REVERT: E 290 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8031 (m-40) REVERT: E 302 TYR cc_start: 0.3915 (t80) cc_final: 0.2518 (m-80) REVERT: E 315 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7809 (tppt) REVERT: D 51 LYS cc_start: 0.9319 (ptpt) cc_final: 0.9016 (ptpp) REVERT: D 54 ARG cc_start: 0.8357 (ttm110) cc_final: 0.8146 (ttm110) REVERT: D 58 LYS cc_start: 0.8964 (mttt) cc_final: 0.8708 (mttm) REVERT: D 64 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7410 (t-90) REVERT: D 121 LYS cc_start: 0.8855 (tptp) cc_final: 0.8558 (tptp) REVERT: F 58 LYS cc_start: 0.8990 (mttt) cc_final: 0.8562 (mmtp) REVERT: F 64 HIS cc_start: 0.7938 (m-70) cc_final: 0.7491 (t-170) REVERT: F 120 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8466 (mm-30) outliers start: 16 outliers final: 11 residues processed: 154 average time/residue: 0.0753 time to fit residues: 13.8408 Evaluate side-chains 156 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 C residue 312 ASN 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 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: 2.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 312 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** ** 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 = 0.4123 r_free = 0.4123 target = 0.134680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094257 restraints weight = 6716.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.096892 restraints weight = 4472.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.098494 restraints weight = 3546.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099256 restraints weight = 3109.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099895 restraints weight = 2909.659| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.175 3906 Z= 0.404 Angle : 1.665 59.181 5286 Z= 0.975 Chirality : 0.078 1.090 627 Planarity : 0.010 0.157 684 Dihedral : 5.540 40.361 561 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.23 % Favored : 94.34 % Rotamer: Outliers : 3.45 % Allowed : 33.33 % Favored : 63.22 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.08 (0.39), residues: 459 helix: 2.25 (0.30), residues: 261 sheet: -3.31 (0.66), residues: 36 loop : -3.04 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 124 TYR 0.013 0.003 TYR C 302 PHE 0.005 0.001 PHE B 70 TRP 0.003 0.001 TRP B 92 HIS 0.014 0.004 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00840 ( 3900) covalent geometry : angle 1.59974 ( 5271) SS BOND : bond 0.00160 ( 3) SS BOND : angle 2.99796 ( 6) hydrogen bonds : bond 0.04516 ( 273) hydrogen bonds : angle 4.33648 ( 792) link_NAG-ASN : bond 0.06632 ( 3) link_NAG-ASN : angle 11.09805 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1066.22 seconds wall clock time: 18 minutes 59.05 seconds (1139.05 seconds total)