Starting phenix.real_space_refine on Wed Mar 4 03:32:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u8g_26383/03_2026/7u8g_26383_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u8g_26383/03_2026/7u8g_26383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u8g_26383/03_2026/7u8g_26383_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u8g_26383/03_2026/7u8g_26383_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u8g_26383/03_2026/7u8g_26383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u8g_26383/03_2026/7u8g_26383.map" } resolution = 3.2 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= 0.001 sd= 0.017 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 3 5.49 5 S 27 5.16 5 C 3292 2.51 5 N 827 2.21 5 O 895 1.98 5 H 4861 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 9907 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 4247 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 248} Chain breaks: 1 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2081 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "D" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1738 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1640 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 182 Unusual residues: {'HEM': 2, 'NAG': 3, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.98, per 1000 atoms: 0.20 Number of scatterers: 9907 At special positions: 0 Unit cell: (57.749, 70.907, 128.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 27 16.00 P 3 15.00 O 895 8.00 N 827 7.00 C 3292 6.00 H 4861 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " 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=2, symmetry=0 Links applied NAG-ASN " NAG A 603 " - " ASN A 240 " " NAG A 604 " - " ASN A 149 " " NAG A 605 " - " ASN A 132 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 219.0 milliseconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1134 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 6 sheets defined 52.0% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 7 through 35 removed outlier: 3.779A pdb=" N SER A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 48 through 68 Proline residue: A 56 - end of helix removed outlier: 4.611A pdb=" N LEU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 131 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 173 through 193 Processing helix chain 'A' and resid 194 through 201 Processing helix chain 'A' and resid 201 through 210 removed outlier: 3.773A pdb=" N HIS A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.568A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.627A pdb=" N VAL A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.614A pdb=" N TRP A 251 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.627A pdb=" N TRP A 272 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'B' and resid 5 through 31 removed outlier: 4.196A pdb=" N TRP B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 12 " --> pdb=" O MET B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 54 removed outlier: 4.020A pdb=" N GLY B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.478A pdb=" N MET B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.601A pdb=" N ARG B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 102 removed outlier: 3.760A pdb=" N ARG B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 104 through 127 removed outlier: 4.330A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLY B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.720A pdb=" N LYS D 65 " --> pdb=" O ARG D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.679A pdb=" N ASP E 82 " --> pdb=" O GLU E 79 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 229 through 231 Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.672A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 110 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR D 99 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU D 108 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.672A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.745A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.664A pdb=" N VAL E 11 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 768 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: 1.90 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 4853 1.08 - 1.33: 893 1.33 - 1.57: 4246 1.57 - 1.82: 43 1.82 - 2.06: 8 Bond restraints: 10043 Sorted by residual: bond pdb=" O12 POV B 201 " pdb=" P POV B 201 " ideal model delta sigma weight residual 1.657 1.463 0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" C31 POV A 601 " pdb=" O31 POV A 601 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C31 POV B 201 " pdb=" O31 POV B 201 " ideal model delta sigma weight residual 1.327 1.421 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C31 POV A 602 " pdb=" O31 POV A 602 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C31 POV A 602 " pdb=" C32 POV A 602 " ideal model delta sigma weight residual 1.502 1.556 -0.054 2.00e-02 2.50e+03 7.39e+00 ... (remaining 10038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.75: 18000 5.75 - 11.51: 13 11.51 - 17.26: 3 17.26 - 23.01: 2 23.01 - 28.76: 3 Bond angle restraints: 18021 Sorted by residual: angle pdb=" C34 POV A 602 " pdb=" C35 POV A 602 " pdb=" C36 POV A 602 " ideal model delta sigma weight residual 112.32 141.08 -28.76 3.00e+00 1.11e-01 9.19e+01 angle pdb=" C34 POV A 601 " pdb=" C35 POV A 601 " pdb=" C36 POV A 601 " ideal model delta sigma weight residual 112.32 140.31 -27.99 3.00e+00 1.11e-01 8.71e+01 angle pdb=" C34 POV B 201 " pdb=" C35 POV B 201 " pdb=" C36 POV B 201 " ideal model delta sigma weight residual 112.32 139.07 -26.75 3.00e+00 1.11e-01 7.95e+01 angle pdb=" O13 POV A 601 " pdb=" P POV A 601 " pdb=" O14 POV A 601 " ideal model delta sigma weight residual 121.11 100.63 20.48 3.00e+00 1.11e-01 4.66e+01 angle pdb=" O13 POV A 602 " pdb=" P POV A 602 " pdb=" O14 POV A 602 " ideal model delta sigma weight residual 121.11 101.14 19.97 3.00e+00 1.11e-01 4.43e+01 ... (remaining 18016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4270 17.18 - 34.36: 354 34.36 - 51.55: 92 51.55 - 68.73: 41 68.73 - 85.91: 16 Dihedral angle restraints: 4773 sinusoidal: 2582 harmonic: 2191 Sorted by residual: dihedral pdb=" CA LEU A 66 " pdb=" C LEU A 66 " pdb=" N ILE A 67 " pdb=" CA ILE A 67 " ideal model delta harmonic sigma weight residual -180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" C1A HEM A 607 " pdb=" C2A HEM A 607 " pdb=" CAA HEM A 607 " pdb=" CBA HEM A 607 " ideal model delta sinusoidal sigma weight residual 0.00 79.89 -79.89 2 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" C2D HEM A 607 " pdb=" C3D HEM A 607 " pdb=" CAD HEM A 607 " pdb=" CBD HEM A 607 " ideal model delta sinusoidal sigma weight residual 180.00 104.07 75.93 2 2.00e+01 2.50e-03 1.13e+01 ... (remaining 4770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 778 0.164 - 0.327: 0 0.327 - 0.491: 0 0.491 - 0.654: 0 0.654 - 0.818: 1 Chirality restraints: 779 Sorted by residual: chirality pdb=" C5 NAG A 603 " pdb=" C4 NAG A 603 " pdb=" C6 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.41 -1.59 -0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" CA ILE E 48 " pdb=" N ILE E 48 " pdb=" C ILE E 48 " pdb=" CB ILE E 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 776 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 276 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 7 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO E 8 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO E 8 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 8 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 199 " 0.098 9.50e-02 1.11e+02 3.28e-02 1.17e+00 pdb=" NE ARG A 199 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 199 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 199 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 199 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 199 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 199 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A 199 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 199 " 0.000 2.00e-02 2.50e+03 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 629 2.20 - 2.80: 20109 2.80 - 3.40: 27202 3.40 - 4.00: 36460 4.00 - 4.60: 56534 Nonbonded interactions: 140934 Sorted by model distance: nonbonded pdb=" OD1 ASN B 11 " pdb="HH22 ARG B 67 " model vdw 1.603 2.450 nonbonded pdb=" HH TYR A 137 " pdb=" O GLU A 245 " model vdw 1.616 2.450 nonbonded pdb=" OE1 GLN D 39 " pdb="HE22 GLN E 38 " model vdw 1.619 2.450 nonbonded pdb=" O GLY E 68 " pdb=" HH TYR E 71 " model vdw 1.636 2.450 nonbonded pdb=" O ALA B 101 " pdb=" HG1 THR B 107 " model vdw 1.637 2.450 ... (remaining 140929 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.760 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: 0.070 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.770 Find NCS groups from input model: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.006 0.194 5191 Z= 0.294 Angle : 0.992 28.765 7077 Z= 0.388 Chirality : 0.049 0.818 779 Planarity : 0.004 0.049 851 Dihedral : 14.761 85.910 1862 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.96 (0.36), residues: 611 helix: 2.04 (0.33), residues: 262 sheet: 0.40 (0.55), residues: 105 loop : -0.81 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.016 0.001 TYR B 121 PHE 0.009 0.001 PHE A 155 TRP 0.007 0.001 TRP A 270 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 5182) covalent geometry : angle 0.99159 ( 7060) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.65239 ( 8) hydrogen bonds : bond 0.12956 ( 256) hydrogen bonds : angle 6.54479 ( 768) Misc. bond : bond 0.08579 ( 2) link_NAG-ASN : bond 0.00157 ( 3) link_NAG-ASN : angle 1.40293 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.260 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2175 time to fit residues: 17.1102 Evaluate side-chains 57 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.119008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100331 restraints weight = 17772.563| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.73 r_work: 0.3016 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 5191 Z= 0.160 Angle : 0.541 10.107 7077 Z= 0.268 Chirality : 0.041 0.147 779 Planarity : 0.004 0.046 851 Dihedral : 10.836 84.648 807 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.20 % Allowed : 4.52 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.81 (0.35), residues: 611 helix: 1.98 (0.32), residues: 263 sheet: 0.32 (0.54), residues: 105 loop : -0.98 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.012 0.001 TYR B 121 PHE 0.010 0.001 PHE D 94 TRP 0.006 0.001 TRP A 106 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5182) covalent geometry : angle 0.53828 ( 7060) SS BOND : bond 0.00284 ( 4) SS BOND : angle 0.92489 ( 8) hydrogen bonds : bond 0.04311 ( 256) hydrogen bonds : angle 5.24633 ( 768) Misc. bond : bond 0.13696 ( 2) link_NAG-ASN : bond 0.00125 ( 3) link_NAG-ASN : angle 1.30917 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.259 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.2536 time to fit residues: 18.7019 Evaluate side-chains 56 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101547 restraints weight = 17654.763| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.79 r_work: 0.3207 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 5191 Z= 0.119 Angle : 0.492 8.640 7077 Z= 0.244 Chirality : 0.040 0.174 779 Planarity : 0.004 0.042 851 Dihedral : 9.976 85.425 807 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.59 % Allowed : 6.29 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.83 (0.35), residues: 611 helix: 2.01 (0.32), residues: 264 sheet: 0.34 (0.55), residues: 105 loop : -1.03 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 38 TYR 0.010 0.001 TYR E 49 PHE 0.008 0.001 PHE A 155 TRP 0.006 0.001 TRP A 106 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5182) covalent geometry : angle 0.48946 ( 7060) SS BOND : bond 0.00251 ( 4) SS BOND : angle 0.91776 ( 8) hydrogen bonds : bond 0.03927 ( 256) hydrogen bonds : angle 4.90735 ( 768) Misc. bond : bond 0.11138 ( 2) link_NAG-ASN : bond 0.00064 ( 3) link_NAG-ASN : angle 1.15338 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.255 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.2427 time to fit residues: 17.4324 Evaluate side-chains 56 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.099540 restraints weight = 17868.082| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.72 r_work: 0.2971 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 5191 Z= 0.163 Angle : 0.512 10.187 7077 Z= 0.252 Chirality : 0.040 0.145 779 Planarity : 0.004 0.040 851 Dihedral : 9.684 89.415 807 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.79 % Allowed : 8.06 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.77 (0.35), residues: 611 helix: 1.99 (0.32), residues: 265 sheet: 0.36 (0.55), residues: 105 loop : -1.13 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 59 TYR 0.013 0.001 TYR E 49 PHE 0.011 0.001 PHE A 155 TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5182) covalent geometry : angle 0.50956 ( 7060) SS BOND : bond 0.00282 ( 4) SS BOND : angle 0.96711 ( 8) hydrogen bonds : bond 0.03859 ( 256) hydrogen bonds : angle 4.74908 ( 768) Misc. bond : bond 0.10292 ( 2) link_NAG-ASN : bond 0.00150 ( 3) link_NAG-ASN : angle 1.33273 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.254 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.2226 time to fit residues: 16.3847 Evaluate side-chains 60 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.099920 restraints weight = 17709.284| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.78 r_work: 0.3004 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 5191 Z= 0.143 Angle : 0.490 9.031 7077 Z= 0.242 Chirality : 0.039 0.144 779 Planarity : 0.003 0.039 851 Dihedral : 9.283 85.493 807 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.59 % Allowed : 7.86 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.82 (0.35), residues: 611 helix: 2.02 (0.32), residues: 267 sheet: 0.41 (0.56), residues: 105 loop : -1.13 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 59 TYR 0.011 0.001 TYR E 49 PHE 0.009 0.001 PHE A 155 TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5182) covalent geometry : angle 0.48763 ( 7060) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.92387 ( 8) hydrogen bonds : bond 0.03711 ( 256) hydrogen bonds : angle 4.61311 ( 768) Misc. bond : bond 0.10266 ( 2) link_NAG-ASN : bond 0.00071 ( 3) link_NAG-ASN : angle 1.24979 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.255 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 63 average time/residue: 0.2513 time to fit residues: 19.1051 Evaluate side-chains 62 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119056 restraints weight = 17268.047| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.52 r_work: 0.3209 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 5191 Z= 0.151 Angle : 0.499 9.499 7077 Z= 0.245 Chirality : 0.039 0.144 779 Planarity : 0.003 0.037 851 Dihedral : 8.960 81.139 807 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.79 % Allowed : 8.45 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.79 (0.35), residues: 611 helix: 2.02 (0.32), residues: 267 sheet: 0.36 (0.56), residues: 105 loop : -1.16 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 59 TYR 0.012 0.001 TYR E 49 PHE 0.009 0.001 PHE A 212 TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5182) covalent geometry : angle 0.49609 ( 7060) SS BOND : bond 0.00229 ( 4) SS BOND : angle 1.00143 ( 8) hydrogen bonds : bond 0.03715 ( 256) hydrogen bonds : angle 4.57382 ( 768) Misc. bond : bond 0.10326 ( 2) link_NAG-ASN : bond 0.00106 ( 3) link_NAG-ASN : angle 1.30159 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.211 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.2422 time to fit residues: 17.4059 Evaluate side-chains 61 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119845 restraints weight = 17255.681| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.52 r_work: 0.3157 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 5191 Z= 0.127 Angle : 0.484 8.685 7077 Z= 0.237 Chirality : 0.039 0.145 779 Planarity : 0.003 0.038 851 Dihedral : 8.588 76.562 807 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.79 % Allowed : 8.64 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.84 (0.35), residues: 611 helix: 2.09 (0.32), residues: 267 sheet: 0.35 (0.55), residues: 105 loop : -1.15 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 59 TYR 0.010 0.001 TYR E 49 PHE 0.009 0.001 PHE A 155 TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5182) covalent geometry : angle 0.48131 ( 7060) SS BOND : bond 0.00229 ( 4) SS BOND : angle 0.94344 ( 8) hydrogen bonds : bond 0.03603 ( 256) hydrogen bonds : angle 4.49659 ( 768) Misc. bond : bond 0.10119 ( 2) link_NAG-ASN : bond 0.00035 ( 3) link_NAG-ASN : angle 1.23182 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.243 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 65 average time/residue: 0.2516 time to fit residues: 19.6018 Evaluate side-chains 62 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.099838 restraints weight = 17743.350| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.72 r_work: 0.3124 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 5191 Z= 0.135 Angle : 0.491 9.139 7077 Z= 0.241 Chirality : 0.040 0.192 779 Planarity : 0.003 0.037 851 Dihedral : 8.414 71.975 807 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.98 % Allowed : 8.84 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.84 (0.35), residues: 611 helix: 2.06 (0.32), residues: 267 sheet: 0.40 (0.56), residues: 105 loop : -1.15 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 59 TYR 0.011 0.001 TYR E 49 PHE 0.009 0.001 PHE A 155 TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5182) covalent geometry : angle 0.48905 ( 7060) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.87291 ( 8) hydrogen bonds : bond 0.03612 ( 256) hydrogen bonds : angle 4.49188 ( 768) Misc. bond : bond 0.09922 ( 2) link_NAG-ASN : bond 0.00061 ( 3) link_NAG-ASN : angle 1.25744 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.175 Fit side-chains REVERT: A 268 MET cc_start: 0.8561 (mmt) cc_final: 0.7790 (mmt) outliers start: 5 outliers final: 5 residues processed: 63 average time/residue: 0.2578 time to fit residues: 19.4645 Evaluate side-chains 63 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120609 restraints weight = 17094.878| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.52 r_work: 0.3197 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 5191 Z= 0.116 Angle : 0.476 8.397 7077 Z= 0.234 Chirality : 0.039 0.144 779 Planarity : 0.003 0.037 851 Dihedral : 8.168 67.086 807 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.98 % Allowed : 9.04 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.89 (0.35), residues: 611 helix: 2.12 (0.32), residues: 267 sheet: 0.40 (0.56), residues: 105 loop : -1.13 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 59 TYR 0.009 0.001 TYR E 49 PHE 0.009 0.001 PHE A 155 TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5182) covalent geometry : angle 0.47445 ( 7060) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.81237 ( 8) hydrogen bonds : bond 0.03518 ( 256) hydrogen bonds : angle 4.42095 ( 768) Misc. bond : bond 0.09536 ( 2) link_NAG-ASN : bond 0.00037 ( 3) link_NAG-ASN : angle 1.16755 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.257 Fit side-chains REVERT: A 268 MET cc_start: 0.8575 (mmt) cc_final: 0.7859 (mmt) REVERT: D 11 VAL cc_start: 0.8771 (t) cc_final: 0.8545 (p) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.2473 time to fit residues: 19.0200 Evaluate side-chains 64 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099734 restraints weight = 17647.798| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.77 r_work: 0.3053 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 5191 Z= 0.143 Angle : 0.496 9.373 7077 Z= 0.242 Chirality : 0.039 0.144 779 Planarity : 0.003 0.037 851 Dihedral : 8.127 63.236 807 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.98 % Allowed : 9.43 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.85 (0.35), residues: 611 helix: 2.14 (0.32), residues: 261 sheet: 0.41 (0.56), residues: 105 loop : -1.16 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 59 TYR 0.012 0.001 TYR E 49 PHE 0.009 0.001 PHE A 212 TRP 0.005 0.001 TRP A 106 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5182) covalent geometry : angle 0.49352 ( 7060) SS BOND : bond 0.00229 ( 4) SS BOND : angle 0.86219 ( 8) hydrogen bonds : bond 0.03585 ( 256) hydrogen bonds : angle 4.43670 ( 768) Misc. bond : bond 0.09449 ( 2) link_NAG-ASN : bond 0.00089 ( 3) link_NAG-ASN : angle 1.26268 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.281 Fit side-chains REVERT: A 268 MET cc_start: 0.8538 (mmt) cc_final: 0.7755 (mmt) outliers start: 5 outliers final: 5 residues processed: 58 average time/residue: 0.2512 time to fit residues: 17.5866 Evaluate side-chains 60 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 0.0570 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100778 restraints weight = 17766.175| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.79 r_work: 0.2996 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 5191 Z= 0.110 Angle : 0.473 8.394 7077 Z= 0.233 Chirality : 0.039 0.144 779 Planarity : 0.003 0.037 851 Dihedral : 7.876 59.642 807 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.98 % Allowed : 9.43 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.93 (0.35), residues: 611 helix: 2.22 (0.32), residues: 261 sheet: 0.45 (0.56), residues: 105 loop : -1.13 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 59 TYR 0.009 0.001 TYR E 49 PHE 0.008 0.001 PHE A 155 TRP 0.005 0.001 TRP A 270 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5182) covalent geometry : angle 0.47104 ( 7060) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.77274 ( 8) hydrogen bonds : bond 0.03476 ( 256) hydrogen bonds : angle 4.37270 ( 768) Misc. bond : bond 0.09394 ( 2) link_NAG-ASN : bond 0.00055 ( 3) link_NAG-ASN : angle 1.14685 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.31 seconds wall clock time: 52 minutes 5.46 seconds (3125.46 seconds total)