Starting phenix.real_space_refine on Thu Jul 2 01:54:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mjs_23883/07_2026/7mjs_23883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjs_23883/07_2026/7mjs_23883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mjs_23883/07_2026/7mjs_23883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjs_23883/07_2026/7mjs_23883.map" model { file = "/net/cci-nas-00/data/ceres_data/7mjs_23883/07_2026/7mjs_23883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjs_23883/07_2026/7mjs_23883.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mjs_23883/07_2026/7mjs_23883.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mjs_23883/07_2026/7mjs_23883.cif" } resolution = 3.03 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= 0.022 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 26 5.16 5 C 3618 2.51 5 N 878 2.21 5 O 1013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5536 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1018 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "L" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 863 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "X" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3592 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'ZGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.27, per 1000 atoms: 0.23 Number of scatterers: 5536 At special positions: 0 Unit cell: (69.72, 69.72, 131.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 1 15.00 O 1013 8.00 N 878 7.00 C 3618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS X 207 " - pdb=" SG CYS X 460 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG X 602 " - " ASN X 227 " " NAG X 603 " - " ASN X 218 " Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 164.1 milliseconds 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 54.8% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'X' and resid 37 through 42 removed outlier: 3.526A pdb=" N LEU X 42 " --> pdb=" O VAL X 38 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 47 removed outlier: 3.594A pdb=" N VAL X 46 " --> pdb=" O LEU X 42 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY X 47 " --> pdb=" O CYS X 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 42 through 47' Processing helix chain 'X' and resid 47 through 69 removed outlier: 4.666A pdb=" N TYR X 51 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN X 52 " --> pdb=" O GLY X 48 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLN X 63 " --> pdb=" O GLY X 59 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE X 64 " --> pdb=" O PHE X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 99 removed outlier: 3.630A pdb=" N ASP X 92 " --> pdb=" O ASP X 88 " (cutoff:3.500A) Proline residue: X 93 - end of helix Processing helix chain 'X' and resid 110 through 127 removed outlier: 3.884A pdb=" N ILE X 114 " --> pdb=" O LEU X 110 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR X 118 " --> pdb=" O ILE X 114 " (cutoff:3.500A) Proline residue: X 119 - end of helix Processing helix chain 'X' and resid 137 through 162 removed outlier: 3.534A pdb=" N TRP X 141 " --> pdb=" O GLY X 137 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR X 142 " --> pdb=" O GLN X 138 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE X 145 " --> pdb=" O TRP X 141 " (cutoff:3.500A) Proline residue: X 159 - end of helix Processing helix chain 'X' and resid 163 through 168 removed outlier: 4.385A pdb=" N SER X 168 " --> pdb=" O THR X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 170 through 202 removed outlier: 3.599A pdb=" N VAL X 200 " --> pdb=" O GLN X 196 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS X 202 " --> pdb=" O GLN X 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 223 removed outlier: 4.088A pdb=" N ALA X 222 " --> pdb=" O ASN X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 264 Processing helix chain 'X' and resid 281 through 289 removed outlier: 3.673A pdb=" N MET X 289 " --> pdb=" O LEU X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 291 through 322 removed outlier: 4.163A pdb=" N THR X 320 " --> pdb=" O ALA X 316 " (cutoff:3.500A) Processing helix chain 'X' and resid 328 through 354 Proline residue: X 345 - end of helix Processing helix chain 'X' and resid 355 through 366 removed outlier: 3.973A pdb=" N TYR X 361 " --> pdb=" O LYS X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 377 removed outlier: 4.321A pdb=" N PHE X 370 " --> pdb=" O SER X 366 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL X 375 " --> pdb=" O LEU X 371 " (cutoff:3.500A) Processing helix chain 'X' and resid 380 through 417 removed outlier: 3.620A pdb=" N TYR X 385 " --> pdb=" O LEU X 381 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE X 386 " --> pdb=" O VAL X 382 " (cutoff:3.500A) Proline residue: X 402 - end of helix Proline residue: X 407 - end of helix Processing helix chain 'X' and resid 425 through 453 removed outlier: 3.628A pdb=" N THR X 438 " --> pdb=" O PHE X 434 " (cutoff:3.500A) Processing helix chain 'X' and resid 463 through 473 Processing helix chain 'X' and resid 475 through 489 Processing helix chain 'X' and resid 490 through 492 No H-bonds generated for 'chain 'X' and resid 490 through 492' Processing helix chain 'X' and resid 497 through 505 removed outlier: 4.238A pdb=" N GLU X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.621A pdb=" N SER H 102 " --> pdb=" O SER H 36 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 60 " --> pdb=" O TYR H 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.781A pdb=" N CYS H 99 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP H 122 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG H 101 " --> pdb=" O ASP H 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.368A pdb=" N LEU L 12 " --> pdb=" O GLU L 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.739A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 969 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: 0.87 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 836 1.31 - 1.44: 1687 1.44 - 1.56: 3112 1.56 - 1.69: 3 1.69 - 1.82: 39 Bond restraints: 5677 Sorted by residual: bond pdb=" C18 ZGS X 601 " pdb=" O20 ZGS X 601 " ideal model delta sigma weight residual 1.345 1.416 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" N VAL X 226 " pdb=" CA VAL X 226 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.19e-02 7.06e+03 1.22e+01 bond pdb=" C32 ZGS X 601 " pdb=" N31 ZGS X 601 " ideal model delta sigma weight residual 1.500 1.441 0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" N ASN X 227 " pdb=" CA ASN X 227 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.72e+00 bond pdb=" N THR X 217 " pdb=" CA THR X 217 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.32e-02 5.74e+03 7.24e+00 ... (remaining 5672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 7623 2.57 - 5.14: 79 5.14 - 7.71: 15 7.71 - 10.28: 2 10.28 - 12.85: 1 Bond angle restraints: 7720 Sorted by residual: angle pdb=" N CYS X 460 " pdb=" CA CYS X 460 " pdb=" C CYS X 460 " ideal model delta sigma weight residual 114.31 108.51 5.80 1.29e+00 6.01e-01 2.02e+01 angle pdb=" O26 ZGS X 601 " pdb=" P25 ZGS X 601 " pdb=" O27 ZGS X 601 " ideal model delta sigma weight residual 121.97 109.12 12.85 3.00e+00 1.11e-01 1.83e+01 angle pdb=" N PHE X 219 " pdb=" CA PHE X 219 " pdb=" C PHE X 219 " ideal model delta sigma weight residual 113.23 108.29 4.94 1.24e+00 6.50e-01 1.59e+01 angle pdb=" C THR X 217 " pdb=" CA THR X 217 " pdb=" CB THR X 217 " ideal model delta sigma weight residual 111.06 117.68 -6.62 1.89e+00 2.80e-01 1.23e+01 angle pdb=" C VAL H 15 " pdb=" N GLN H 16 " pdb=" CA GLN H 16 " ideal model delta sigma weight residual 120.97 111.17 9.80 2.84e+00 1.24e-01 1.19e+01 ... (remaining 7715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 2960 17.64 - 35.28: 263 35.28 - 52.91: 45 52.91 - 70.55: 14 70.55 - 88.19: 3 Dihedral angle restraints: 3285 sinusoidal: 1247 harmonic: 2038 Sorted by residual: dihedral pdb=" CB CYS X 207 " pdb=" SG CYS X 207 " pdb=" SG CYS X 460 " pdb=" CB CYS X 460 " ideal model delta sinusoidal sigma weight residual -86.00 -31.66 -54.34 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CA ASN L 96 " pdb=" C ASN L 96 " pdb=" N GLN L 97 " pdb=" CA GLN L 97 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" C THR X 217 " pdb=" N THR X 217 " pdb=" CA THR X 217 " pdb=" CB THR X 217 " ideal model delta harmonic sigma weight residual -122.00 -131.98 9.98 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 3282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 881 0.198 - 0.396: 3 0.396 - 0.595: 0 0.595 - 0.793: 0 0.793 - 0.991: 1 Chirality restraints: 885 Sorted by residual: chirality pdb=" C1 NAG X 603 " pdb=" ND2 ASN X 218 " pdb=" C2 NAG X 603 " pdb=" O5 NAG X 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG X 602 " pdb=" ND2 ASN X 227 " pdb=" C2 NAG X 602 " pdb=" O5 NAG X 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA THR X 217 " pdb=" N THR X 217 " pdb=" C THR X 217 " pdb=" CB THR X 217 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 882 not shown) Planarity restraints: 953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 602 " -0.114 2.00e-02 2.50e+03 9.38e-02 1.10e+02 pdb=" C7 NAG X 602 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG X 602 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG X 602 " 0.150 2.00e-02 2.50e+03 pdb=" O7 NAG X 602 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 603 " 0.091 2.00e-02 2.50e+03 7.74e-02 7.48e+01 pdb=" C7 NAG X 603 " -0.015 2.00e-02 2.50e+03 pdb=" C8 NAG X 603 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG X 603 " -0.125 2.00e-02 2.50e+03 pdb=" O7 NAG X 603 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 44 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO L 45 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " 0.022 5.00e-02 4.00e+02 ... (remaining 950 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 999 2.76 - 3.30: 5470 3.30 - 3.83: 9160 3.83 - 4.37: 11223 4.37 - 4.90: 19596 Nonbonded interactions: 46448 Sorted by model distance: nonbonded pdb=" O SER H 66 " pdb=" NH1 ARG H 70 " model vdw 2.228 3.120 nonbonded pdb=" OG SER H 58 " pdb=" O PHE X 213 " model vdw 2.247 3.040 nonbonded pdb=" O GLY X 363 " pdb=" OG SER X 366 " model vdw 2.287 3.040 nonbonded pdb=" NH1 ARG H 41 " pdb=" OD1 ASP H 93 " model vdw 2.304 3.120 nonbonded pdb=" OH TYR H 105 " pdb=" OG SER L 92 " model vdw 2.333 3.040 ... (remaining 46443 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: 2.940 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.005 0.071 5682 Z= 0.270 Angle : 0.781 13.101 7732 Z= 0.428 Chirality : 0.057 0.991 885 Planarity : 0.006 0.094 951 Dihedral : 14.153 88.191 1976 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.26), residues: 695 helix: -1.42 (0.23), residues: 341 sheet: -2.47 (0.41), residues: 114 loop : -2.35 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 67 TYR 0.014 0.001 TYR X 146 PHE 0.015 0.002 PHE X 318 TRP 0.009 0.001 TRP X 349 HIS 0.003 0.001 HIS X 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.27 ( 5677) covalent geometry : angle 0.75615 / 0.42 ( 7720) SS BOND : bond 0.00261 / 0.13 ( 3) SS BOND : angle 0.76706 / 0.38 ( 6) hydrogen bonds : bond 0.12120 / 7.65 ( 331) hydrogen bonds : angle 6.90881 / 4.60 ( 969) link_NAG-ASN : bond 0.01681 / 0.88 ( 2) link_NAG-ASN : angle 6.98969 / 3.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.153 Fit side-chains REVERT: H 46 LYS cc_start: 0.8527 (mttp) cc_final: 0.8313 (mttp) REVERT: H 49 GLU cc_start: 0.7553 (tt0) cc_final: 0.7207 (tt0) REVERT: L 46 LYS cc_start: 0.8591 (mttt) cc_final: 0.8258 (mttp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0729 time to fit residues: 10.8402 Evaluate side-chains 93 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0050 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN H 112 GLN L 38 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 240 ASN X 290 ASN X 291 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125996 restraints weight = 7054.562| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.94 r_work: 0.3415 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5682 Z= 0.137 Angle : 0.558 8.080 7732 Z= 0.291 Chirality : 0.043 0.255 885 Planarity : 0.004 0.041 951 Dihedral : 6.347 59.424 797 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.18 % Allowed : 10.47 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.30), residues: 695 helix: 0.19 (0.27), residues: 345 sheet: -1.86 (0.45), residues: 103 loop : -1.66 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 70 TYR 0.017 0.001 TYR X 65 PHE 0.014 0.001 PHE X 318 TRP 0.007 0.001 TRP X 349 HIS 0.006 0.001 HIS X 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 5677) covalent geometry : angle 0.54961 / 0.29 ( 7720) SS BOND : bond 0.00365 / 0.18 ( 3) SS BOND : angle 0.82750 / 0.43 ( 6) hydrogen bonds : bond 0.04386 / 2.90 ( 331) hydrogen bonds : angle 5.02712 / 3.41 ( 969) link_NAG-ASN : bond 0.00817 / 0.43 ( 2) link_NAG-ASN : angle 3.35135 / 1.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.150 Fit side-chains REVERT: H 46 LYS cc_start: 0.8692 (mttp) cc_final: 0.8450 (mttp) REVERT: H 49 GLU cc_start: 0.8253 (tt0) cc_final: 0.8041 (tt0) REVERT: L 46 LYS cc_start: 0.8998 (mttt) cc_final: 0.8747 (mttp) REVERT: X 170 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7366 (mm-30) REVERT: X 240 ASN cc_start: 0.8753 (m-40) cc_final: 0.8384 (m-40) outliers start: 7 outliers final: 6 residues processed: 112 average time/residue: 0.0518 time to fit residues: 7.9997 Evaluate side-chains 102 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 429 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.143724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125319 restraints weight = 6982.317| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.05 r_work: 0.3410 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5682 Z= 0.145 Angle : 0.547 7.178 7732 Z= 0.284 Chirality : 0.042 0.237 885 Planarity : 0.004 0.044 951 Dihedral : 5.708 57.648 797 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.70 % Allowed : 11.66 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.31), residues: 695 helix: 0.65 (0.27), residues: 347 sheet: -1.60 (0.45), residues: 103 loop : -1.41 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.018 0.001 TYR H 33 PHE 0.015 0.001 PHE X 318 TRP 0.007 0.001 TRP X 349 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 5677) covalent geometry : angle 0.54017 / 0.28 ( 7720) SS BOND : bond 0.00296 / 0.14 ( 3) SS BOND : angle 1.01619 / 0.51 ( 6) hydrogen bonds : bond 0.04325 / 2.87 ( 331) hydrogen bonds : angle 4.81325 / 3.27 ( 969) link_NAG-ASN : bond 0.00671 / 0.34 ( 2) link_NAG-ASN : angle 2.94670 / 1.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.172 Fit side-chains REVERT: L 46 LYS cc_start: 0.9024 (mttt) cc_final: 0.8721 (mttp) REVERT: X 170 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7399 (mm-30) REVERT: X 314 ASN cc_start: 0.7518 (m110) cc_final: 0.7239 (m-40) outliers start: 16 outliers final: 11 residues processed: 113 average time/residue: 0.0601 time to fit residues: 9.4372 Evaluate side-chains 114 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.140948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122258 restraints weight = 7077.996| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.07 r_work: 0.3364 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5682 Z= 0.228 Angle : 0.600 6.675 7732 Z= 0.314 Chirality : 0.045 0.239 885 Planarity : 0.004 0.044 951 Dihedral : 5.791 57.502 797 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.89 % Allowed : 12.67 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.31), residues: 695 helix: 0.60 (0.27), residues: 345 sheet: -1.74 (0.43), residues: 116 loop : -1.32 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.026 0.002 TYR X 492 PHE 0.017 0.002 PHE X 318 TRP 0.006 0.001 TRP H 39 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 ( 5677) covalent geometry : angle 0.59468 / 0.31 ( 7720) SS BOND : bond 0.00423 / 0.21 ( 3) SS BOND : angle 0.99550 / 0.51 ( 6) hydrogen bonds : bond 0.04795 / 3.18 ( 331) hydrogen bonds : angle 4.94248 / 3.37 ( 969) link_NAG-ASN : bond 0.00506 / 0.26 ( 2) link_NAG-ASN : angle 2.72328 / 1.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.169 Fit side-chains REVERT: L 46 LYS cc_start: 0.9014 (mttt) cc_final: 0.8775 (mttp) REVERT: X 170 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7404 (mm-30) REVERT: X 240 ASN cc_start: 0.8791 (m-40) cc_final: 0.8454 (m-40) REVERT: X 297 LEU cc_start: 0.8743 (tt) cc_final: 0.8515 (tp) REVERT: X 314 ASN cc_start: 0.7813 (m110) cc_final: 0.7523 (m-40) REVERT: X 418 PRO cc_start: 0.8862 (Cg_endo) cc_final: 0.8594 (Cg_exo) outliers start: 23 outliers final: 18 residues processed: 112 average time/residue: 0.0544 time to fit residues: 8.6144 Evaluate side-chains 117 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 43 CYS Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 chunk 59 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123895 restraints weight = 7361.121| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.89 r_work: 0.3361 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5682 Z= 0.134 Angle : 0.547 6.963 7732 Z= 0.283 Chirality : 0.042 0.227 885 Planarity : 0.004 0.044 951 Dihedral : 5.502 54.699 797 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.70 % Allowed : 15.37 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.32), residues: 695 helix: 0.93 (0.28), residues: 351 sheet: -1.33 (0.45), residues: 103 loop : -1.23 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.023 0.001 TYR X 492 PHE 0.015 0.001 PHE X 318 TRP 0.009 0.001 TRP X 349 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 5677) covalent geometry : angle 0.54219 / 0.28 ( 7720) SS BOND : bond 0.00332 / 0.16 ( 3) SS BOND : angle 0.86724 / 0.46 ( 6) hydrogen bonds : bond 0.04299 / 2.84 ( 331) hydrogen bonds : angle 4.71860 / 3.22 ( 969) link_NAG-ASN : bond 0.00591 / 0.30 ( 2) link_NAG-ASN : angle 2.58741 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.175 Fit side-chains REVERT: L 46 LYS cc_start: 0.8982 (mttt) cc_final: 0.8672 (mttp) REVERT: X 170 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7377 (mm-30) REVERT: X 200 VAL cc_start: 0.8925 (t) cc_final: 0.8549 (m) REVERT: X 240 ASN cc_start: 0.8743 (m-40) cc_final: 0.8399 (m-40) REVERT: X 314 ASN cc_start: 0.7448 (m110) cc_final: 0.7089 (m-40) REVERT: X 418 PRO cc_start: 0.8846 (Cg_endo) cc_final: 0.8592 (Cg_exo) outliers start: 16 outliers final: 13 residues processed: 120 average time/residue: 0.0591 time to fit residues: 9.9784 Evaluate side-chains 116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 39 GLN X 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124536 restraints weight = 7220.050| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.87 r_work: 0.3374 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5682 Z= 0.138 Angle : 0.549 6.966 7732 Z= 0.284 Chirality : 0.043 0.221 885 Planarity : 0.004 0.044 951 Dihedral : 5.374 53.634 797 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.70 % Allowed : 16.22 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.32), residues: 695 helix: 1.12 (0.28), residues: 351 sheet: -1.20 (0.46), residues: 103 loop : -1.18 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.022 0.001 TYR X 492 PHE 0.015 0.001 PHE X 318 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 5677) covalent geometry : angle 0.54358 / 0.28 ( 7720) SS BOND : bond 0.00675 / 0.34 ( 3) SS BOND : angle 1.16475 / 0.56 ( 6) hydrogen bonds : bond 0.04228 / 2.80 ( 331) hydrogen bonds : angle 4.64476 / 3.16 ( 969) link_NAG-ASN : bond 0.00582 / 0.30 ( 2) link_NAG-ASN : angle 2.51174 / 1.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.192 Fit side-chains REVERT: L 46 LYS cc_start: 0.8960 (mttt) cc_final: 0.8654 (mttp) REVERT: X 170 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7377 (mm-30) REVERT: X 240 ASN cc_start: 0.8729 (m-40) cc_final: 0.8359 (m-40) REVERT: X 314 ASN cc_start: 0.7378 (m110) cc_final: 0.7015 (m-40) REVERT: X 418 PRO cc_start: 0.8851 (Cg_endo) cc_final: 0.8643 (Cg_exo) outliers start: 16 outliers final: 15 residues processed: 116 average time/residue: 0.0542 time to fit residues: 8.7582 Evaluate side-chains 118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123040 restraints weight = 7346.313| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.89 r_work: 0.3355 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5682 Z= 0.166 Angle : 0.563 6.732 7732 Z= 0.292 Chirality : 0.044 0.223 885 Planarity : 0.004 0.043 951 Dihedral : 5.422 54.127 797 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.55 % Allowed : 15.54 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.32), residues: 695 helix: 1.09 (0.28), residues: 351 sheet: -1.12 (0.46), residues: 103 loop : -1.16 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 62 TYR 0.027 0.002 TYR X 492 PHE 0.016 0.001 PHE X 318 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 ( 5677) covalent geometry : angle 0.55859 / 0.29 ( 7720) SS BOND : bond 0.00337 / 0.17 ( 3) SS BOND : angle 0.90925 / 0.46 ( 6) hydrogen bonds : bond 0.04376 / 2.90 ( 331) hydrogen bonds : angle 4.69969 / 3.21 ( 969) link_NAG-ASN : bond 0.00533 / 0.27 ( 2) link_NAG-ASN : angle 2.41593 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.210 Fit side-chains REVERT: L 46 LYS cc_start: 0.8972 (mttt) cc_final: 0.8661 (mttp) REVERT: X 170 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7420 (mm-30) REVERT: X 240 ASN cc_start: 0.8734 (m-40) cc_final: 0.8373 (m-40) REVERT: X 314 ASN cc_start: 0.7509 (m110) cc_final: 0.7143 (m-40) REVERT: X 418 PRO cc_start: 0.8846 (Cg_endo) cc_final: 0.8643 (Cg_exo) outliers start: 21 outliers final: 17 residues processed: 116 average time/residue: 0.0607 time to fit residues: 9.7851 Evaluate side-chains 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 43 CYS Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 285 LEU Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 0.0010 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125152 restraints weight = 7171.550| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.86 r_work: 0.3379 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5682 Z= 0.133 Angle : 0.544 7.037 7732 Z= 0.281 Chirality : 0.042 0.216 885 Planarity : 0.004 0.043 951 Dihedral : 5.270 52.896 797 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.38 % Allowed : 16.72 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.32), residues: 695 helix: 1.28 (0.28), residues: 351 sheet: -1.04 (0.47), residues: 103 loop : -1.12 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.037 0.001 TYR X 492 PHE 0.015 0.001 PHE X 318 TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 5677) covalent geometry : angle 0.53975 / 0.28 ( 7720) SS BOND : bond 0.00338 / 0.17 ( 3) SS BOND : angle 0.76318 / 0.40 ( 6) hydrogen bonds : bond 0.04099 / 2.72 ( 331) hydrogen bonds : angle 4.58520 / 3.13 ( 969) link_NAG-ASN : bond 0.00548 / 0.28 ( 2) link_NAG-ASN : angle 2.31580 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.183 Fit side-chains REVERT: L 46 LYS cc_start: 0.8969 (mttt) cc_final: 0.8651 (mttp) REVERT: X 170 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7396 (mm-30) REVERT: X 240 ASN cc_start: 0.8718 (m-40) cc_final: 0.8374 (m-40) REVERT: X 314 ASN cc_start: 0.7336 (m110) cc_final: 0.6959 (m-40) REVERT: X 418 PRO cc_start: 0.8854 (Cg_endo) cc_final: 0.8633 (Cg_exo) outliers start: 20 outliers final: 17 residues processed: 117 average time/residue: 0.0518 time to fit residues: 8.5494 Evaluate side-chains 120 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 285 LEU Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 423 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125087 restraints weight = 7094.745| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.05 r_work: 0.3400 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5682 Z= 0.168 Angle : 0.568 7.532 7732 Z= 0.295 Chirality : 0.044 0.218 885 Planarity : 0.004 0.043 951 Dihedral : 5.360 53.772 797 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.04 % Allowed : 17.74 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.32), residues: 695 helix: 1.20 (0.28), residues: 351 sheet: -1.29 (0.44), residues: 116 loop : -1.00 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.040 0.002 TYR X 492 PHE 0.016 0.001 PHE X 318 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 5677) covalent geometry : angle 0.56464 / 0.29 ( 7720) SS BOND : bond 0.00374 / 0.18 ( 3) SS BOND : angle 0.76669 / 0.39 ( 6) hydrogen bonds : bond 0.04321 / 2.87 ( 331) hydrogen bonds : angle 4.66710 / 3.18 ( 969) link_NAG-ASN : bond 0.00514 / 0.26 ( 2) link_NAG-ASN : angle 2.24978 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.152 Fit side-chains REVERT: L 46 LYS cc_start: 0.9014 (mttt) cc_final: 0.8696 (mttp) REVERT: X 170 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7393 (mm-30) REVERT: X 240 ASN cc_start: 0.8767 (m-40) cc_final: 0.8408 (m-40) REVERT: X 314 ASN cc_start: 0.7553 (m110) cc_final: 0.7156 (m-40) REVERT: X 418 PRO cc_start: 0.8839 (Cg_endo) cc_final: 0.8602 (Cg_exo) outliers start: 18 outliers final: 16 residues processed: 112 average time/residue: 0.0531 time to fit residues: 8.3976 Evaluate side-chains 118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126987 restraints weight = 7035.909| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.03 r_work: 0.3425 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5682 Z= 0.136 Angle : 0.549 7.949 7732 Z= 0.284 Chirality : 0.042 0.210 885 Planarity : 0.004 0.043 951 Dihedral : 5.242 52.531 797 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.70 % Allowed : 18.24 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.32), residues: 695 helix: 1.38 (0.28), residues: 351 sheet: -0.92 (0.48), residues: 103 loop : -1.01 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.038 0.001 TYR X 492 PHE 0.015 0.001 PHE X 318 TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 5677) covalent geometry : angle 0.54585 / 0.28 ( 7720) SS BOND : bond 0.00365 / 0.18 ( 3) SS BOND : angle 0.73543 / 0.39 ( 6) hydrogen bonds : bond 0.04058 / 2.69 ( 331) hydrogen bonds : angle 4.55790 / 3.11 ( 969) link_NAG-ASN : bond 0.00541 / 0.28 ( 2) link_NAG-ASN : angle 2.14098 / 1.21 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.223 Fit side-chains REVERT: L 46 LYS cc_start: 0.9021 (mttt) cc_final: 0.8692 (mttp) REVERT: X 170 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7376 (mm-30) REVERT: X 240 ASN cc_start: 0.8763 (m-40) cc_final: 0.8416 (m-40) REVERT: X 314 ASN cc_start: 0.7360 (m110) cc_final: 0.6968 (m-40) REVERT: X 418 PRO cc_start: 0.8869 (Cg_endo) cc_final: 0.8617 (Cg_exo) outliers start: 16 outliers final: 16 residues processed: 113 average time/residue: 0.0571 time to fit residues: 9.1992 Evaluate side-chains 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 435 THR Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 0.0040 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126555 restraints weight = 7073.418| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.04 r_work: 0.3422 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5682 Z= 0.144 Angle : 0.556 7.581 7732 Z= 0.287 Chirality : 0.043 0.237 885 Planarity : 0.004 0.043 951 Dihedral : 5.226 52.705 797 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.70 % Allowed : 18.41 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.32), residues: 695 helix: 1.38 (0.28), residues: 357 sheet: -0.83 (0.48), residues: 103 loop : -1.04 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.037 0.001 TYR X 492 PHE 0.016 0.001 PHE X 318 TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 5677) covalent geometry : angle 0.55289 / 0.29 ( 7720) SS BOND : bond 0.00380 / 0.19 ( 3) SS BOND : angle 0.68540 / 0.36 ( 6) hydrogen bonds : bond 0.04179 / 2.76 ( 331) hydrogen bonds : angle 4.55578 / 3.10 ( 969) link_NAG-ASN : bond 0.00528 / 0.27 ( 2) link_NAG-ASN : angle 2.08570 / 1.18 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1489.82 seconds wall clock time: 26 minutes 15.09 seconds (1575.09 seconds total)