Starting phenix.real_space_refine on Thu Jul 2 01:14:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iv4_35740/07_2026/8iv4_35740.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv4_35740/07_2026/8iv4_35740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8iv4_35740/07_2026/8iv4_35740.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iv4_35740/07_2026/8iv4_35740.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iv4_35740/07_2026/8iv4_35740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv4_35740/07_2026/8iv4_35740.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv4_35740/07_2026/8iv4_35740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv4_35740/07_2026/8iv4_35740.cif" } resolution = 3.59 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= 0.013 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 3173 2.51 5 N 841 2.21 5 O 980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s 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: 5027 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 921 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "C" 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 chiralities: 2 Time building chain proxies: 0.81, per 1000 atoms: 0.16 Number of scatterers: 5027 At special positions: 0 Unit cell: (86.358, 66.908, 109.698, 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 980 8.00 N 841 7.00 C 3173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN G 343 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 176.8 milliseconds 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 12 sheets defined 6.2% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.002A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.801A pdb=" N ASP B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 83 " --> pdb=" O CYS B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.918A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 370 removed outlier: 3.923A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.482A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 removed outlier: 3.698A pdb=" N TYR G 421 " --> pdb=" O LYS G 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.745A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR L 68 " --> pdb=" O VAL L 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.532A pdb=" N GLU L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.560A pdb=" N TYR L 48 " --> pdb=" O ASN L 52 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN L 36 " --> pdb=" O VAL L 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.521A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.535A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR H 94 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.535A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR H 94 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.565A pdb=" N GLU B 105 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP B 35 " --> pdb=" O MET B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.519A pdb=" N GLY A 10 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET A 34 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'G' and resid 452 through 454 146 hydrogen bonds defined for protein. 357 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: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1593 1.34 - 1.46: 1294 1.46 - 1.58: 2212 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5147 Sorted by residual: bond pdb=" C LEU G 335 " pdb=" N CYS G 336 " ideal model delta sigma weight residual 1.331 1.269 0.062 2.07e-02 2.33e+03 8.86e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.31e+00 bond pdb=" N CYS G 488 " pdb=" CA CYS G 488 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.10e+00 ... (remaining 5142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 6609 1.69 - 3.39: 323 3.39 - 5.08: 29 5.08 - 6.77: 10 6.77 - 8.47: 4 Bond angle restraints: 6975 Sorted by residual: angle pdb=" C SER L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N TYR B 94 " pdb=" CA TYR B 94 " pdb=" C TYR B 94 " ideal model delta sigma weight residual 109.81 118.28 -8.47 2.21e+00 2.05e-01 1.47e+01 angle pdb=" C GLN L 89 " pdb=" N TRP L 90 " pdb=" CA TRP L 90 " ideal model delta sigma weight residual 120.63 126.24 -5.61 1.61e+00 3.86e-01 1.21e+01 angle pdb=" N GLN A 111 " pdb=" CA GLN A 111 " pdb=" C GLN A 111 " ideal model delta sigma weight residual 114.56 110.26 4.30 1.27e+00 6.20e-01 1.14e+01 ... (remaining 6970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 2706 17.91 - 35.81: 249 35.81 - 53.72: 45 53.72 - 71.62: 4 71.62 - 89.53: 5 Dihedral angle restraints: 3009 sinusoidal: 1159 harmonic: 1850 Sorted by residual: dihedral pdb=" CA ASN G 487 " pdb=" C ASN G 487 " pdb=" N CYS G 488 " pdb=" CA CYS G 488 " ideal model delta harmonic sigma weight residual -180.00 -131.59 -48.41 0 5.00e+00 4.00e-02 9.38e+01 dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 58.47 34.53 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 3006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 514 0.047 - 0.094: 171 0.094 - 0.141: 56 0.141 - 0.188: 9 0.188 - 0.235: 4 Chirality restraints: 754 Sorted by residual: chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 28 " pdb=" CA THR A 28 " pdb=" OG1 THR A 28 " pdb=" CG2 THR A 28 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA TYR B 94 " pdb=" N TYR B 94 " pdb=" C TYR B 94 " pdb=" CB TYR B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 751 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 487 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ASN G 487 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN G 487 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS G 488 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO B 95 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO G 521 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " 0.035 5.00e-02 4.00e+02 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1626 2.83 - 3.35: 3861 3.35 - 3.87: 8003 3.87 - 4.38: 8760 4.38 - 4.90: 16095 Nonbonded interactions: 38345 Sorted by model distance: nonbonded pdb=" O SER G 438 " pdb=" OG SER G 438 " model vdw 2.315 3.040 nonbonded pdb=" O SER H 30 " pdb=" OG SER H 30 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.336 3.040 nonbonded pdb=" O ARG H 67 " pdb=" OG SER H 84 " model vdw 2.354 3.040 nonbonded pdb=" OG SER G 438 " pdb=" OD2 ASP G 442 " model vdw 2.361 3.040 ... (remaining 38340 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.860 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.680 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 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 0.062 5157 Z= 0.258 Angle : 0.853 8.871 6997 Z= 0.495 Chirality : 0.054 0.235 754 Planarity : 0.007 0.069 891 Dihedral : 14.079 89.529 1813 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.55 % Allowed : 6.96 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.00 (0.27), residues: 634 helix: -4.95 (0.21), residues: 21 sheet: -1.94 (0.31), residues: 250 loop : -3.14 (0.24), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 408 TYR 0.026 0.002 TYR B 94 PHE 0.022 0.002 PHE L 46 TRP 0.022 0.002 TRP H 47 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.26 ( 5147) covalent geometry : angle 0.84205 / 0.49 ( 6975) SS BOND : bond 0.00296 / 0.17 ( 8) SS BOND : angle 0.84826 / 0.53 ( 16) hydrogen bonds : bond 0.27686 / 19.67 ( 144) hydrogen bonds : angle 10.62234 / 6.97 ( 357) link_BETA1-4 : bond 0.01097 / 0.58 ( 1) link_BETA1-4 : angle 1.24981 / 0.70 ( 3) link_NAG-ASN : bond 0.00084 / 0.04 ( 1) link_NAG-ASN : angle 6.51442 / 3.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.126 Fit side-chains REVERT: L 11 MET cc_start: 0.7400 (mtt) cc_final: 0.6839 (mtt) REVERT: L 19 ILE cc_start: 0.8245 (tt) cc_final: 0.8027 (tt) REVERT: L 32 MET cc_start: 0.7936 (tpp) cc_final: 0.7538 (tpp) REVERT: L 90 TRP cc_start: 0.7295 (t60) cc_final: 0.7030 (t60) REVERT: H 3 MET cc_start: 0.6729 (mtm) cc_final: 0.5999 (tpt) REVERT: H 19 LYS cc_start: 0.7516 (tttt) cc_final: 0.7136 (tttp) REVERT: H 82 GLN cc_start: 0.7352 (pp30) cc_final: 0.7113 (pp30) REVERT: H 93 MET cc_start: 0.6589 (ttm) cc_final: 0.6235 (ttm) REVERT: H 109 ASP cc_start: 0.8068 (m-30) cc_final: 0.7446 (m-30) REVERT: B 1 ASP cc_start: 0.7827 (p0) cc_final: 0.7625 (p0) REVERT: B 4 MET cc_start: 0.6457 (mmm) cc_final: 0.5943 (mmt) REVERT: B 47 MET cc_start: 0.7245 (mmp) cc_final: 0.6926 (mmp) REVERT: B 52 SER cc_start: 0.8365 (t) cc_final: 0.8140 (m) REVERT: B 54 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7763 (ttp80) REVERT: B 79 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7432 (mm110) REVERT: B 82 ASP cc_start: 0.8596 (m-30) cc_final: 0.8361 (m-30) REVERT: A 18 MET cc_start: 0.6312 (ttm) cc_final: 0.6020 (ttt) REVERT: A 19 LYS cc_start: 0.7633 (tttt) cc_final: 0.6873 (tttp) REVERT: A 35 ASP cc_start: 0.6952 (m-30) cc_final: 0.6540 (m-30) REVERT: A 50 GLN cc_start: 0.7547 (tt0) cc_final: 0.6930 (tt0) REVERT: A 69 ARG cc_start: 0.7396 (mtm110) cc_final: 0.7149 (mtp180) REVERT: A 108 PHE cc_start: 0.7478 (t80) cc_final: 0.7176 (t80) REVERT: G 347 PHE cc_start: 0.8147 (m-10) cc_final: 0.7860 (m-80) REVERT: G 369 TYR cc_start: 0.8841 (t80) cc_final: 0.8477 (t80) REVERT: G 442 ASP cc_start: 0.8779 (m-30) cc_final: 0.8099 (m-30) outliers start: 3 outliers final: 1 residues processed: 128 average time/residue: 0.0640 time to fit residues: 10.2777 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN G 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120926 restraints weight = 6660.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124299 restraints weight = 3760.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126719 restraints weight = 2576.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128352 restraints weight = 1938.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129457 restraints weight = 1564.826| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5157 Z= 0.198 Angle : 0.628 7.976 6997 Z= 0.330 Chirality : 0.046 0.159 754 Planarity : 0.005 0.063 891 Dihedral : 6.108 67.912 710 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.89 % Favored : 91.96 % Rotamer: Outliers : 3.48 % Allowed : 10.26 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.23 (0.29), residues: 634 helix: -4.36 (0.46), residues: 15 sheet: -1.44 (0.31), residues: 252 loop : -2.65 (0.27), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 346 TYR 0.018 0.002 TYR B 94 PHE 0.016 0.002 PHE L 46 TRP 0.013 0.002 TRP G 436 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 5147) covalent geometry : angle 0.61999 / 0.33 ( 6975) SS BOND : bond 0.00392 / 0.20 ( 8) SS BOND : angle 1.07893 / 0.72 ( 16) hydrogen bonds : bond 0.04180 / 2.86 ( 144) hydrogen bonds : angle 7.00887 / 4.60 ( 357) link_BETA1-4 : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : angle 0.97360 / 0.52 ( 3) link_NAG-ASN : bond 0.00342 / 0.18 ( 1) link_NAG-ASN : angle 4.34580 / 2.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: L 18 GLU cc_start: 0.7608 (pp20) cc_final: 0.7354 (pp20) REVERT: L 32 MET cc_start: 0.8624 (tpp) cc_final: 0.8079 (tpp) REVERT: L 66 SER cc_start: 0.8730 (p) cc_final: 0.8152 (m) REVERT: L 90 TRP cc_start: 0.8453 (t60) cc_final: 0.7439 (t60) REVERT: H 19 LYS cc_start: 0.8490 (tttt) cc_final: 0.8114 (tttm) REVERT: H 105 ASP cc_start: 0.8951 (p0) cc_final: 0.8566 (p0) REVERT: B 30 ARG cc_start: 0.7784 (mpt90) cc_final: 0.7497 (mmt-90) REVERT: B 42 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7929 (mt0) REVERT: A 3 LYS cc_start: 0.8579 (pptt) cc_final: 0.8242 (pttp) REVERT: A 19 LYS cc_start: 0.8527 (tttt) cc_final: 0.8122 (ttmm) REVERT: G 503 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.8743 (t) outliers start: 19 outliers final: 13 residues processed: 121 average time/residue: 0.0683 time to fit residues: 10.3000 Evaluate side-chains 116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS A 50 GLN G 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107686 restraints weight = 6825.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111324 restraints weight = 3773.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113835 restraints weight = 2538.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115590 restraints weight = 1906.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116824 restraints weight = 1537.090| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5157 Z= 0.194 Angle : 0.612 8.895 6997 Z= 0.320 Chirality : 0.045 0.169 754 Planarity : 0.005 0.057 891 Dihedral : 5.881 58.381 710 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 5.49 % Allowed : 13.00 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.30), residues: 634 helix: -3.81 (0.64), residues: 15 sheet: -0.98 (0.32), residues: 245 loop : -2.35 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 346 TYR 0.017 0.002 TYR B 94 PHE 0.010 0.001 PHE A 70 TRP 0.011 0.002 TRP L 90 HIS 0.002 0.001 HIS L 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 ( 5147) covalent geometry : angle 0.60391 / 0.32 ( 6975) SS BOND : bond 0.00268 / 0.14 ( 8) SS BOND : angle 1.06341 / 0.75 ( 16) hydrogen bonds : bond 0.03645 / 2.45 ( 144) hydrogen bonds : angle 6.39316 / 4.20 ( 357) link_BETA1-4 : bond 0.00586 / 0.31 ( 1) link_BETA1-4 : angle 0.81031 / 0.47 ( 3) link_NAG-ASN : bond 0.00241 / 0.13 ( 1) link_NAG-ASN : angle 4.26678 / 2.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: L 18 GLU cc_start: 0.7596 (pp20) cc_final: 0.7358 (pp20) REVERT: L 32 MET cc_start: 0.8599 (tpp) cc_final: 0.8037 (tpp) REVERT: L 66 SER cc_start: 0.8759 (p) cc_final: 0.8201 (m) REVERT: H 19 LYS cc_start: 0.8485 (tttt) cc_final: 0.8086 (tttm) REVERT: H 91 THR cc_start: 0.9128 (m) cc_final: 0.8912 (t) REVERT: H 105 ASP cc_start: 0.8906 (p0) cc_final: 0.8704 (p0) REVERT: B 42 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7941 (mt0) REVERT: A 3 LYS cc_start: 0.8478 (pptt) cc_final: 0.8190 (pttp) REVERT: A 19 LYS cc_start: 0.8675 (tttt) cc_final: 0.8228 (tttp) REVERT: G 369 TYR cc_start: 0.8581 (t80) cc_final: 0.8372 (t80) REVERT: G 503 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.8981 (t) outliers start: 30 outliers final: 23 residues processed: 126 average time/residue: 0.0609 time to fit residues: 9.6021 Evaluate side-chains 128 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122385 restraints weight = 6648.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.125931 restraints weight = 3836.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128371 restraints weight = 2646.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.130077 restraints weight = 2005.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131198 restraints weight = 1620.260| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5157 Z= 0.144 Angle : 0.565 6.971 6997 Z= 0.296 Chirality : 0.044 0.157 754 Planarity : 0.005 0.058 891 Dihedral : 5.517 50.267 710 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.49 % Allowed : 15.38 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.31), residues: 634 helix: -3.10 (0.92), residues: 15 sheet: -0.74 (0.32), residues: 257 loop : -2.12 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 346 TYR 0.017 0.001 TYR H 32 PHE 0.008 0.001 PHE A 70 TRP 0.014 0.002 TRP A 33 HIS 0.003 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5147) covalent geometry : angle 0.55761 / 0.29 ( 6975) SS BOND : bond 0.00244 / 0.12 ( 8) SS BOND : angle 0.94086 / 0.64 ( 16) hydrogen bonds : bond 0.03121 / 2.09 ( 144) hydrogen bonds : angle 5.94974 / 3.90 ( 357) link_BETA1-4 : bond 0.00683 / 0.36 ( 1) link_BETA1-4 : angle 0.77707 / 0.45 ( 3) link_NAG-ASN : bond 0.00098 / 0.05 ( 1) link_NAG-ASN : angle 3.88586 / 2.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: L 32 MET cc_start: 0.8570 (tpp) cc_final: 0.8019 (tpp) REVERT: L 66 SER cc_start: 0.8742 (p) cc_final: 0.8138 (m) REVERT: H 19 LYS cc_start: 0.8429 (tttt) cc_final: 0.8053 (tttm) REVERT: H 91 THR cc_start: 0.9115 (m) cc_final: 0.8868 (t) REVERT: B 4 MET cc_start: 0.8198 (mmm) cc_final: 0.6778 (mmm) REVERT: B 42 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7906 (mt0) REVERT: A 3 LYS cc_start: 0.8497 (pptt) cc_final: 0.8273 (pttp) REVERT: A 19 LYS cc_start: 0.8695 (tttt) cc_final: 0.8288 (tttp) REVERT: A 25 SER cc_start: 0.8179 (m) cc_final: 0.7936 (p) REVERT: G 369 TYR cc_start: 0.8529 (t80) cc_final: 0.8310 (t80) REVERT: G 468 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7952 (mt) outliers start: 30 outliers final: 23 residues processed: 122 average time/residue: 0.0663 time to fit residues: 10.1863 Evaluate side-chains 126 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.126756 restraints weight = 6767.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130485 restraints weight = 3863.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133026 restraints weight = 2633.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134794 restraints weight = 1985.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135912 restraints weight = 1596.065| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5157 Z= 0.201 Angle : 0.598 7.118 6997 Z= 0.314 Chirality : 0.045 0.168 754 Planarity : 0.005 0.057 891 Dihedral : 5.611 46.662 710 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 6.41 % Allowed : 15.75 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.32), residues: 634 helix: -2.80 (1.05), residues: 15 sheet: -0.69 (0.32), residues: 257 loop : -2.05 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.027 0.002 TYR G 473 PHE 0.009 0.001 PHE A 70 TRP 0.012 0.002 TRP A 33 HIS 0.010 0.002 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 5147) covalent geometry : angle 0.58966 / 0.31 ( 6975) SS BOND : bond 0.00268 / 0.13 ( 8) SS BOND : angle 1.03395 / 0.74 ( 16) hydrogen bonds : bond 0.03247 / 2.18 ( 144) hydrogen bonds : angle 5.89321 / 3.87 ( 357) link_BETA1-4 : bond 0.00658 / 0.35 ( 1) link_BETA1-4 : angle 0.74979 / 0.44 ( 3) link_NAG-ASN : bond 0.00046 / 0.02 ( 1) link_NAG-ASN : angle 4.39321 / 2.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.119 Fit side-chains REVERT: L 32 MET cc_start: 0.8608 (tpp) cc_final: 0.8043 (tpp) REVERT: L 66 SER cc_start: 0.8782 (p) cc_final: 0.8253 (m) REVERT: H 19 LYS cc_start: 0.8526 (tttt) cc_final: 0.8058 (tttm) REVERT: H 91 THR cc_start: 0.9169 (m) cc_final: 0.8947 (t) REVERT: B 4 MET cc_start: 0.8156 (mmm) cc_final: 0.6626 (mmm) REVERT: B 42 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8046 (mt0) REVERT: A 19 LYS cc_start: 0.8728 (tttt) cc_final: 0.8207 (tttp) REVERT: A 25 SER cc_start: 0.8173 (m) cc_final: 0.7883 (p) REVERT: G 369 TYR cc_start: 0.8670 (t80) cc_final: 0.8435 (t80) outliers start: 35 outliers final: 26 residues processed: 123 average time/residue: 0.0618 time to fit residues: 9.8008 Evaluate side-chains 127 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 5 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 88 HIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.122615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.103145 restraints weight = 6905.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.106449 restraints weight = 4062.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.108755 restraints weight = 2798.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110334 restraints weight = 2123.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111560 restraints weight = 1729.454| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5157 Z= 0.132 Angle : 0.570 7.002 6997 Z= 0.297 Chirality : 0.044 0.159 754 Planarity : 0.005 0.056 891 Dihedral : 5.378 44.760 710 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.76 % Allowed : 17.22 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.32), residues: 634 helix: -2.54 (1.16), residues: 15 sheet: -0.54 (0.32), residues: 255 loop : -1.95 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 346 TYR 0.012 0.001 TYR H 32 PHE 0.008 0.001 PHE A 70 TRP 0.010 0.002 TRP H 111 HIS 0.007 0.002 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 5147) covalent geometry : angle 0.56551 / 0.30 ( 6975) SS BOND : bond 0.00194 / 0.10 ( 8) SS BOND : angle 0.91561 / 0.63 ( 16) hydrogen bonds : bond 0.03024 / 2.05 ( 144) hydrogen bonds : angle 5.67218 / 3.72 ( 357) link_BETA1-4 : bond 0.00363 / 0.19 ( 1) link_BETA1-4 : angle 0.76140 / 0.45 ( 3) link_NAG-ASN : bond 0.00100 / 0.05 ( 1) link_NAG-ASN : angle 3.05431 / 1.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.146 Fit side-chains REVERT: L 32 MET cc_start: 0.8598 (tpp) cc_final: 0.8081 (tpp) REVERT: L 66 SER cc_start: 0.8742 (p) cc_final: 0.8190 (m) REVERT: H 19 LYS cc_start: 0.8471 (tttt) cc_final: 0.8160 (tttm) REVERT: H 91 THR cc_start: 0.9176 (m) cc_final: 0.8931 (t) REVERT: B 4 MET cc_start: 0.8157 (mmm) cc_final: 0.6698 (mmm) REVERT: B 42 GLN cc_start: 0.8260 (mm-40) cc_final: 0.8030 (mt0) REVERT: A 19 LYS cc_start: 0.8693 (tttt) cc_final: 0.8215 (tttp) REVERT: A 25 SER cc_start: 0.8130 (m) cc_final: 0.7850 (p) REVERT: G 369 TYR cc_start: 0.8634 (t80) cc_final: 0.8406 (t80) outliers start: 26 outliers final: 21 residues processed: 118 average time/residue: 0.0562 time to fit residues: 8.4712 Evaluate side-chains 121 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 2 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.149379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129120 restraints weight = 6645.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133124 restraints weight = 3629.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135795 restraints weight = 2416.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137532 restraints weight = 1797.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138815 restraints weight = 1445.105| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5157 Z= 0.148 Angle : 0.577 6.848 6997 Z= 0.300 Chirality : 0.045 0.163 754 Planarity : 0.005 0.058 891 Dihedral : 5.305 43.231 710 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.49 % Allowed : 16.85 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.91 (0.33), residues: 634 helix: -2.46 (1.19), residues: 15 sheet: -0.46 (0.33), residues: 255 loop : -1.87 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 346 TYR 0.022 0.001 TYR H 32 PHE 0.008 0.001 PHE A 70 TRP 0.022 0.002 TRP A 33 HIS 0.002 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 5147) covalent geometry : angle 0.57072 / 0.30 ( 6975) SS BOND : bond 0.00233 / 0.12 ( 8) SS BOND : angle 0.92704 / 0.63 ( 16) hydrogen bonds : bond 0.02985 / 2.03 ( 144) hydrogen bonds : angle 5.56697 / 3.66 ( 357) link_BETA1-4 : bond 0.00575 / 0.30 ( 1) link_BETA1-4 : angle 0.71127 / 0.41 ( 3) link_NAG-ASN : bond 0.00368 / 0.19 ( 1) link_NAG-ASN : angle 3.57513 / 2.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.118 Fit side-chains REVERT: L 32 MET cc_start: 0.8557 (tpp) cc_final: 0.7990 (tpp) REVERT: L 66 SER cc_start: 0.8743 (p) cc_final: 0.8139 (m) REVERT: H 28 SER cc_start: 0.8886 (t) cc_final: 0.8587 (p) REVERT: H 91 THR cc_start: 0.9165 (m) cc_final: 0.8891 (t) REVERT: B 4 MET cc_start: 0.8202 (mmm) cc_final: 0.6781 (mmm) REVERT: B 42 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7949 (mt0) REVERT: A 19 LYS cc_start: 0.8687 (tttt) cc_final: 0.8257 (tttp) REVERT: G 466 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7313 (ttp-170) outliers start: 30 outliers final: 26 residues processed: 123 average time/residue: 0.0599 time to fit residues: 9.4271 Evaluate side-chains 128 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 466 ARG Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.0060 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128369 restraints weight = 6717.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132468 restraints weight = 3646.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135156 restraints weight = 2393.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136968 restraints weight = 1768.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138270 restraints weight = 1405.066| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5157 Z= 0.152 Angle : 0.592 8.389 6997 Z= 0.305 Chirality : 0.045 0.175 754 Planarity : 0.005 0.057 891 Dihedral : 5.296 43.125 710 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 6.23 % Allowed : 16.48 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.84 (0.33), residues: 634 helix: -2.17 (1.20), residues: 15 sheet: -0.44 (0.33), residues: 255 loop : -1.81 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 346 TYR 0.020 0.001 TYR H 32 PHE 0.008 0.001 PHE A 70 TRP 0.024 0.002 TRP A 33 HIS 0.002 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 5147) covalent geometry : angle 0.58407 / 0.30 ( 6975) SS BOND : bond 0.00232 / 0.12 ( 8) SS BOND : angle 0.96150 / 0.68 ( 16) hydrogen bonds : bond 0.02986 / 2.03 ( 144) hydrogen bonds : angle 5.53721 / 3.65 ( 357) link_BETA1-4 : bond 0.00403 / 0.21 ( 1) link_BETA1-4 : angle 1.19641 / 0.69 ( 3) link_NAG-ASN : bond 0.00661 / 0.35 ( 1) link_NAG-ASN : angle 4.19292 / 2.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: L 32 MET cc_start: 0.8606 (tpp) cc_final: 0.8011 (tpp) REVERT: L 66 SER cc_start: 0.8770 (p) cc_final: 0.8186 (m) REVERT: H 28 SER cc_start: 0.9071 (t) cc_final: 0.8801 (p) REVERT: H 91 THR cc_start: 0.9188 (m) cc_final: 0.8915 (t) REVERT: B 4 MET cc_start: 0.8240 (mmm) cc_final: 0.6780 (mmm) REVERT: B 42 GLN cc_start: 0.8222 (mm-40) cc_final: 0.8008 (mt0) REVERT: A 3 LYS cc_start: 0.8507 (pptt) cc_final: 0.8175 (pttp) REVERT: A 19 LYS cc_start: 0.8702 (tttt) cc_final: 0.8219 (tttp) REVERT: G 466 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7521 (ttp-170) outliers start: 34 outliers final: 30 residues processed: 124 average time/residue: 0.0881 time to fit residues: 13.6631 Evaluate side-chains 131 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 466 ARG Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.120713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.101142 restraints weight = 6913.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.104358 restraints weight = 4099.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106681 restraints weight = 2833.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.108238 restraints weight = 2169.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109409 restraints weight = 1775.957| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5157 Z= 0.148 Angle : 0.585 7.603 6997 Z= 0.303 Chirality : 0.045 0.183 754 Planarity : 0.005 0.057 891 Dihedral : 5.260 42.430 710 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 6.04 % Allowed : 16.85 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.78 (0.33), residues: 634 helix: -2.12 (1.23), residues: 15 sheet: -0.43 (0.33), residues: 255 loop : -1.74 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 346 TYR 0.019 0.001 TYR H 32 PHE 0.006 0.001 PHE G 400 TRP 0.037 0.002 TRP A 33 HIS 0.003 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 5147) covalent geometry : angle 0.57905 / 0.30 ( 6975) SS BOND : bond 0.00233 / 0.12 ( 8) SS BOND : angle 0.94335 / 0.65 ( 16) hydrogen bonds : bond 0.02952 / 2.01 ( 144) hydrogen bonds : angle 5.46168 / 3.61 ( 357) link_BETA1-4 : bond 0.00583 / 0.31 ( 1) link_BETA1-4 : angle 0.95515 / 0.56 ( 3) link_NAG-ASN : bond 0.00481 / 0.25 ( 1) link_NAG-ASN : angle 3.45827 / 1.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: L 32 MET cc_start: 0.8622 (tpp) cc_final: 0.8063 (tpp) REVERT: L 46 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7930 (t80) REVERT: L 66 SER cc_start: 0.8754 (p) cc_final: 0.8175 (m) REVERT: H 28 SER cc_start: 0.9053 (t) cc_final: 0.8814 (p) REVERT: H 91 THR cc_start: 0.9193 (m) cc_final: 0.8931 (t) REVERT: B 4 MET cc_start: 0.8218 (mmm) cc_final: 0.6756 (mmm) REVERT: B 42 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8041 (mt0) REVERT: A 3 LYS cc_start: 0.8459 (pptt) cc_final: 0.8247 (pttp) REVERT: A 19 LYS cc_start: 0.8647 (tttt) cc_final: 0.8133 (tttm) REVERT: G 466 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7574 (ttp-170) REVERT: G 505 TYR cc_start: 0.9324 (OUTLIER) cc_final: 0.9022 (m-10) outliers start: 33 outliers final: 28 residues processed: 125 average time/residue: 0.0864 time to fit residues: 13.4977 Evaluate side-chains 134 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 466 ARG Chi-restraints excluded: chain G residue 478 THR Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 0.2980 chunk 40 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.101946 restraints weight = 6816.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.105095 restraints weight = 4016.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.107351 restraints weight = 2769.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.109060 restraints weight = 2117.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110229 restraints weight = 1710.189| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5157 Z= 0.142 Angle : 0.587 7.218 6997 Z= 0.305 Chirality : 0.045 0.188 754 Planarity : 0.005 0.056 891 Dihedral : 5.234 42.523 710 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.49 % Allowed : 17.77 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.75 (0.33), residues: 634 helix: -2.10 (1.24), residues: 15 sheet: -0.42 (0.32), residues: 255 loop : -1.71 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 346 TYR 0.020 0.001 TYR H 32 PHE 0.010 0.001 PHE A 29 TRP 0.056 0.002 TRP A 33 HIS 0.005 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5147) covalent geometry : angle 0.58198 / 0.30 ( 6975) SS BOND : bond 0.00221 / 0.11 ( 8) SS BOND : angle 0.94191 / 0.65 ( 16) hydrogen bonds : bond 0.02960 / 1.99 ( 144) hydrogen bonds : angle 5.44328 / 3.59 ( 357) link_BETA1-4 : bond 0.00572 / 0.30 ( 1) link_BETA1-4 : angle 0.91536 / 0.54 ( 3) link_NAG-ASN : bond 0.00331 / 0.17 ( 1) link_NAG-ASN : angle 3.31327 / 1.85 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: L 32 MET cc_start: 0.8525 (tpp) cc_final: 0.7960 (tpp) REVERT: L 46 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7918 (t80) REVERT: L 66 SER cc_start: 0.8762 (p) cc_final: 0.8133 (m) REVERT: H 28 SER cc_start: 0.8821 (t) cc_final: 0.8577 (p) REVERT: H 91 THR cc_start: 0.9149 (m) cc_final: 0.8870 (t) REVERT: B 4 MET cc_start: 0.8292 (mmm) cc_final: 0.6931 (mmm) REVERT: A 3 LYS cc_start: 0.8573 (pptt) cc_final: 0.8322 (pttp) REVERT: A 19 LYS cc_start: 0.8584 (tttt) cc_final: 0.8266 (ttmm) REVERT: G 466 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7505 (ttp-170) outliers start: 30 outliers final: 25 residues processed: 121 average time/residue: 0.0893 time to fit residues: 13.4765 Evaluate side-chains 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 466 ARG Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.100052 restraints weight = 7014.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.103335 restraints weight = 4079.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.105766 restraints weight = 2808.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.107320 restraints weight = 2133.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.108578 restraints weight = 1743.239| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5157 Z= 0.157 Angle : 0.601 7.462 6997 Z= 0.311 Chirality : 0.045 0.197 754 Planarity : 0.005 0.064 891 Dihedral : 5.287 42.589 710 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 5.31 % Allowed : 17.58 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.73 (0.33), residues: 634 helix: -2.03 (1.24), residues: 15 sheet: -0.38 (0.33), residues: 255 loop : -1.72 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 408 TYR 0.020 0.001 TYR H 32 PHE 0.026 0.001 PHE A 29 TRP 0.051 0.002 TRP A 33 HIS 0.005 0.002 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 5147) covalent geometry : angle 0.59554 / 0.31 ( 6975) SS BOND : bond 0.00236 / 0.12 ( 8) SS BOND : angle 0.93720 / 0.64 ( 16) hydrogen bonds : bond 0.02952 / 2.00 ( 144) hydrogen bonds : angle 5.48429 / 3.63 ( 357) link_BETA1-4 : bond 0.00578 / 0.30 ( 1) link_BETA1-4 : angle 0.86999 / 0.51 ( 3) link_NAG-ASN : bond 0.00300 / 0.16 ( 1) link_NAG-ASN : angle 3.35258 / 1.86 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1150.89 seconds wall clock time: 20 minutes 41.99 seconds (1241.99 seconds total)