Starting phenix.real_space_refine on Wed Aug 5 11:43:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wac_65811/08_2026/9wac_65811.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wac_65811/08_2026/9wac_65811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wac_65811/08_2026/9wac_65811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wac_65811/08_2026/9wac_65811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wac_65811/08_2026/9wac_65811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wac_65811/08_2026/9wac_65811.map" } resolution = 2.89 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= 0.002 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 138 5.49 5 S 19 5.16 5 C 5496 2.51 5 N 1719 2.21 5 O 2130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9502 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6599 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 10 Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2053 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 46} Link IDs: {'rna2p': 6, 'rna3p': 90} Chain breaks: 3 Chain: "C" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 663 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 187 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 1.84, per 1000 atoms: 0.19 Number of scatterers: 9502 At special positions: 0 Unit cell: (84, 112.35, 121.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 138 15.00 O 2130 8.00 N 1719 7.00 C 5496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 271.8 milliseconds 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 38.3% alpha, 13.5% beta 59 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 53 through 84 removed outlier: 4.201A pdb=" N ARG A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 235 through 248 Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.996A pdb=" N VAL A 281 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 406 through 420 Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.744A pdb=" N THR A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 505 through 526 removed outlier: 3.873A pdb=" N ARG A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 removed outlier: 3.982A pdb=" N MET A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA A 714 " --> pdb=" O ASN A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 766 removed outlier: 3.739A pdb=" N ALA A 759 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.809A pdb=" N SER A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 929 through 932 Processing helix chain 'A' and resid 933 through 947 removed outlier: 3.514A pdb=" N TYR A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 955 Processing helix chain 'A' and resid 1019 through 1022 removed outlier: 3.803A pdb=" N LEU A1022 " --> pdb=" O ALA A1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1019 through 1022' Processing helix chain 'A' and resid 1036 through 1040 removed outlier: 3.695A pdb=" N TRP A1040 " --> pdb=" O TYR A1037 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 8.910A pdb=" N HIS A 533 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 5 " --> pdb=" O HIS A 533 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 294 removed outlier: 5.759A pdb=" N LEU A 454 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA5, first strand: chain 'A' and resid 890 through 894 Processing sheet with id=AA6, first strand: chain 'A' and resid 959 through 962 removed outlier: 4.605A pdb=" N VAL A 959 " --> pdb=" O VAL A 972 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 970 " --> pdb=" O LYS A 961 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 985 through 987 Processing sheet with id=AA8, first strand: chain 'A' and resid 1010 through 1017 removed outlier: 3.516A pdb=" N ARG A1001 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A1002 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER A1052 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A1004 " --> pdb=" O LYS A1050 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1029 through 1030 removed outlier: 3.641A pdb=" N ARG A1041 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 4.628A pdb=" N LYS A1107 " --> pdb=" O LEU A1097 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A1097 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG A1098 " --> pdb=" O PHE A1085 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHE A1085 " --> pdb=" O ARG A1098 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A1058 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A1116 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1068 through 1070 260 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 146 hydrogen bonds 276 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2129 1.33 - 1.45: 2700 1.45 - 1.57: 4822 1.57 - 1.69: 270 1.69 - 1.81: 31 Bond restraints: 9952 Sorted by residual: bond pdb=" C3' DT C 10 " pdb=" C2' DT C 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.99e+00 bond pdb=" C3' DG D 7 " pdb=" C2' DG D 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.77e+00 bond pdb=" N LEU A 446 " pdb=" CA LEU A 446 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 8.87e+00 bond pdb=" N LYS A 202 " pdb=" CA LYS A 202 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.30e-02 5.92e+03 8.24e+00 bond pdb=" N ILE A 852 " pdb=" CA ILE A 852 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.01e+00 ... (remaining 9947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 12969 1.30 - 2.60: 865 2.60 - 3.90: 192 3.90 - 5.20: 24 5.20 - 6.50: 7 Bond angle restraints: 14057 Sorted by residual: angle pdb=" C4' DC C 14 " pdb=" O4' DC C 14 " pdb=" C1' DC C 14 " ideal model delta sigma weight residual 110.10 105.04 5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" N1 C B 91 " pdb=" C2 C B 91 " pdb=" O2 C B 91 " ideal model delta sigma weight residual 118.90 121.93 -3.03 6.00e-01 2.78e+00 2.55e+01 angle pdb=" N ARG A 853 " pdb=" CA ARG A 853 " pdb=" C ARG A 853 " ideal model delta sigma weight residual 112.93 107.47 5.46 1.12e+00 7.97e-01 2.37e+01 angle pdb=" C1' C B 91 " pdb=" N1 C B 91 " pdb=" C2 C B 91 " ideal model delta sigma weight residual 118.80 124.03 -5.23 1.10e+00 8.26e-01 2.26e+01 angle pdb=" C1' C B 12 " pdb=" N1 C B 12 " pdb=" C2 C B 12 " ideal model delta sigma weight residual 118.80 123.98 -5.18 1.10e+00 8.26e-01 2.22e+01 ... (remaining 14052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.12: 5003 19.12 - 38.24: 620 38.24 - 57.36: 270 57.36 - 76.48: 132 76.48 - 95.60: 10 Dihedral angle restraints: 6035 sinusoidal: 3647 harmonic: 2388 Sorted by residual: dihedral pdb=" CG ARG A 71 " pdb=" CD ARG A 71 " pdb=" NE ARG A 71 " pdb=" CZ ARG A 71 " ideal model delta sinusoidal sigma weight residual 180.00 135.56 44.44 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA ASN A 438 " pdb=" CB ASN A 438 " pdb=" CG ASN A 438 " pdb=" OD1 ASN A 438 " ideal model delta sinusoidal sigma weight residual 120.00 -175.13 -64.87 2 2.00e+01 2.50e-03 9.84e+00 dihedral pdb=" CA ARG A 295 " pdb=" CB ARG A 295 " pdb=" CG ARG A 295 " pdb=" CD ARG A 295 " ideal model delta sinusoidal sigma weight residual -60.00 -119.65 59.65 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1236 0.050 - 0.100: 263 0.100 - 0.150: 144 0.150 - 0.200: 13 0.200 - 0.250: 1 Chirality restraints: 1657 Sorted by residual: chirality pdb=" CA VAL A 439 " pdb=" N VAL A 439 " pdb=" C VAL A 439 " pdb=" CB VAL A 439 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ARG A 397 " pdb=" N ARG A 397 " pdb=" C ARG A 397 " pdb=" CB ARG A 397 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA LEU A 446 " pdb=" N LEU A 446 " pdb=" C LEU A 446 " pdb=" CB LEU A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 1654 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 530 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" CD GLU A 530 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU A 530 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 530 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 88 " 0.026 2.00e-02 2.50e+03 1.12e-02 3.78e+00 pdb=" N9 G B 88 " -0.027 2.00e-02 2.50e+03 pdb=" C8 G B 88 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 88 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G B 88 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 88 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 88 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G B 88 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G B 88 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G B 88 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 88 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 88 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC C 14 " 0.023 2.00e-02 2.50e+03 1.15e-02 2.99e+00 pdb=" N1 DC C 14 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DC C 14 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC C 14 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DC C 14 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC C 14 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC C 14 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC C 14 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC C 14 " -0.005 2.00e-02 2.50e+03 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1524 2.76 - 3.30: 8009 3.30 - 3.83: 16971 3.83 - 4.37: 20763 4.37 - 4.90: 31978 Nonbonded interactions: 79245 Sorted by model distance: nonbonded pdb=" OD1 ASP A 253 " pdb=" OD1 ASP A 254 " model vdw 2.231 3.040 nonbonded pdb=" O PRO A 496 " pdb=" NE2 HIS A 711 " model vdw 2.276 3.120 nonbonded pdb=" OD1 ASP A1101 " pdb=" OG SER A1103 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 3 " pdb=" O GLY A 527 " model vdw 2.293 3.040 nonbonded pdb=" NE2 HIS A 189 " pdb=" O2' G B 51 " model vdw 2.309 3.120 ... (remaining 79240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9952 Z= 0.347 Angle : 0.738 6.501 14057 Z= 0.592 Chirality : 0.054 0.250 1657 Planarity : 0.004 0.031 1298 Dihedral : 20.493 95.597 4495 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.56 % Allowed : 19.89 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.29), residues: 805 helix: 1.47 (0.32), residues: 294 sheet: 0.21 (0.51), residues: 92 loop : -1.69 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 973 TYR 0.007 0.001 TYR A 3 PHE 0.012 0.001 PHE A 303 TRP 0.006 0.001 TRP A 415 HIS 0.003 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.35 ( 9952) covalent geometry : angle 0.73793 / 0.59 (14057) hydrogen bonds : bond 0.12174 / 8.16 ( 406) hydrogen bonds : angle 4.39821 / 3.25 ( 1005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 196 VAL cc_start: 0.8745 (m) cc_final: 0.8460 (t) outliers start: 4 outliers final: 1 residues processed: 92 average time/residue: 0.6808 time to fit residues: 66.3803 Evaluate side-chains 76 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 851 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.200602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.187217 restraints weight = 7547.674| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 0.35 r_work: 0.3823 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work: 0.3533 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9952 Z= 0.163 Angle : 0.551 5.306 14057 Z= 0.320 Chirality : 0.040 0.228 1657 Planarity : 0.005 0.042 1298 Dihedral : 20.727 93.060 2856 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 2.26 % Allowed : 19.46 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.29), residues: 805 helix: 1.56 (0.31), residues: 295 sheet: 0.17 (0.52), residues: 92 loop : -1.66 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 397 TYR 0.009 0.001 TYR A 927 PHE 0.013 0.001 PHE A 303 TRP 0.008 0.001 TRP A 415 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 ( 9952) covalent geometry : angle 0.55055 / 0.32 (14057) hydrogen bonds : bond 0.05765 / 3.76 ( 406) hydrogen bonds : angle 3.76882 / 2.79 ( 1005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 196 VAL cc_start: 0.8746 (m) cc_final: 0.8470 (t) outliers start: 16 outliers final: 7 residues processed: 90 average time/residue: 0.6626 time to fit residues: 63.2955 Evaluate side-chains 80 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 7 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.0670 chunk 72 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 946 GLN A 996 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.204533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.192937 restraints weight = 7609.333| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 0.37 r_work: 0.3877 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work: 0.3624 rms_B_bonded: 4.70 restraints_weight: 0.1250 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9952 Z= 0.107 Angle : 0.469 4.958 14057 Z= 0.282 Chirality : 0.036 0.139 1657 Planarity : 0.004 0.030 1298 Dihedral : 20.673 93.301 2854 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 2.40 % Allowed : 20.17 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.30), residues: 805 helix: 1.81 (0.31), residues: 295 sheet: 0.24 (0.52), residues: 93 loop : -1.57 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 973 TYR 0.005 0.001 TYR A 242 PHE 0.011 0.001 PHE A 483 TRP 0.005 0.001 TRP A 415 HIS 0.002 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.11 ( 9952) covalent geometry : angle 0.46911 / 0.28 (14057) hydrogen bonds : bond 0.04837 / 3.12 ( 406) hydrogen bonds : angle 3.52876 / 2.63 ( 1005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 162 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.6851 (mpp) REVERT: A 195 TYR cc_start: 0.8027 (m-80) cc_final: 0.7826 (m-80) REVERT: A 196 VAL cc_start: 0.8723 (m) cc_final: 0.8477 (t) REVERT: A 950 ASP cc_start: 0.7815 (t0) cc_final: 0.7478 (p0) outliers start: 17 outliers final: 5 residues processed: 92 average time/residue: 0.6441 time to fit residues: 62.8433 Evaluate side-chains 80 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 1118 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.202442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.189864 restraints weight = 7560.703| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 0.38 r_work: 0.3850 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work: 0.3610 rms_B_bonded: 4.75 restraints_weight: 0.1250 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9952 Z= 0.130 Angle : 0.497 5.608 14057 Z= 0.292 Chirality : 0.037 0.160 1657 Planarity : 0.004 0.061 1298 Dihedral : 20.606 93.525 2854 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 2.40 % Allowed : 20.87 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.30), residues: 805 helix: 1.83 (0.31), residues: 295 sheet: 0.09 (0.50), residues: 98 loop : -1.51 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 66 TYR 0.008 0.001 TYR A 3 PHE 0.013 0.001 PHE A 483 TRP 0.006 0.001 TRP A 415 HIS 0.004 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 ( 9952) covalent geometry : angle 0.49684 / 0.29 (14057) hydrogen bonds : bond 0.04903 / 3.18 ( 406) hydrogen bonds : angle 3.50166 / 2.60 ( 1005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 196 VAL cc_start: 0.8743 (m) cc_final: 0.8518 (t) REVERT: A 950 ASP cc_start: 0.7813 (t0) cc_final: 0.7531 (p0) REVERT: A 952 LYS cc_start: 0.7880 (mppt) cc_final: 0.7635 (mptt) outliers start: 17 outliers final: 6 residues processed: 92 average time/residue: 0.5924 time to fit residues: 57.8257 Evaluate side-chains 81 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 455 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.199087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.185570 restraints weight = 7551.875| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 0.36 r_work: 0.3795 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work: 0.3518 rms_B_bonded: 4.37 restraints_weight: 0.1250 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9952 Z= 0.214 Angle : 0.605 5.639 14057 Z= 0.339 Chirality : 0.044 0.265 1657 Planarity : 0.005 0.056 1298 Dihedral : 20.609 93.893 2854 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.10 % Allowed : 20.59 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.29), residues: 805 helix: 1.55 (0.31), residues: 294 sheet: -0.08 (0.49), residues: 97 loop : -1.57 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 66 TYR 0.015 0.002 TYR A 927 PHE 0.018 0.002 PHE A1013 TRP 0.009 0.002 TRP A 415 HIS 0.008 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 ( 9952) covalent geometry : angle 0.60491 / 0.34 (14057) hydrogen bonds : bond 0.05926 / 3.88 ( 406) hydrogen bonds : angle 3.69864 / 2.73 ( 1005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 196 VAL cc_start: 0.8770 (m) cc_final: 0.8546 (t) REVERT: A 279 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7030 (ptm160) REVERT: A 925 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8475 (mtpp) REVERT: A 950 ASP cc_start: 0.7767 (t0) cc_final: 0.7411 (p0) REVERT: A 952 LYS cc_start: 0.7920 (mppt) cc_final: 0.7644 (mptt) REVERT: A 1098 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7434 (ptt180) outliers start: 22 outliers final: 8 residues processed: 99 average time/residue: 0.6589 time to fit residues: 68.8212 Evaluate side-chains 88 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 1098 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 90 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.200197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186526 restraints weight = 7545.382| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 0.35 r_work: 0.3810 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work: 0.3506 rms_B_bonded: 4.45 restraints_weight: 0.1250 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9952 Z= 0.163 Angle : 0.544 5.363 14057 Z= 0.314 Chirality : 0.040 0.199 1657 Planarity : 0.005 0.052 1298 Dihedral : 20.601 94.020 2854 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.68 % Allowed : 20.87 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.29), residues: 805 helix: 1.62 (0.31), residues: 295 sheet: -0.05 (0.50), residues: 97 loop : -1.59 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 973 TYR 0.010 0.001 TYR A 927 PHE 0.015 0.002 PHE A 303 TRP 0.008 0.001 TRP A 415 HIS 0.005 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 9952) covalent geometry : angle 0.54447 / 0.31 (14057) hydrogen bonds : bond 0.05404 / 3.51 ( 406) hydrogen bonds : angle 3.63352 / 2.69 ( 1005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 196 VAL cc_start: 0.8760 (m) cc_final: 0.8549 (t) REVERT: A 925 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8446 (mtpp) REVERT: A 950 ASP cc_start: 0.7712 (t0) cc_final: 0.7318 (p0) REVERT: A 1098 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7370 (ptt180) outliers start: 19 outliers final: 12 residues processed: 95 average time/residue: 0.6034 time to fit residues: 60.6988 Evaluate side-chains 91 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1118 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 28 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.198883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.185397 restraints weight = 7598.358| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 0.35 r_work: 0.3789 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9952 Z= 0.195 Angle : 0.586 5.499 14057 Z= 0.332 Chirality : 0.042 0.232 1657 Planarity : 0.005 0.051 1298 Dihedral : 20.603 94.119 2854 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.10 % Allowed : 20.45 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.29), residues: 805 helix: 1.49 (0.31), residues: 295 sheet: -0.12 (0.49), residues: 97 loop : -1.63 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 973 TYR 0.013 0.002 TYR A 927 PHE 0.015 0.002 PHE A 483 TRP 0.008 0.002 TRP A 415 HIS 0.006 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 ( 9952) covalent geometry : angle 0.58641 / 0.33 (14057) hydrogen bonds : bond 0.05754 / 3.74 ( 406) hydrogen bonds : angle 3.69476 / 2.73 ( 1005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 212 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.6484 (ttp80) REVERT: A 950 ASP cc_start: 0.7695 (t0) cc_final: 0.7465 (p0) REVERT: A 952 LYS cc_start: 0.7832 (mppt) cc_final: 0.7564 (mptt) REVERT: A 1098 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7423 (ptt180) outliers start: 22 outliers final: 11 residues processed: 97 average time/residue: 0.6389 time to fit residues: 65.6429 Evaluate side-chains 90 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1098 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.201791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.189164 restraints weight = 7568.218| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 0.37 r_work: 0.3831 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9952 Z= 0.128 Angle : 0.504 5.192 14057 Z= 0.296 Chirality : 0.037 0.150 1657 Planarity : 0.004 0.042 1298 Dihedral : 20.584 94.036 2854 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.41 % Allowed : 22.99 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.30), residues: 805 helix: 1.74 (0.31), residues: 295 sheet: 0.06 (0.50), residues: 97 loop : -1.57 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 973 TYR 0.008 0.001 TYR A 937 PHE 0.015 0.001 PHE A 303 TRP 0.007 0.001 TRP A 415 HIS 0.003 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 ( 9952) covalent geometry : angle 0.50429 / 0.30 (14057) hydrogen bonds : bond 0.04904 / 3.16 ( 406) hydrogen bonds : angle 3.52726 / 2.62 ( 1005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 952 LYS cc_start: 0.7766 (mppt) cc_final: 0.7506 (mptt) outliers start: 10 outliers final: 9 residues processed: 87 average time/residue: 0.5926 time to fit residues: 54.7500 Evaluate side-chains 86 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 968 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.202118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.189825 restraints weight = 7550.825| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 0.35 r_work: 0.3848 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9952 Z= 0.124 Angle : 0.496 5.615 14057 Z= 0.291 Chirality : 0.037 0.147 1657 Planarity : 0.004 0.038 1298 Dihedral : 20.541 93.931 2854 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.26 % Allowed : 22.28 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.30), residues: 805 helix: 1.82 (0.31), residues: 295 sheet: 0.07 (0.50), residues: 97 loop : -1.54 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 973 TYR 0.008 0.001 TYR A 937 PHE 0.014 0.001 PHE A 483 TRP 0.006 0.001 TRP A 415 HIS 0.003 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 9952) covalent geometry : angle 0.49618 / 0.29 (14057) hydrogen bonds : bond 0.04760 / 3.07 ( 406) hydrogen bonds : angle 3.47254 / 2.59 ( 1005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 212 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.6509 (ttp80) REVERT: A 925 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8356 (mtpp) REVERT: A 952 LYS cc_start: 0.7713 (mppt) cc_final: 0.7472 (mptt) outliers start: 16 outliers final: 7 residues processed: 92 average time/residue: 0.6233 time to fit residues: 60.4468 Evaluate side-chains 86 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 968 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.201382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.187432 restraints weight = 7627.458| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 0.37 r_work: 0.3837 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work: 0.3534 rms_B_bonded: 4.96 restraints_weight: 0.1250 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9952 Z= 0.195 Angle : 0.584 6.136 14057 Z= 0.329 Chirality : 0.042 0.240 1657 Planarity : 0.005 0.047 1298 Dihedral : 20.535 94.114 2854 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.83 % Allowed : 22.85 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.29), residues: 805 helix: 1.63 (0.31), residues: 294 sheet: -0.06 (0.50), residues: 97 loop : -1.57 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 973 TYR 0.013 0.002 TYR A 927 PHE 0.017 0.002 PHE A 483 TRP 0.008 0.002 TRP A 415 HIS 0.006 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 9952) covalent geometry : angle 0.58414 / 0.33 (14057) hydrogen bonds : bond 0.05585 / 3.64 ( 406) hydrogen bonds : angle 3.62461 / 2.68 ( 1005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 212 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.6563 (ttp80) REVERT: A 952 LYS cc_start: 0.7848 (mppt) cc_final: 0.7575 (mptt) REVERT: A 1098 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7396 (ptt180) outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 0.6136 time to fit residues: 57.5797 Evaluate side-chains 89 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1098 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.201610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.186940 restraints weight = 7603.359| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 0.39 r_work: 0.3838 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work: 0.3525 rms_B_bonded: 4.52 restraints_weight: 0.1250 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9952 Z= 0.180 Angle : 0.569 6.630 14057 Z= 0.324 Chirality : 0.041 0.215 1657 Planarity : 0.005 0.045 1298 Dihedral : 20.545 94.228 2854 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.26 % Allowed : 22.57 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.29), residues: 805 helix: 1.59 (0.31), residues: 295 sheet: -0.11 (0.50), residues: 97 loop : -1.61 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 973 TYR 0.011 0.001 TYR A 937 PHE 0.017 0.002 PHE A 483 TRP 0.008 0.001 TRP A 415 HIS 0.006 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 9952) covalent geometry : angle 0.56921 / 0.32 (14057) hydrogen bonds : bond 0.05476 / 3.56 ( 406) hydrogen bonds : angle 3.62478 / 2.68 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2966.47 seconds wall clock time: 51 minutes 11.94 seconds (3071.94 seconds total)