Starting phenix.real_space_refine on Tue Aug 4 15:25:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21aq_67524/08_2026/21aq_67524.cif Found real_map, /net/cci-nas-00/data/ceres_data/21aq_67524/08_2026/21aq_67524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21aq_67524/08_2026/21aq_67524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21aq_67524/08_2026/21aq_67524.map" model { file = "/net/cci-nas-00/data/ceres_data/21aq_67524/08_2026/21aq_67524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21aq_67524/08_2026/21aq_67524.cif" } resolution = 2.97 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= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 2664 2.51 5 N 725 2.21 5 O 854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4276 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 928 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "B" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 813 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "H" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2424 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.24, per 1000 atoms: 0.29 Number of scatterers: 4276 At special positions: 0 Unit cell: (58.9, 78.85, 109.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 854 8.00 N 725 7.00 C 2664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 49 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 156 " distance=2.03 Simple disulfide: pdb=" SG CYS H 180 " - pdb=" SG CYS H 327 " distance=2.03 Simple disulfide: pdb=" SG CYS H 206 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 258 " - pdb=" SG CYS H 266 " distance=2.05 Simple disulfide: pdb=" SG CYS H 258 " - pdb=" SG CYS H 305 " distance=2.06 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 303 " distance=2.04 Simple disulfide: pdb=" SG CYS H 274 " - pdb=" SG CYS H 280 " distance=2.03 Simple disulfide: pdb=" SG CYS H 287 " - pdb=" SG CYS H 292 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 7 " " MAN C 4 " - " MAN C 5 " ALPHA1-6 " BMA C 3 " - " MAN C 4 " " MAN C 4 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN H 63 " " NAG D 1 " - " ASN H 33 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 206.8 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 974 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 14 sheets defined 17.4% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.874A pdb=" N THR A 91 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.569A pdb=" N SER B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.716A pdb=" N GLU B 82 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 53 Processing helix chain 'H' and resid 54 through 65 Processing helix chain 'H' and resid 76 through 80 removed outlier: 3.552A pdb=" N GLN H 79 " --> pdb=" O GLY H 76 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL H 80 " --> pdb=" O ARG H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 80' Processing helix chain 'H' and resid 97 through 104 removed outlier: 3.697A pdb=" N TRP H 103 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 252 through 254 No H-bonds generated for 'chain 'H' and resid 252 through 254' Processing helix chain 'H' and resid 270 through 278 removed outlier: 3.505A pdb=" N THR H 276 " --> pdb=" O LYS H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.094A pdb=" N MET A 34 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.184A pdb=" N HIS A 112 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.574A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP B 34 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.574A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'H' and resid 70 through 71 removed outlier: 6.712A pdb=" N TYR H 70 " --> pdb=" O LEU H 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.530A pdb=" N PHE H 129 " --> pdb=" O LEU H 173 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE H 175 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU H 131 " --> pdb=" O ILE H 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 147 through 149 Processing sheet with id=AB1, first strand: chain 'H' and resid 177 through 180 removed outlier: 3.509A pdb=" N ASP H 177 " --> pdb=" O PHE H 330 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS H 207 " --> pdb=" O THR H 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 177 through 180 removed outlier: 3.509A pdb=" N ASP H 177 " --> pdb=" O PHE H 330 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS H 327 " --> pdb=" O ASP H 231 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA H 228 " --> pdb=" O MET H 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 218 through 219 removed outlier: 7.353A pdb=" N GLY H 218 " --> pdb=" O ASN H 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 244 through 248 Processing sheet with id=AB5, first strand: chain 'H' and resid 256 through 257 157 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.43 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 1391 1.36 - 1.49: 1173 1.49 - 1.62: 1764 1.62 - 1.75: 1 1.75 - 1.88: 45 Bond restraints: 4374 Sorted by residual: bond pdb=" CB PRO A 14 " pdb=" CG PRO A 14 " ideal model delta sigma weight residual 1.492 1.662 -0.170 5.00e-02 4.00e+02 1.16e+01 bond pdb=" CB CYS H 305 " pdb=" SG CYS H 305 " ideal model delta sigma weight residual 1.808 1.883 -0.075 3.30e-02 9.18e+02 5.21e+00 bond pdb=" C1 MAN C 4 " pdb=" C2 MAN C 4 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" N PRO A 14 " pdb=" CD PRO A 14 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.54e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 ... (remaining 4369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 5861 2.78 - 5.55: 47 5.55 - 8.33: 10 8.33 - 11.11: 0 11.11 - 13.89: 1 Bond angle restraints: 5919 Sorted by residual: angle pdb=" CA PRO A 14 " pdb=" N PRO A 14 " pdb=" CD PRO A 14 " ideal model delta sigma weight residual 112.00 98.11 13.89 1.40e+00 5.10e-01 9.84e+01 angle pdb=" N PRO A 14 " pdb=" CD PRO A 14 " pdb=" CG PRO A 14 " ideal model delta sigma weight residual 103.20 95.53 7.67 1.50e+00 4.44e-01 2.62e+01 angle pdb=" N CYS H 258 " pdb=" CA CYS H 258 " pdb=" C CYS H 258 " ideal model delta sigma weight residual 108.74 113.12 -4.38 1.38e+00 5.25e-01 1.01e+01 angle pdb=" CA PRO A 14 " pdb=" CB PRO A 14 " pdb=" CG PRO A 14 " ideal model delta sigma weight residual 104.50 98.49 6.01 1.90e+00 2.77e-01 1.00e+01 angle pdb=" CA CYS H 258 " pdb=" CB CYS H 258 " pdb=" SG CYS H 258 " ideal model delta sigma weight residual 114.40 121.59 -7.19 2.30e+00 1.89e-01 9.77e+00 ... (remaining 5914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 2565 21.59 - 43.19: 135 43.19 - 64.78: 24 64.78 - 86.37: 9 86.37 - 107.96: 5 Dihedral angle restraints: 2738 sinusoidal: 1200 harmonic: 1538 Sorted by residual: dihedral pdb=" CB CYS H 266 " pdb=" SG CYS H 266 " pdb=" SG CYS H 303 " pdb=" CB CYS H 303 " ideal model delta sinusoidal sigma weight residual -86.00 -165.55 79.55 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CB CYS H 258 " pdb=" SG CYS H 258 " pdb=" SG CYS H 305 " pdb=" CB CYS H 305 " ideal model delta sinusoidal sigma weight residual 93.00 35.06 57.94 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS H 274 " pdb=" SG CYS H 274 " pdb=" SG CYS H 280 " pdb=" CB CYS H 280 " ideal model delta sinusoidal sigma weight residual 93.00 148.91 -55.91 1 1.00e+01 1.00e-02 4.22e+01 ... (remaining 2735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 521 0.054 - 0.108: 104 0.108 - 0.162: 29 0.162 - 0.216: 0 0.216 - 0.270: 1 Chirality restraints: 655 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN H 33 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA CYS H 258 " pdb=" N CYS H 258 " pdb=" C CYS H 258 " pdb=" CB CYS H 258 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 652 not shown) Planarity restraints: 757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 13 " 0.083 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 14 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 119 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO H 120 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 120 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 120 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 14 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C PRO A 14 " -0.027 2.00e-02 2.50e+03 pdb=" O PRO A 14 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY A 15 " 0.009 2.00e-02 2.50e+03 ... (remaining 754 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 631 2.77 - 3.30: 3697 3.30 - 3.83: 6784 3.83 - 4.37: 8042 4.37 - 4.90: 14539 Nonbonded interactions: 33693 Sorted by model distance: nonbonded pdb=" OD2 ASP B 91 " pdb=" OG1 THR B 94 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLU H 201 " pdb=" OH TYR H 318 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR B 35 " pdb=" OE1 GLN B 88 " model vdw 2.292 3.040 nonbonded pdb=" O GLU H 268 " pdb=" OG SER H 269 " model vdw 2.323 3.040 nonbonded pdb=" NH1 ARG H 77 " pdb=" OD2 ASP H 100 " model vdw 2.349 3.120 ... (remaining 33688 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.780 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 4394 Z= 0.174 Angle : 0.708 13.886 5968 Z= 0.360 Chirality : 0.048 0.270 655 Planarity : 0.006 0.115 755 Dihedral : 14.189 107.964 1731 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.54 (0.35), residues: 538 helix: 0.17 (0.65), residues: 69 sheet: 0.32 (0.44), residues: 146 loop : -0.79 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.009 0.001 TYR A 80 PHE 0.013 0.001 PHE H 130 TRP 0.008 0.001 TRP H 141 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.17 ( 4374) covalent geometry : angle 0.67807 / 0.35 ( 5919) SS BOND : bond 0.00978 / 0.48 ( 11) SS BOND : angle 2.31742 / 1.53 ( 22) hydrogen bonds : bond 0.26491 / 18.80 ( 147) hydrogen bonds : angle 8.78356 / 6.36 ( 384) link_ALPHA1-3 : bond 0.00422 / 0.21 ( 2) link_ALPHA1-3 : angle 1.55676 / 0.76 ( 6) link_ALPHA1-6 : bond 0.00343 / 0.17 ( 2) link_ALPHA1-6 : angle 1.54420 / 0.76 ( 6) link_BETA1-4 : bond 0.00650 / 0.33 ( 3) link_BETA1-4 : angle 3.39219 / 1.55 ( 9) link_NAG-ASN : bond 0.00376 / 0.20 ( 2) link_NAG-ASN : angle 1.86162 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.6820 time to fit residues: 51.2203 Evaluate side-chains 52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.0040 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109951 restraints weight = 5065.316| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.14 r_work: 0.3138 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 4394 Z= 0.140 Angle : 0.619 8.402 5968 Z= 0.322 Chirality : 0.047 0.207 655 Planarity : 0.005 0.043 755 Dihedral : 10.404 79.770 773 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.53 % Allowed : 9.15 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.27 (0.36), residues: 538 helix: 0.29 (0.64), residues: 70 sheet: 0.67 (0.43), residues: 154 loop : -0.72 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 77 TYR 0.008 0.001 TYR H 83 PHE 0.013 0.002 PHE H 130 TRP 0.014 0.001 TRP H 141 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 4374) covalent geometry : angle 0.58530 / 0.31 ( 5919) SS BOND : bond 0.00996 / 0.50 ( 11) SS BOND : angle 2.14301 / 1.35 ( 22) hydrogen bonds : bond 0.04653 / 3.22 ( 147) hydrogen bonds : angle 5.86237 / 4.26 ( 384) link_ALPHA1-3 : bond 0.00793 / 0.40 ( 2) link_ALPHA1-3 : angle 1.77438 / 0.90 ( 6) link_ALPHA1-6 : bond 0.00391 / 0.20 ( 2) link_ALPHA1-6 : angle 1.83451 / 0.91 ( 6) link_BETA1-4 : bond 0.00411 / 0.21 ( 3) link_BETA1-4 : angle 3.26688 / 1.51 ( 9) link_NAG-ASN : bond 0.00260 / 0.14 ( 2) link_NAG-ASN : angle 2.02559 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.190 Fit side-chains REVERT: H 79 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8923 (mm110) outliers start: 7 outliers final: 2 residues processed: 57 average time/residue: 0.6633 time to fit residues: 39.0152 Evaluate side-chains 53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 253 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.5015 > 50:) chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106410 restraints weight = 5077.314| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.15 r_work: 0.3089 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 4394 Z= 0.175 Angle : 0.651 8.419 5968 Z= 0.333 Chirality : 0.049 0.251 655 Planarity : 0.005 0.040 755 Dihedral : 9.642 70.458 773 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.40 % Allowed : 11.55 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.51 (0.35), residues: 538 helix: -0.09 (0.62), residues: 76 sheet: 0.56 (0.43), residues: 149 loop : -0.85 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.011 0.001 TYR H 83 PHE 0.014 0.002 PHE H 130 TRP 0.014 0.002 TRP H 141 HIS 0.008 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.17 ( 4374) covalent geometry : angle 0.60955 / 0.32 ( 5919) SS BOND : bond 0.01065 / 0.53 ( 11) SS BOND : angle 2.64269 / 1.65 ( 22) hydrogen bonds : bond 0.04048 / 2.85 ( 147) hydrogen bonds : angle 5.13908 / 3.70 ( 384) link_ALPHA1-3 : bond 0.00938 / 0.48 ( 2) link_ALPHA1-3 : angle 1.42598 / 0.70 ( 6) link_ALPHA1-6 : bond 0.00233 / 0.12 ( 2) link_ALPHA1-6 : angle 1.85832 / 0.93 ( 6) link_BETA1-4 : bond 0.00445 / 0.22 ( 3) link_BETA1-4 : angle 3.31607 / 1.55 ( 9) link_NAG-ASN : bond 0.00237 / 0.12 ( 2) link_NAG-ASN : angle 2.66987 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.166 Fit side-chains REVERT: A 89 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 41 GLN cc_start: 0.8371 (mt0) cc_final: 0.8115 (mt0) REVERT: B 50 ASP cc_start: 0.7895 (m-30) cc_final: 0.7585 (m-30) REVERT: H 79 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8979 (mm110) REVERT: H 219 GLU cc_start: 0.7236 (pt0) cc_final: 0.7027 (pt0) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.6024 time to fit residues: 38.0079 Evaluate side-chains 57 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain H residue 323 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN H 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107442 restraints weight = 4986.939| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.13 r_work: 0.3108 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 4394 Z= 0.132 Angle : 0.608 8.397 5968 Z= 0.310 Chirality : 0.047 0.242 655 Planarity : 0.004 0.038 755 Dihedral : 9.183 64.857 773 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.96 % Allowed : 14.38 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.35), residues: 538 helix: 0.55 (0.64), residues: 70 sheet: 0.57 (0.42), residues: 154 loop : -0.84 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.014 0.001 TYR H 259 PHE 0.014 0.001 PHE H 130 TRP 0.013 0.001 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 4374) covalent geometry : angle 0.56774 / 0.30 ( 5919) SS BOND : bond 0.00916 / 0.47 ( 11) SS BOND : angle 2.43875 / 1.54 ( 22) hydrogen bonds : bond 0.03335 / 2.34 ( 147) hydrogen bonds : angle 4.89111 / 3.53 ( 384) link_ALPHA1-3 : bond 0.00804 / 0.41 ( 2) link_ALPHA1-3 : angle 1.55583 / 0.78 ( 6) link_ALPHA1-6 : bond 0.00246 / 0.13 ( 2) link_ALPHA1-6 : angle 1.77771 / 0.89 ( 6) link_BETA1-4 : bond 0.00471 / 0.23 ( 3) link_BETA1-4 : angle 3.27450 / 1.52 ( 9) link_NAG-ASN : bond 0.00416 / 0.22 ( 2) link_NAG-ASN : angle 2.48122 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.162 Fit side-chains REVERT: A 43 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7808 (mtmt) REVERT: A 89 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 19 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.7986 (mtm-85) REVERT: B 41 GLN cc_start: 0.8344 (mt0) cc_final: 0.8086 (mt0) REVERT: B 50 ASP cc_start: 0.7843 (m-30) cc_final: 0.7525 (m-30) REVERT: H 79 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8925 (mm110) REVERT: H 219 GLU cc_start: 0.7316 (pt0) cc_final: 0.7095 (pt0) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.6647 time to fit residues: 41.9188 Evaluate side-chains 57 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 253 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107984 restraints weight = 5006.450| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.12 r_work: 0.3113 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 4394 Z= 0.125 Angle : 0.598 8.346 5968 Z= 0.304 Chirality : 0.046 0.233 655 Planarity : 0.004 0.038 755 Dihedral : 8.855 60.487 773 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.53 % Allowed : 15.69 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.35), residues: 538 helix: 0.68 (0.65), residues: 70 sheet: 0.46 (0.41), residues: 154 loop : -0.80 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.014 0.001 TYR H 259 PHE 0.013 0.001 PHE H 130 TRP 0.013 0.001 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.12 ( 4374) covalent geometry : angle 0.55941 / 0.29 ( 5919) SS BOND : bond 0.00845 / 0.43 ( 11) SS BOND : angle 2.34570 / 1.48 ( 22) hydrogen bonds : bond 0.03138 / 2.20 ( 147) hydrogen bonds : angle 4.71085 / 3.40 ( 384) link_ALPHA1-3 : bond 0.00794 / 0.41 ( 2) link_ALPHA1-3 : angle 1.56384 / 0.78 ( 6) link_ALPHA1-6 : bond 0.00231 / 0.12 ( 2) link_ALPHA1-6 : angle 1.78325 / 0.89 ( 6) link_BETA1-4 : bond 0.00472 / 0.23 ( 3) link_BETA1-4 : angle 3.22845 / 1.49 ( 9) link_NAG-ASN : bond 0.00398 / 0.21 ( 2) link_NAG-ASN : angle 2.44522 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.161 Fit side-chains REVERT: A 89 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7254 (tm-30) REVERT: B 19 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8039 (mtm-85) REVERT: B 41 GLN cc_start: 0.8336 (mt0) cc_final: 0.8100 (mt0) REVERT: B 50 ASP cc_start: 0.7788 (m-30) cc_final: 0.7586 (m-30) REVERT: H 79 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8905 (mm110) REVERT: H 131 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8830 (pp20) REVERT: H 219 GLU cc_start: 0.7257 (pt0) cc_final: 0.7044 (pt0) REVERT: H 271 GLU cc_start: 0.8394 (tt0) cc_final: 0.7985 (tt0) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.7273 time to fit residues: 44.9882 Evaluate side-chains 56 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 253 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 38 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 12 optimal weight: 0.0370 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109130 restraints weight = 5125.370| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.15 r_work: 0.3133 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4394 Z= 0.104 Angle : 0.567 8.155 5968 Z= 0.287 Chirality : 0.046 0.214 655 Planarity : 0.004 0.038 755 Dihedral : 8.407 57.125 773 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.18 % Allowed : 16.12 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.24 (0.35), residues: 538 helix: 0.80 (0.66), residues: 70 sheet: 0.50 (0.41), residues: 154 loop : -0.72 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.013 0.001 TYR H 259 PHE 0.013 0.001 PHE H 130 TRP 0.011 0.001 TRP H 141 HIS 0.003 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.10 ( 4374) covalent geometry : angle 0.53023 / 0.28 ( 5919) SS BOND : bond 0.00767 / 0.39 ( 11) SS BOND : angle 2.13501 / 1.35 ( 22) hydrogen bonds : bond 0.02835 / 1.98 ( 147) hydrogen bonds : angle 4.55751 / 3.29 ( 384) link_ALPHA1-3 : bond 0.00798 / 0.41 ( 2) link_ALPHA1-3 : angle 1.66730 / 0.84 ( 6) link_ALPHA1-6 : bond 0.00257 / 0.14 ( 2) link_ALPHA1-6 : angle 1.74395 / 0.87 ( 6) link_BETA1-4 : bond 0.00499 / 0.25 ( 3) link_BETA1-4 : angle 3.16062 / 1.46 ( 9) link_NAG-ASN : bond 0.00435 / 0.23 ( 2) link_NAG-ASN : angle 2.24689 / 1.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.172 Fit side-chains REVERT: A 43 LYS cc_start: 0.8284 (mmmm) cc_final: 0.7544 (mptm) REVERT: A 89 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7272 (tm-30) REVERT: B 19 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8046 (mtm-85) REVERT: H 79 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8956 (mm110) REVERT: H 131 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8823 (pp20) REVERT: H 219 GLU cc_start: 0.7279 (pt0) cc_final: 0.7069 (pt0) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 0.6427 time to fit residues: 39.1989 Evaluate side-chains 55 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106850 restraints weight = 5127.928| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.15 r_work: 0.3097 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 4394 Z= 0.142 Angle : 0.614 7.984 5968 Z= 0.311 Chirality : 0.048 0.233 655 Planarity : 0.004 0.038 755 Dihedral : 8.399 55.996 773 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.96 % Allowed : 16.99 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.35), residues: 538 helix: 0.63 (0.65), residues: 70 sheet: 0.45 (0.42), residues: 153 loop : -0.72 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 241 TYR 0.012 0.001 TYR H 259 PHE 0.012 0.001 PHE H 130 TRP 0.013 0.001 TRP H 141 HIS 0.006 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 4374) covalent geometry : angle 0.57688 / 0.30 ( 5919) SS BOND : bond 0.00861 / 0.44 ( 11) SS BOND : angle 2.35450 / 1.47 ( 22) hydrogen bonds : bond 0.03260 / 2.31 ( 147) hydrogen bonds : angle 4.57913 / 3.31 ( 384) link_ALPHA1-3 : bond 0.00831 / 0.43 ( 2) link_ALPHA1-3 : angle 1.53941 / 0.77 ( 6) link_ALPHA1-6 : bond 0.00185 / 0.10 ( 2) link_ALPHA1-6 : angle 1.85395 / 0.93 ( 6) link_BETA1-4 : bond 0.00503 / 0.25 ( 3) link_BETA1-4 : angle 3.07274 / 1.42 ( 9) link_NAG-ASN : bond 0.00269 / 0.14 ( 2) link_NAG-ASN : angle 2.47242 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.172 Fit side-chains REVERT: A 89 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7367 (tm-30) REVERT: B 19 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.8025 (mtm-85) REVERT: B 50 ASP cc_start: 0.7789 (m-30) cc_final: 0.7494 (m-30) REVERT: H 131 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8828 (pp20) REVERT: H 313 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6911 (mt-10) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.6306 time to fit residues: 39.1495 Evaluate side-chains 59 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain H residue 313 GLU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106954 restraints weight = 5071.588| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.14 r_work: 0.3094 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 4394 Z= 0.139 Angle : 0.611 8.176 5968 Z= 0.310 Chirality : 0.047 0.242 655 Planarity : 0.004 0.038 755 Dihedral : 8.208 55.275 773 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.18 % Allowed : 16.78 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.32 (0.35), residues: 538 helix: 0.66 (0.65), residues: 70 sheet: 0.43 (0.42), residues: 153 loop : -0.74 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 241 TYR 0.011 0.001 TYR H 259 PHE 0.013 0.001 PHE H 130 TRP 0.013 0.001 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 4374) covalent geometry : angle 0.57338 / 0.30 ( 5919) SS BOND : bond 0.00847 / 0.43 ( 11) SS BOND : angle 2.36902 / 1.48 ( 22) hydrogen bonds : bond 0.03185 / 2.24 ( 147) hydrogen bonds : angle 4.58462 / 3.31 ( 384) link_ALPHA1-3 : bond 0.00846 / 0.44 ( 2) link_ALPHA1-3 : angle 1.59745 / 0.80 ( 6) link_ALPHA1-6 : bond 0.00198 / 0.10 ( 2) link_ALPHA1-6 : angle 1.81502 / 0.91 ( 6) link_BETA1-4 : bond 0.00467 / 0.23 ( 3) link_BETA1-4 : angle 3.12938 / 1.44 ( 9) link_NAG-ASN : bond 0.00355 / 0.19 ( 2) link_NAG-ASN : angle 2.49881 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.163 Fit side-chains REVERT: A 43 LYS cc_start: 0.8241 (mmmm) cc_final: 0.7478 (mptm) REVERT: A 89 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 19 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8018 (mtm-85) REVERT: B 50 ASP cc_start: 0.7913 (m-30) cc_final: 0.7618 (m-30) REVERT: H 131 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8874 (pp20) REVERT: H 313 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6896 (mt-10) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.6942 time to fit residues: 42.9681 Evaluate side-chains 59 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain H residue 313 GLU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108363 restraints weight = 5132.666| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.13 r_work: 0.3113 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4394 Z= 0.112 Angle : 0.581 8.103 5968 Z= 0.294 Chirality : 0.046 0.222 655 Planarity : 0.004 0.039 755 Dihedral : 7.848 56.428 773 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.18 % Allowed : 16.78 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.24 (0.35), residues: 538 helix: 0.79 (0.65), residues: 70 sheet: 0.46 (0.42), residues: 153 loop : -0.69 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 241 TYR 0.012 0.001 TYR H 259 PHE 0.013 0.001 PHE H 130 TRP 0.012 0.001 TRP A 47 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 4374) covalent geometry : angle 0.54460 / 0.28 ( 5919) SS BOND : bond 0.00751 / 0.39 ( 11) SS BOND : angle 2.15070 / 1.35 ( 22) hydrogen bonds : bond 0.02891 / 2.02 ( 147) hydrogen bonds : angle 4.48432 / 3.24 ( 384) link_ALPHA1-3 : bond 0.00838 / 0.43 ( 2) link_ALPHA1-3 : angle 1.67016 / 0.84 ( 6) link_ALPHA1-6 : bond 0.00262 / 0.14 ( 2) link_ALPHA1-6 : angle 1.76465 / 0.89 ( 6) link_BETA1-4 : bond 0.00476 / 0.24 ( 3) link_BETA1-4 : angle 3.10642 / 1.43 ( 9) link_NAG-ASN : bond 0.00395 / 0.21 ( 2) link_NAG-ASN : angle 2.30942 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.163 Fit side-chains REVERT: A 43 LYS cc_start: 0.8307 (mmmm) cc_final: 0.7583 (mptm) REVERT: A 89 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7428 (tm-30) REVERT: B 19 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8050 (mtm-85) REVERT: H 131 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8809 (pp20) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.6625 time to fit residues: 41.7052 Evaluate side-chains 58 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105595 restraints weight = 5075.131| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.12 r_work: 0.3071 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 4394 Z= 0.176 Angle : 0.659 8.125 5968 Z= 0.334 Chirality : 0.049 0.255 655 Planarity : 0.005 0.040 755 Dihedral : 8.070 54.045 773 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.53 % Allowed : 18.08 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.38 (0.35), residues: 538 helix: 0.66 (0.65), residues: 70 sheet: 0.38 (0.41), residues: 153 loop : -0.78 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 241 TYR 0.012 0.002 TYR H 259 PHE 0.014 0.002 PHE H 130 TRP 0.015 0.002 TRP H 141 HIS 0.008 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.17 ( 4374) covalent geometry : angle 0.61981 / 0.32 ( 5919) SS BOND : bond 0.00938 / 0.48 ( 11) SS BOND : angle 2.63768 / 1.64 ( 22) hydrogen bonds : bond 0.03519 / 2.50 ( 147) hydrogen bonds : angle 4.59466 / 3.34 ( 384) link_ALPHA1-3 : bond 0.00799 / 0.41 ( 2) link_ALPHA1-3 : angle 1.49954 / 0.75 ( 6) link_ALPHA1-6 : bond 0.00191 / 0.10 ( 2) link_ALPHA1-6 : angle 1.92216 / 0.97 ( 6) link_BETA1-4 : bond 0.00485 / 0.24 ( 3) link_BETA1-4 : angle 3.09254 / 1.42 ( 9) link_NAG-ASN : bond 0.00241 / 0.12 ( 2) link_NAG-ASN : angle 2.74153 / 1.59 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.169 Fit side-chains REVERT: A 43 LYS cc_start: 0.8341 (mmmm) cc_final: 0.7869 (mtmt) REVERT: A 89 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 50 ASP cc_start: 0.8020 (m-30) cc_final: 0.7669 (m-30) REVERT: H 131 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8875 (pp20) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 0.6769 time to fit residues: 38.3703 Evaluate side-chains 55 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106070 restraints weight = 5015.287| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.14 r_work: 0.3079 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 4394 Z= 0.151 Angle : 0.626 8.311 5968 Z= 0.317 Chirality : 0.048 0.258 655 Planarity : 0.005 0.045 755 Dihedral : 7.906 53.034 773 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.96 % Allowed : 18.08 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.38 (0.35), residues: 538 helix: 0.69 (0.65), residues: 70 sheet: 0.40 (0.42), residues: 153 loop : -0.79 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.012 0.001 TYR H 259 PHE 0.013 0.002 PHE H 130 TRP 0.014 0.001 TRP H 141 HIS 0.006 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 ( 4374) covalent geometry : angle 0.58686 / 0.31 ( 5919) SS BOND : bond 0.00861 / 0.44 ( 11) SS BOND : angle 2.48964 / 1.55 ( 22) hydrogen bonds : bond 0.03292 / 2.32 ( 147) hydrogen bonds : angle 4.55288 / 3.31 ( 384) link_ALPHA1-3 : bond 0.00847 / 0.44 ( 2) link_ALPHA1-3 : angle 1.58535 / 0.79 ( 6) link_ALPHA1-6 : bond 0.00218 / 0.11 ( 2) link_ALPHA1-6 : angle 1.84225 / 0.93 ( 6) link_BETA1-4 : bond 0.00439 / 0.22 ( 3) link_BETA1-4 : angle 3.14637 / 1.44 ( 9) link_NAG-ASN : bond 0.00372 / 0.19 ( 2) link_NAG-ASN : angle 2.64817 / 1.52 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1697.72 seconds wall clock time: 29 minutes 43.04 seconds (1783.04 seconds total)