Starting phenix.real_space_refine on Mon Jul 28 16:51:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u8g_26383/07_2025/7u8g_26383_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u8g_26383/07_2025/7u8g_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u8g_26383/07_2025/7u8g_26383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u8g_26383/07_2025/7u8g_26383.map" model { file = "/net/cci-nas-00/data/ceres_data/7u8g_26383/07_2025/7u8g_26383_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u8g_26383/07_2025/7u8g_26383_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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-2': 2, 'POV:plan-1': 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-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.80, per 1000 atoms: 0.69 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: 3.31 Conformation dependent library (CDL) restraints added in 682.7 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: 0.86 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: 3.61 Time building geometry restraints manager: 3.92 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: 2.920 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: 0.190 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.360 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.200 ------------------------------------------------------------------------------- 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 : 5.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (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 TRP 0.007 0.001 TRP A 270 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.016 0.001 TYR B 121 ARG 0.003 0.000 ARG A 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 3) link_NAG-ASN : angle 1.40293 ( 9) hydrogen bonds : bond 0.12956 ( 256) hydrogen bonds : angle 6.54479 ( 768) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.65239 ( 8) covalent geometry : bond 0.00617 ( 5182) covalent geometry : angle 0.99159 ( 7060) Misc. bond : bond 0.08579 ( 2) *********************** 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 : 0.947 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.4485 time to fit residues: 35.8358 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 : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.119833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101217 restraints weight = 17493.229| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.72 r_work: 0.3055 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 5191 Z= 0.140 Angle : 0.525 9.640 7077 Z= 0.261 Chirality : 0.040 0.150 779 Planarity : 0.004 0.046 851 Dihedral : 10.808 84.860 807 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.95 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.35), residues: 611 helix: 2.01 (0.32), residues: 263 sheet: 0.35 (0.54), residues: 105 loop : -0.95 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 270 HIS 0.003 0.001 HIS A 115 PHE 0.010 0.001 PHE D 94 TYR 0.011 0.001 TYR B 121 ARG 0.003 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 3) link_NAG-ASN : angle 1.25619 ( 9) hydrogen bonds : bond 0.04348 ( 256) hydrogen bonds : angle 5.25507 ( 768) SS BOND : bond 0.00273 ( 4) SS BOND : angle 0.92170 ( 8) covalent geometry : bond 0.00329 ( 5182) covalent geometry : angle 0.52238 ( 7060) Misc. bond : bond 0.13411 ( 2) *********************** 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 60 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.733 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4949 time to fit residues: 36.2799 Evaluate side-chains 53 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.117749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.099222 restraints weight = 17953.413| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.72 r_work: 0.3183 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 5191 Z= 0.177 Angle : 0.532 10.352 7077 Z= 0.264 Chirality : 0.040 0.155 779 Planarity : 0.004 0.043 851 Dihedral : 10.222 88.088 807 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.18 % Allowed : 6.68 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.34), residues: 611 helix: 1.90 (0.32), residues: 264 sheet: 0.28 (0.55), residues: 105 loop : -1.13 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.010 0.001 PHE A 212 TYR 0.013 0.001 TYR E 49 ARG 0.005 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 3) link_NAG-ASN : angle 1.36020 ( 9) hydrogen bonds : bond 0.04099 ( 256) hydrogen bonds : angle 4.97005 ( 768) SS BOND : bond 0.00292 ( 4) SS BOND : angle 1.01534 ( 8) covalent geometry : bond 0.00420 ( 5182) covalent geometry : angle 0.52950 ( 7060) Misc. bond : bond 0.11273 ( 2) *********************** 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 63 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 1.121 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.6572 time to fit residues: 49.6603 Evaluate side-chains 58 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.118889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.100433 restraints weight = 17774.654| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.72 r_work: 0.3067 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 5191 Z= 0.135 Angle : 0.490 8.736 7077 Z= 0.243 Chirality : 0.039 0.145 779 Planarity : 0.003 0.040 851 Dihedral : 9.606 89.386 807 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.59 % Allowed : 8.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.35), residues: 611 helix: 1.99 (0.32), residues: 267 sheet: 0.39 (0.56), residues: 105 loop : -1.09 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.003 0.001 HIS A 239 PHE 0.011 0.001 PHE A 155 TYR 0.010 0.001 TYR E 49 ARG 0.004 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 3) link_NAG-ASN : angle 1.21269 ( 9) hydrogen bonds : bond 0.03768 ( 256) hydrogen bonds : angle 4.69899 ( 768) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.90348 ( 8) covalent geometry : bond 0.00326 ( 5182) covalent geometry : angle 0.48728 ( 7060) Misc. bond : bond 0.10918 ( 2) *********************** 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 65 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.797 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 0.5518 time to fit residues: 43.2389 Evaluate side-chains 59 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 3 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 = 0.118962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099801 restraints weight = 17731.334| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.78 r_work: 0.3050 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 5191 Z= 0.138 Angle : 0.493 9.218 7077 Z= 0.242 Chirality : 0.039 0.145 779 Planarity : 0.003 0.039 851 Dihedral : 9.237 85.461 807 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.59 % Allowed : 8.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.35), residues: 611 helix: 2.01 (0.32), residues: 267 sheet: 0.34 (0.56), residues: 105 loop : -1.11 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.011 0.001 TYR E 49 ARG 0.007 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00060 ( 3) link_NAG-ASN : angle 1.25332 ( 9) hydrogen bonds : bond 0.03702 ( 256) hydrogen bonds : angle 4.60341 ( 768) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.97972 ( 8) covalent geometry : bond 0.00339 ( 5182) covalent geometry : angle 0.49020 ( 7060) Misc. bond : bond 0.10127 ( 2) *********************** 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 63 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.843 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 0.5251 time to fit residues: 40.2196 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 : 0.820 ------------------------------------------------------------------------------- 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 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.119689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100513 restraints weight = 17604.721| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.78 r_work: 0.3034 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1287 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= 0.121 Angle : 0.479 8.618 7077 Z= 0.236 Chirality : 0.039 0.144 779 Planarity : 0.003 0.037 851 Dihedral : 8.814 82.233 807 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.59 % Allowed : 8.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.35), residues: 611 helix: 2.08 (0.32), residues: 267 sheet: 0.39 (0.55), residues: 105 loop : -1.13 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 239 PHE 0.009 0.001 PHE A 155 TYR 0.010 0.001 TYR E 49 ARG 0.007 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 3) link_NAG-ASN : angle 1.19451 ( 9) hydrogen bonds : bond 0.03606 ( 256) hydrogen bonds : angle 4.52055 ( 768) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.95633 ( 8) covalent geometry : bond 0.00297 ( 5182) covalent geometry : angle 0.47685 ( 7060) Misc. bond : bond 0.09979 ( 2) *********************** 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 65 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.820 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 0.6709 time to fit residues: 53.8395 Evaluate side-chains 63 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.119122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099910 restraints weight = 17876.550| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.79 r_work: 0.3055 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 5191 Z= 0.136 Angle : 0.491 9.188 7077 Z= 0.241 Chirality : 0.040 0.188 779 Planarity : 0.003 0.037 851 Dihedral : 8.628 77.269 807 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.79 % Allowed : 9.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.35), residues: 611 helix: 2.04 (0.32), residues: 267 sheet: 0.40 (0.56), residues: 105 loop : -1.16 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 212 TYR 0.012 0.001 TYR E 49 ARG 0.006 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00067 ( 3) link_NAG-ASN : angle 1.25148 ( 9) hydrogen bonds : bond 0.03625 ( 256) hydrogen bonds : angle 4.50647 ( 768) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.88207 ( 8) covalent geometry : bond 0.00333 ( 5182) covalent geometry : angle 0.48846 ( 7060) Misc. bond : bond 0.09822 ( 2) *********************** 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 62 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.841 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 61 average time/residue: 0.6388 time to fit residues: 47.5202 Evaluate side-chains 60 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 51 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.117679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099163 restraints weight = 17920.511| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.73 r_work: 0.3048 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1381 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= 0.153 Angle : 0.501 9.433 7077 Z= 0.246 Chirality : 0.040 0.146 779 Planarity : 0.003 0.037 851 Dihedral : 8.407 70.443 807 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.79 % Allowed : 9.43 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.35), residues: 611 helix: 2.00 (0.32), residues: 267 sheet: 0.36 (0.56), residues: 105 loop : -1.18 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.010 0.001 PHE A 212 TYR 0.013 0.001 TYR E 49 ARG 0.006 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 3) link_NAG-ASN : angle 1.31688 ( 9) hydrogen bonds : bond 0.03680 ( 256) hydrogen bonds : angle 4.51796 ( 768) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.90252 ( 8) covalent geometry : bond 0.00373 ( 5182) covalent geometry : angle 0.49883 ( 7060) Misc. bond : bond 0.10096 ( 2) *********************** 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 60 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.847 Fit side-chains REVERT: A 268 MET cc_start: 0.8586 (mmt) cc_final: 0.7832 (mmt) outliers start: 4 outliers final: 4 residues processed: 59 average time/residue: 0.6158 time to fit residues: 46.1381 Evaluate side-chains 59 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 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 = 0.3292 r_free = 0.3292 target = 0.118828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099608 restraints weight = 17716.035| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.79 r_work: 0.3050 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1451 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 : 0.492 8.892 7077 Z= 0.241 Chirality : 0.040 0.145 779 Planarity : 0.003 0.038 851 Dihedral : 8.254 66.211 807 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.79 % Allowed : 9.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.35), residues: 611 helix: 2.04 (0.32), residues: 267 sheet: 0.38 (0.56), residues: 105 loop : -1.16 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.011 0.001 TYR E 49 ARG 0.006 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 3) link_NAG-ASN : angle 1.25284 ( 9) hydrogen bonds : bond 0.03606 ( 256) hydrogen bonds : angle 4.46555 ( 768) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.81637 ( 8) covalent geometry : bond 0.00330 ( 5182) covalent geometry : angle 0.48962 ( 7060) Misc. bond : bond 0.09867 ( 2) *********************** 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 59 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.726 Fit side-chains REVERT: A 268 MET cc_start: 0.8551 (mmt) cc_final: 0.7780 (mmt) outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 0.5465 time to fit residues: 39.2992 Evaluate side-chains 57 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.119448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100206 restraints weight = 17739.749| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.78 r_work: 0.2988 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 5191 Z= 0.125 Angle : 0.484 8.621 7077 Z= 0.237 Chirality : 0.039 0.145 779 Planarity : 0.003 0.038 851 Dihedral : 8.020 61.559 807 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.79 % Allowed : 9.82 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.35), residues: 611 helix: 2.08 (0.32), residues: 267 sheet: 0.41 (0.56), residues: 105 loop : -1.18 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.011 0.001 PHE B 38 TYR 0.010 0.001 TYR E 49 ARG 0.006 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00038 ( 3) link_NAG-ASN : angle 1.21206 ( 9) hydrogen bonds : bond 0.03550 ( 256) hydrogen bonds : angle 4.42063 ( 768) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.80782 ( 8) covalent geometry : bond 0.00307 ( 5182) covalent geometry : angle 0.48157 ( 7060) Misc. bond : bond 0.09547 ( 2) ********************** 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 59 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.634 Fit side-chains REVERT: A 268 MET cc_start: 0.8513 (mmt) cc_final: 0.7709 (mmt) outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 0.5734 time to fit residues: 40.8447 Evaluate side-chains 58 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.118360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099797 restraints weight = 17762.510| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.72 r_work: 0.2973 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1515 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= 0.132 Angle : 0.488 8.971 7077 Z= 0.239 Chirality : 0.039 0.145 779 Planarity : 0.003 0.038 851 Dihedral : 7.884 59.655 807 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.79 % Allowed : 9.82 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.35), residues: 611 helix: 2.15 (0.32), residues: 261 sheet: 0.40 (0.56), residues: 105 loop : -1.17 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.012 0.001 TYR E 49 ARG 0.006 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 3) link_NAG-ASN : angle 1.22971 ( 9) hydrogen bonds : bond 0.03552 ( 256) hydrogen bonds : angle 4.40661 ( 768) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.77639 ( 8) covalent geometry : bond 0.00326 ( 5182) covalent geometry : angle 0.48621 ( 7060) Misc. bond : bond 0.09426 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7961.05 seconds wall clock time: 145 minutes 40.93 seconds (8740.93 seconds total)