Starting phenix.real_space_refine on Thu Oct 22 18:49:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y5l_10701/10_2026/6y5l_10701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5l_10701/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5l_10701/10_2026/6y5l_10701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5l_10701/10_2026/6y5l_10701.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5l_10701/10_2026/6y5l_10701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5l_10701/10_2026/6y5l_10701.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6y5l_10701/10_2026/6y5l_10701.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y5l_10701/10_2026/6y5l_10701.cif" } 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-2.3rc1-6221/lib/python3.11/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 chiralities: 1 Restraints were copied for chains: C, E, D, F Time building chain proxies: 0.75, per 1000 atoms: 0.19 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: 0.35 Conformation dependent library (CDL) restraints added in 150.5 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 55.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 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: 0.58 Time building geometry restraints manager: 0.48 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: 2151 17.34 - 34.67: 204 34.67 - 52.01: 48 52.01 - 69.35: 6 69.35 - 86.69: 3 Dihedral angle restraints: 2412 sinusoidal: 1014 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 2409 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: 6.790 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.950 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 : 14.581 86.685 1485 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/Z covalent geometry : bond 0.00352 / 0.17 ( 3900) covalent geometry : angle 0.70143 / 0.40 ( 5271) SS BOND : bond 0.00126 / 0.06 ( 3) SS BOND : angle 1.19134 / 0.70 ( 6) hydrogen bonds : bond 0.08119 / 5.82 ( 273) hydrogen bonds : angle 4.50729 / 3.11 ( 792) link_NAG-ASN : bond 0.00245 / 0.11 ( 3) link_NAG-ASN : angle 1.40889 / 0.85 ( 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 : 0.164 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: 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: 0.0793 time to fit residues: 19.1823 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 : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] 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... 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 = 0.4075 r_free = 0.4075 target = 0.131297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091265 restraints weight = 6922.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.093569 restraints weight = 4694.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094784 restraints weight = 3778.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.095621 restraints weight = 3373.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.095854 restraints weight = 3161.754| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3906 Z= 0.197 Angle : 0.703 4.857 5286 Z= 0.378 Chirality : 0.047 0.158 627 Planarity : 0.006 0.042 684 Dihedral : 5.494 37.020 498 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.22 % Allowed : 19.31 % Favored : 77.47 % 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: -0.39 (0.38), residues: 459 helix: 2.52 (0.26), residues: 261 sheet: -4.25 (0.45), residues: 30 loop : -4.37 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 123 TYR 0.015 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/Z covalent geometry : bond 0.00449 / 0.20 ( 3900) covalent geometry : angle 0.69254 / 0.38 ( 5271) SS BOND : bond 0.00502 / 0.22 ( 3) SS BOND : angle 2.15815 / 1.24 ( 6) hydrogen bonds : bond 0.03366 / 2.18 ( 273) hydrogen bonds : angle 3.66068 / 2.47 ( 792) link_NAG-ASN : bond 0.00319 / 0.13 ( 3) link_NAG-ASN : angle 2.45876 / 1.48 ( 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: 14 poor density : 172 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: A 307 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7408 (mtpp) REVERT: A 320 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.5656 (ttm) REVERT: B 51 LYS cc_start: 0.9226 (mmtt) cc_final: 0.8830 (ptpp) REVERT: B 58 LYS cc_start: 0.9065 (mttp) cc_final: 0.8826 (mmtp) REVERT: B 64 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7411 (t-90) REVERT: B 110 LEU cc_start: 0.8925 (mt) cc_final: 0.8509 (mt) REVERT: B 112 ASP cc_start: 0.8676 (p0) cc_final: 0.8455 (p0) REVERT: B 121 LYS cc_start: 0.9269 (mtpt) cc_final: 0.9013 (tmtt) REVERT: C 41 GLU cc_start: 0.7918 (tp30) cc_final: 0.7677 (tp30) REVERT: C 307 LYS cc_start: 0.7634 (mmmt) cc_final: 0.7274 (mtpp) REVERT: E 22 ASN cc_start: 0.7067 (m-40) cc_final: 0.6482 (t0) REVERT: E 320 MET cc_start: 0.6925 (ttm) cc_final: 0.6625 (ttm) REVERT: D 51 LYS cc_start: 0.9254 (mmtt) cc_final: 0.8753 (ptpt) REVERT: D 54 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8323 (ttm110) REVERT: D 58 LYS cc_start: 0.9090 (mttt) cc_final: 0.8744 (mttm) REVERT: D 110 LEU cc_start: 0.9094 (mt) cc_final: 0.8887 (mt) REVERT: F 51 LYS cc_start: 0.9343 (mmtt) cc_final: 0.8989 (ptpt) REVERT: F 54 ARG cc_start: 0.8783 (mtp85) cc_final: 0.8395 (ttm110) REVERT: F 58 LYS cc_start: 0.9148 (mttt) cc_final: 0.8859 (mmtt) REVERT: F 64 HIS cc_start: 0.8196 (m-70) cc_final: 0.7740 (m-70) REVERT: F 121 LYS cc_start: 0.9238 (mtpt) cc_final: 0.8973 (tptp) outliers start: 14 outliers final: 6 residues processed: 173 average time/residue: 0.0791 time to fit residues: 16.3909 Evaluate side-chains 163 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [30, 28, 11, 43, 22, 27, 26, 23, 37, 6, 5] chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 GLN C 322 ASN E 296 ASN E 322 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4066 r_free = 0.4066 target = 0.130536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.098128 restraints weight = 6938.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097095 restraints weight = 7299.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097805 restraints weight = 6886.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099273 restraints weight = 4624.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.100188 restraints weight = 3885.461| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3865 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= 0.191 Angle : 0.773 11.252 5286 Z= 0.413 Chirality : 0.047 0.161 627 Planarity : 0.006 0.046 684 Dihedral : 5.402 36.499 498 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.68 % Allowed : 22.30 % Favored : 74.02 % 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: 0.30 (0.40), residues: 459 helix: 3.16 (0.27), residues: 261 sheet: -4.20 (0.49), residues: 30 loop : -4.16 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 124 TYR 0.014 0.003 TYR C 302 PHE 0.011 0.002 PHE B 70 TRP 0.003 0.001 TRP B 92 HIS 0.012 0.003 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 3900) covalent geometry : angle 0.76260 / 0.41 ( 5271) SS BOND : bond 0.00122 / 0.05 ( 3) SS BOND : angle 1.99224 / 1.14 ( 6) hydrogen bonds : bond 0.03484 / 2.24 ( 273) hydrogen bonds : angle 3.69751 / 2.46 ( 792) link_NAG-ASN : bond 0.00348 / 0.13 ( 3) link_NAG-ASN : angle 2.73613 / 1.63 ( 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 183 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 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: A 307 LYS cc_start: 0.7513 (mmmt) cc_final: 0.7148 (mtpp) REVERT: A 322 ASN cc_start: 0.7495 (t0) cc_final: 0.7025 (t0) REVERT: B 64 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7343 (t-90) REVERT: B 121 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8973 (tmtt) REVERT: C 41 GLU cc_start: 0.7843 (tp30) cc_final: 0.7558 (tp30) REVERT: C 307 LYS cc_start: 0.7475 (mmmt) cc_final: 0.7158 (mtpp) REVERT: E 22 ASN cc_start: 0.6885 (m-40) cc_final: 0.6455 (t0) REVERT: E 320 MET cc_start: 0.7041 (ttm) cc_final: 0.6730 (ttm) REVERT: D 58 LYS cc_start: 0.8908 (mttt) cc_final: 0.8655 (mttm) REVERT: D 112 ASP cc_start: 0.8747 (p0) cc_final: 0.8527 (p0) REVERT: D 116 ASN cc_start: 0.8754 (m110) cc_final: 0.8124 (t0) REVERT: D 121 LYS cc_start: 0.8899 (tptp) cc_final: 0.8673 (tptp) REVERT: F 54 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7826 (ttm110) REVERT: F 58 LYS cc_start: 0.8931 (mttt) cc_final: 0.8630 (mmtp) REVERT: F 64 HIS cc_start: 0.8119 (m-70) cc_final: 0.7793 (m170) outliers start: 16 outliers final: 10 residues processed: 175 average time/residue: 0.0753 time to fit residues: 15.7834 Evaluate side-chains 163 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 64 HIS 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: [19, 42, 18, 36, 39, 14, 20, 17, 8, 40, 31] chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN C 322 ASN E 296 ASN E 322 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4043 r_free = 0.4043 target = 0.128543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095881 restraints weight = 6882.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096112 restraints weight = 6171.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.097046 restraints weight = 5344.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097815 restraints weight = 4054.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098658 restraints weight = 3740.058| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3906 Z= 0.216 Angle : 0.843 10.726 5286 Z= 0.445 Chirality : 0.049 0.204 627 Planarity : 0.006 0.048 684 Dihedral : 5.436 36.472 498 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.06 % Allowed : 27.36 % Favored : 67.59 % 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: 3.08 (0.28), residues: 261 sheet: -3.74 (0.57), residues: 30 loop : -4.03 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 124 TYR 0.016 0.003 TYR C 302 PHE 0.009 0.001 PHE B 70 TRP 0.004 0.001 TRP B 92 HIS 0.010 0.003 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 ( 3900) covalent geometry : angle 0.83258 / 0.44 ( 5271) SS BOND : bond 0.00268 / 0.12 ( 3) SS BOND : angle 2.10333 / 1.20 ( 6) hydrogen bonds : bond 0.03747 / 2.43 ( 273) hydrogen bonds : angle 3.79850 / 2.52 ( 792) link_NAG-ASN : bond 0.00150 / 0.06 ( 3) link_NAG-ASN : angle 2.88745 / 1.73 ( 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 178 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.101 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: 0.7521 (mmmt) cc_final: 0.7158 (mtpp) REVERT: A 320 MET cc_start: 0.6974 (ttm) cc_final: 0.6727 (ttp) REVERT: B 64 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7343 (t-90) REVERT: B 121 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8911 (tmtt) REVERT: C 307 LYS cc_start: 0.7489 (mmmt) cc_final: 0.7118 (mtpp) REVERT: E 22 ASN cc_start: 0.7000 (m-40) cc_final: 0.6610 (t0) REVERT: E 320 MET cc_start: 0.7086 (ttm) cc_final: 0.6759 (ttm) REVERT: D 58 LYS cc_start: 0.8913 (mttt) cc_final: 0.8666 (mttm) REVERT: D 121 LYS cc_start: 0.8815 (tptp) cc_final: 0.8579 (tptp) REVERT: F 51 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8450 (mtmm) REVERT: F 58 LYS cc_start: 0.8893 (mttt) cc_final: 0.8497 (mmtp) REVERT: F 64 HIS cc_start: 0.7986 (m-70) cc_final: 0.7335 (t-170) outliers start: 22 outliers final: 14 residues processed: 164 average time/residue: 0.0789 time to fit residues: 15.4343 Evaluate side-chains 167 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain F residue 51 LYS 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: [44, 25, 26, 12, 21, 31, 2, 20, 32, 8, 19] chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.0070 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN 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 47 GLN ** 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 = 0.4122 r_free = 0.4122 target = 0.134686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.102554 restraints weight = 6855.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.102824 restraints weight = 6026.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.104060 restraints weight = 4691.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.105266 restraints weight = 3734.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.105866 restraints weight = 3370.453| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3906 Z= 0.168 Angle : 0.871 13.530 5286 Z= 0.462 Chirality : 0.047 0.185 627 Planarity : 0.006 0.048 684 Dihedral : 5.258 36.708 498 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.83 % Allowed : 28.97 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.97 (0.28), residues: 261 sheet: -3.43 (0.63), residues: 30 loop : -3.88 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 54 TYR 0.010 0.002 TYR C 302 PHE 0.006 0.001 PHE F 70 TRP 0.002 0.001 TRP B 92 HIS 0.010 0.003 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 3900) covalent geometry : angle 0.86305 / 0.46 ( 5271) SS BOND : bond 0.00095 / 0.04 ( 3) SS BOND : angle 1.73377 / 0.99 ( 6) hydrogen bonds : bond 0.03764 / 2.39 ( 273) hydrogen bonds : angle 3.87451 / 2.58 ( 792) link_NAG-ASN : bond 0.00606 / 0.27 ( 3) link_NAG-ASN : angle 2.64821 / 1.60 ( 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: 21 poor density : 154 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: A 307 LYS cc_start: 0.7430 (mmmt) cc_final: 0.6903 (mtpp) REVERT: B 58 LYS cc_start: 0.8969 (mttp) cc_final: 0.8729 (mmtp) REVERT: B 64 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7366 (t-90) REVERT: C 290 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7946 (m-40) REVERT: C 307 LYS cc_start: 0.7523 (mmmt) cc_final: 0.7161 (mtpp) REVERT: E 22 ASN cc_start: 0.7111 (m-40) cc_final: 0.6831 (t0) REVERT: E 320 MET cc_start: 0.7152 (ttm) cc_final: 0.6783 (ttm) REVERT: D 51 LYS cc_start: 0.9281 (ptpt) cc_final: 0.9065 (ptpp) REVERT: D 58 LYS cc_start: 0.8950 (mttt) cc_final: 0.8697 (mttm) REVERT: D 64 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7371 (t-90) REVERT: F 58 LYS cc_start: 0.8948 (mttt) cc_final: 0.8497 (mmtp) outliers start: 21 outliers final: 13 residues processed: 166 average time/residue: 0.0830 time to fit residues: 16.4316 Evaluate side-chains 157 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 43 VAL 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 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: [16, 4, 37, 5, 24, 26, 34, 31, 23, 17, 44] chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.0010 chunk 17 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN ** B 105 GLN ** 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 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.135627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103541 restraints weight = 6831.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.103333 restraints weight = 6688.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.103771 restraints weight = 7140.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.105444 restraints weight = 4377.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.106560 restraints weight = 3582.504| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 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 0.034 3906 Z= 0.162 Angle : 0.879 14.387 5286 Z= 0.468 Chirality : 0.048 0.190 627 Planarity : 0.006 0.049 684 Dihedral : 5.184 36.360 498 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.60 % Allowed : 30.34 % Favored : 65.06 % 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: 0.22 (0.39), residues: 459 helix: 2.76 (0.28), residues: 261 sheet: -3.32 (0.66), residues: 30 loop : -3.77 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 124 TYR 0.010 0.002 TYR C 302 PHE 0.004 0.001 PHE F 70 TRP 0.002 0.001 TRP B 92 HIS 0.012 0.003 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 3900) covalent geometry : angle 0.87069 / 0.47 ( 5271) SS BOND : bond 0.00020 / 0.01 ( 3) SS BOND : angle 1.52789 / 0.88 ( 6) hydrogen bonds : bond 0.03910 / 2.49 ( 273) hydrogen bonds : angle 3.92160 / 2.63 ( 792) link_NAG-ASN : bond 0.00354 / 0.16 ( 3) link_NAG-ASN : angle 2.93082 / 1.77 ( 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 167 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7476 (mmmt) cc_final: 0.7000 (mtpp) REVERT: A 320 MET cc_start: 0.6516 (ttp) cc_final: 0.5972 (ttm) REVERT: B 58 LYS cc_start: 0.8965 (mttp) cc_final: 0.8754 (mmtp) REVERT: B 121 LYS cc_start: 0.8745 (tmtt) cc_final: 0.8432 (tptp) REVERT: C 290 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8148 (m-40) REVERT: C 307 LYS cc_start: 0.7600 (mmmt) cc_final: 0.7192 (mtpp) REVERT: E 22 ASN cc_start: 0.7162 (m-40) cc_final: 0.6952 (t0) REVERT: E 290 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8070 (m-40) REVERT: E 320 MET cc_start: 0.7024 (ttm) cc_final: 0.6755 (ttm) REVERT: D 51 LYS cc_start: 0.9247 (ptpt) cc_final: 0.9024 (ptpp) REVERT: D 58 LYS cc_start: 0.8915 (mttt) cc_final: 0.8671 (mttm) REVERT: D 64 HIS cc_start: 0.8001 (m-70) cc_final: 0.7339 (t-90) REVERT: F 54 ARG cc_start: 0.8288 (ttm110) cc_final: 0.8028 (ptp-110) outliers start: 20 outliers final: 9 residues processed: 158 average time/residue: 0.0747 time to fit residues: 14.0117 Evaluate side-chains 154 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 312 ASN 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 88 LYS Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [15, 27, 11, 22, 16, 35, 44, 36, 39, 32, 10] chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN ** B 105 GLN ** 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** ** 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 = 0.4111 r_free = 0.4111 target = 0.133786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.102099 restraints weight = 6913.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.103280 restraints weight = 5564.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104268 restraints weight = 4634.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104942 restraints weight = 3555.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105516 restraints weight = 3353.561| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5372 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= 0.192 Angle : 0.898 12.747 5286 Z= 0.484 Chirality : 0.049 0.190 627 Planarity : 0.006 0.048 684 Dihedral : 5.192 36.460 498 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.83 % Allowed : 31.49 % 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: 0.05 (0.39), residues: 459 helix: 2.51 (0.28), residues: 261 sheet: -3.18 (0.70), residues: 30 loop : -3.68 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 124 TYR 0.014 0.003 TYR C 302 PHE 0.005 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/Z covalent geometry : bond 0.00432 / 0.19 ( 3900) covalent geometry : angle 0.88853 / 0.48 ( 5271) SS BOND : bond 0.00101 / 0.05 ( 3) SS BOND : angle 0.57420 / 0.33 ( 6) hydrogen bonds : bond 0.04120 / 2.66 ( 273) hydrogen bonds : angle 4.04156 / 2.73 ( 792) link_NAG-ASN : bond 0.00528 / 0.24 ( 3) link_NAG-ASN : angle 3.29224 / 1.97 ( 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 173 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7093 (mtpp) REVERT: B 58 LYS cc_start: 0.8943 (mttt) cc_final: 0.8688 (mttp) REVERT: C 290 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: C 307 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7185 (mtpp) REVERT: C 315 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7801 (mmtm) REVERT: D 51 LYS cc_start: 0.9208 (ptpt) cc_final: 0.8952 (ptpp) REVERT: D 54 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7964 (ttm110) REVERT: D 58 LYS cc_start: 0.8825 (mttt) cc_final: 0.8599 (mttm) REVERT: D 64 HIS cc_start: 0.7922 (m-70) cc_final: 0.7317 (t-90) REVERT: F 58 LYS cc_start: 0.8879 (mttt) cc_final: 0.8551 (mttm) REVERT: F 110 LEU cc_start: 0.8887 (mm) cc_final: 0.8680 (mp) REVERT: F 120 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8395 (mm-30) outliers start: 21 outliers final: 13 residues processed: 165 average time/residue: 0.0784 time to fit residues: 15.3648 Evaluate side-chains 159 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 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 66 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [32, 25, 14, 19, 21, 10, 0, 24, 42, 40, 17] chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.133733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.101962 restraints weight = 6848.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.103134 restraints weight = 5599.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.104135 restraints weight = 4660.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104820 restraints weight = 3566.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.105426 restraints weight = 3353.883| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3906 Z= 0.200 Angle : 0.988 16.055 5286 Z= 0.521 Chirality : 0.051 0.186 627 Planarity : 0.006 0.044 684 Dihedral : 5.288 36.671 498 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.98 % Allowed : 33.56 % Favored : 60.46 % 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: -0.03 (0.39), residues: 459 helix: 2.31 (0.29), residues: 261 sheet: -3.48 (0.63), residues: 36 loop : -3.33 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 124 TYR 0.013 0.003 TYR C 302 PHE 0.007 0.001 PHE B 63 TRP 0.003 0.001 TRP B 92 HIS 0.015 0.004 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 3900) covalent geometry : angle 0.97242 / 0.52 ( 5271) SS BOND : bond 0.00053 / 0.02 ( 3) SS BOND : angle 0.40018 / 0.24 ( 6) hydrogen bonds : bond 0.04416 / 2.87 ( 273) hydrogen bonds : angle 4.28737 / 2.88 ( 792) link_NAG-ASN : bond 0.00152 / 0.08 ( 3) link_NAG-ASN : angle 4.40719 / 2.66 ( 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 177 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7730 (mmmt) cc_final: 0.7261 (mtpp) REVERT: B 58 LYS cc_start: 0.8939 (mttt) cc_final: 0.8653 (mttp) REVERT: C 290 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8203 (m-40) REVERT: C 307 LYS cc_start: 0.7541 (mmmt) cc_final: 0.7100 (mtpp) REVERT: C 315 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7773 (mmtm) REVERT: C 322 ASN cc_start: 0.7160 (t0) cc_final: 0.6414 (t0) REVERT: E 302 TYR cc_start: 0.3903 (t80) cc_final: 0.2539 (m-80) REVERT: D 58 LYS cc_start: 0.8838 (mttt) cc_final: 0.8626 (mttm) REVERT: D 64 HIS cc_start: 0.7926 (m-70) cc_final: 0.7372 (t-90) REVERT: D 115 MET cc_start: 0.8776 (mmm) cc_final: 0.8483 (mmm) REVERT: F 37 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7883 (t70) REVERT: F 38 LEU cc_start: 0.9198 (pt) cc_final: 0.8998 (tp) REVERT: F 54 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7904 (ptp-110) outliers start: 26 outliers final: 14 residues processed: 165 average time/residue: 0.0827 time to fit residues: 16.3094 Evaluate side-chains 163 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 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 43 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [19, 15, 20, 4, 35, 13, 2, 1, 6, 25, 28] chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 35 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.135596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095737 restraints weight = 6710.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098489 restraints weight = 4433.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100110 restraints weight = 3501.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.101092 restraints weight = 3068.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.101525 restraints weight = 2845.187| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3906 Z= 0.179 Angle : 0.997 14.404 5286 Z= 0.527 Chirality : 0.050 0.184 627 Planarity : 0.006 0.043 684 Dihedral : 5.147 36.669 498 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.52 % Allowed : 33.10 % Favored : 61.38 % 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: -0.06 (0.39), residues: 459 helix: 2.17 (0.30), residues: 261 sheet: -3.49 (0.62), residues: 36 loop : -3.13 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 124 TYR 0.009 0.002 TYR C 302 PHE 0.005 0.001 PHE B 63 TRP 0.002 0.001 TRP B 92 HIS 0.016 0.004 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 3900) covalent geometry : angle 0.97905 / 0.52 ( 5271) SS BOND : bond 0.00092 / 0.04 ( 3) SS BOND : angle 0.35469 / 0.21 ( 6) hydrogen bonds : bond 0.04449 / 2.87 ( 273) hydrogen bonds : angle 4.33100 / 2.91 ( 792) link_NAG-ASN : bond 0.00263 / 0.10 ( 3) link_NAG-ASN : angle 4.72278 / 2.84 ( 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 179 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7401 (mtpp) REVERT: B 58 LYS cc_start: 0.9152 (mttt) cc_final: 0.8778 (mttp) REVERT: B 121 LYS cc_start: 0.8936 (tmtt) cc_final: 0.8735 (tptp) REVERT: C 307 LYS cc_start: 0.7668 (mmmt) cc_final: 0.7215 (mtpp) REVERT: E 290 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.8043 (m-40) REVERT: E 302 TYR cc_start: 0.4027 (t80) cc_final: 0.2593 (m-80) REVERT: E 315 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7822 (tppt) REVERT: D 51 LYS cc_start: 0.9442 (ptpt) cc_final: 0.9204 (ptpp) REVERT: D 54 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8372 (ttm110) REVERT: D 58 LYS cc_start: 0.9071 (mttt) cc_final: 0.8742 (mttm) REVERT: D 64 HIS cc_start: 0.8097 (m-70) cc_final: 0.7593 (t-90) REVERT: D 115 MET cc_start: 0.8780 (mmm) cc_final: 0.8493 (mmm) REVERT: F 37 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8029 (t70) REVERT: F 54 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8307 (ptp-110) REVERT: F 120 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8515 (mm-30) REVERT: F 121 LYS cc_start: 0.8707 (tptp) cc_final: 0.8498 (tptp) outliers start: 24 outliers final: 13 residues processed: 168 average time/residue: 0.0750 time to fit residues: 15.0589 Evaluate side-chains 162 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 296 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 43 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 70 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 88 LYS 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: [21, 26, 25, 43, 23, 15, 10, 31, 4, 17, 27] chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 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 = 0.4106 r_free = 0.4106 target = 0.133272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093231 restraints weight = 6792.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095988 restraints weight = 4477.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097597 restraints weight = 3531.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098407 restraints weight = 3084.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.099068 restraints weight = 2877.046| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 3906 Z= 0.233 Angle : 1.125 16.586 5286 Z= 0.585 Chirality : 0.055 0.198 627 Planarity : 0.006 0.042 684 Dihedral : 5.463 36.749 498 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.14 % Allowed : 34.94 % Favored : 60.92 % 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: -0.13 (0.39), residues: 459 helix: 2.06 (0.30), residues: 261 sheet: -3.39 (0.68), residues: 36 loop : -3.08 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 124 TYR 0.014 0.003 TYR C 302 PHE 0.006 0.001 PHE E 294 TRP 0.004 0.001 TRP B 92 HIS 0.017 0.005 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 ( 3900) covalent geometry : angle 1.10283 / 0.58 ( 5271) SS BOND : bond 0.00089 / 0.04 ( 3) SS BOND : angle 0.48423 / 0.26 ( 6) hydrogen bonds : bond 0.04903 / 3.18 ( 273) hydrogen bonds : angle 4.53556 / 3.04 ( 792) link_NAG-ASN : bond 0.00490 / 0.21 ( 3) link_NAG-ASN : angle 5.60449 / 3.35 ( 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 168 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7348 (mtpp) REVERT: B 58 LYS cc_start: 0.9182 (mttt) cc_final: 0.8808 (mttp) REVERT: C 307 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7321 (mtpp) REVERT: C 315 LYS cc_start: 0.8037 (mmtm) cc_final: 0.7720 (mmtm) REVERT: E 302 TYR cc_start: 0.3905 (t80) cc_final: 0.2434 (m-80) REVERT: D 51 LYS cc_start: 0.9499 (ptpt) cc_final: 0.9189 (ptpp) REVERT: D 54 ARG cc_start: 0.8668 (ttm110) cc_final: 0.8415 (ttm110) REVERT: D 58 LYS cc_start: 0.9094 (mttt) cc_final: 0.8764 (mttm) REVERT: D 64 HIS cc_start: 0.8055 (m-70) cc_final: 0.7589 (t-90) REVERT: F 54 ARG cc_start: 0.8714 (ttm110) cc_final: 0.8331 (ptp-110) REVERT: F 121 LYS cc_start: 0.8718 (tptp) cc_final: 0.8498 (tptp) outliers start: 18 outliers final: 14 residues processed: 160 average time/residue: 0.0763 time to fit residues: 14.5844 Evaluate side-chains 159 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: [31, 36, 39, 5, 37, 22, 38, 15, 34, 8, 27] chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.134106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093844 restraints weight = 6785.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.096661 restraints weight = 4469.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.098330 restraints weight = 3511.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.099140 restraints weight = 3061.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099700 restraints weight = 2852.513| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3906 Z= 0.222 Angle : 1.191 18.747 5286 Z= 0.612 Chirality : 0.055 0.205 627 Planarity : 0.006 0.042 684 Dihedral : 5.526 37.219 498 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.37 % Allowed : 35.63 % Favored : 60.00 % 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: 1.96 (0.30), residues: 261 sheet: -3.36 (0.69), residues: 36 loop : -2.98 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 124 TYR 0.012 0.003 TYR C 302 PHE 0.004 0.001 PHE F 70 TRP 0.003 0.001 TRP B 92 HIS 0.017 0.005 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 ( 3900) covalent geometry : angle 1.16193 / 0.61 ( 5271) SS BOND : bond 0.00119 / 0.06 ( 3) SS BOND : angle 2.39031 / 1.45 ( 6) hydrogen bonds : bond 0.04857 / 3.17 ( 273) hydrogen bonds : angle 4.55540 / 3.07 ( 792) link_NAG-ASN : bond 0.00766 / 0.35 ( 3) link_NAG-ASN : angle 6.20463 / 3.70 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1100.05 seconds wall clock time: 19 minutes 43.18 seconds (1183.18 seconds total)