Starting phenix.real_space_refine on Thu Jul 2 05:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v93_64859/07_2026/9v93_64859.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v93_64859/07_2026/9v93_64859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v93_64859/07_2026/9v93_64859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v93_64859/07_2026/9v93_64859.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v93_64859/07_2026/9v93_64859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v93_64859/07_2026/9v93_64859.map" } resolution = 2.81 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= 0.039 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: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 3 5.21 5 S 15 5.16 5 C 4128 2.51 5 N 1221 2.21 5 O 1325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 6724 Number of models: 1 Model: "" Number of chains: 4 Chain: "a" Number of atoms: 6050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6050 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 42, 'TRANS': 717} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "b" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "c" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 310 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 9} Link IDs: {'rna3p': 14} Chain: "a" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3, 'water': 2} Link IDs: {None: 4} Time building chain proxies: 1.27, per 1000 atoms: 0.19 Number of scatterers: 6724 At special positions: 0 Unit cell: (89.355, 86.802, 102.971, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 15 16.00 P 32 15.00 Mg 3 11.99 O 1325 8.00 N 1221 7.00 C 4128 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: 0.47 Conformation dependent library (CDL) restraints added in 242.5 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 34.1% alpha, 23.2% beta 11 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'a' and resid 37 through 54 removed outlier: 3.585A pdb=" N GLN a 48 " --> pdb=" O ARG a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 130 removed outlier: 3.654A pdb=" N ALA a 127 " --> pdb=" O ALA a 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE a 128 " --> pdb=" O ILE a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 195 through 203 Processing helix chain 'a' and resid 203 through 208 Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.948A pdb=" N ARG a 216 " --> pdb=" O ALA a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 254 through 263 Processing helix chain 'a' and resid 299 through 304 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 325 through 327 No H-bonds generated for 'chain 'a' and resid 325 through 327' Processing helix chain 'a' and resid 360 through 362 No H-bonds generated for 'chain 'a' and resid 360 through 362' Processing helix chain 'a' and resid 372 through 392 removed outlier: 4.492A pdb=" N MET a 385 " --> pdb=" O ARG a 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR a 386 " --> pdb=" O GLN a 382 " (cutoff:3.500A) Processing helix chain 'a' and resid 411 through 431 Processing helix chain 'a' and resid 451 through 464 Processing helix chain 'a' and resid 481 through 491 removed outlier: 4.514A pdb=" N ASP a 485 " --> pdb=" O GLU a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 501 through 510 Processing helix chain 'a' and resid 516 through 531 Processing helix chain 'a' and resid 587 through 606 Processing helix chain 'a' and resid 621 through 638 Processing helix chain 'a' and resid 697 through 702 Processing helix chain 'a' and resid 723 through 734 Processing helix chain 'a' and resid 749 through 763 removed outlier: 4.263A pdb=" N SER a 755 " --> pdb=" O THR a 751 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU a 761 " --> pdb=" O GLU a 757 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE a 762 " --> pdb=" O ARG a 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 344 through 346 removed outlier: 3.553A pdb=" N PHE a 344 " --> pdb=" O ALA a 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.686A pdb=" N ARG a 137 " --> pdb=" O PHE a 144 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE a 144 " --> pdb=" O ARG a 137 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG a 162 " --> pdb=" O ARG a 145 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL a 330 " --> pdb=" O LEU a 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 58 through 60 removed outlier: 3.687A pdb=" N ALA a 67 " --> pdb=" O THR a 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR a 70 " --> pdb=" O ARG a 24 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL a 25 " --> pdb=" O ILE a 97 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE a 97 " --> pdb=" O VAL a 25 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG a 90 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 286 through 287 removed outlier: 7.563A pdb=" N ALA a 272 " --> pdb=" O THR a 236 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY a 234 " --> pdb=" O PHE a 274 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG a 276 " --> pdb=" O PHE a 232 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N PHE a 232 " --> pdb=" O ARG a 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 244 through 247 Processing sheet with id=AA6, first strand: chain 'a' and resid 364 through 365 Processing sheet with id=AA7, first strand: chain 'a' and resid 436 through 442 removed outlier: 6.785A pdb=" N LEU a 402 " --> pdb=" O ARG a 438 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE a 440 " --> pdb=" O LEU a 402 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU a 404 " --> pdb=" O ILE a 440 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TYR a 442 " --> pdb=" O LEU a 404 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR a 406 " --> pdb=" O TYR a 442 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP a 401 " --> pdb=" O LEU a 470 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL a 472 " --> pdb=" O ASP a 401 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL a 403 " --> pdb=" O VAL a 472 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL a 474 " --> pdb=" O VAL a 403 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU a 405 " --> pdb=" O VAL a 474 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLN a 497 " --> pdb=" O PHE a 469 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL a 499 " --> pdb=" O PRO a 471 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE a 473 " --> pdb=" O VAL a 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'a' and resid 568 through 575 removed outlier: 6.301A pdb=" N LEU a 551 " --> pdb=" O ASP a 617 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU a 612 " --> pdb=" O GLY a 648 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL a 650 " --> pdb=" O LEU a 612 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL a 614 " --> pdb=" O VAL a 650 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL a 652 " --> pdb=" O VAL a 614 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG a 616 " --> pdb=" O VAL a 652 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL a 649 " --> pdb=" O THR a 714 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER a 679 " --> pdb=" O THR a 691 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.64 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: 1799 1.33 - 1.45: 1362 1.45 - 1.57: 3683 1.57 - 1.69: 62 1.69 - 1.81: 23 Bond restraints: 6929 Sorted by residual: bond pdb=" C3' DT b 14 " pdb=" C2' DT b 14 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.71e+00 bond pdb=" C3' DT b 9 " pdb=" C2' DT b 9 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.53e+00 bond pdb=" C3' DG b 12 " pdb=" C2' DG b 12 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.15e+00 bond pdb=" O4' DG b 15 " pdb=" C1' DG b 15 " ideal model delta sigma weight residual 1.420 1.398 0.022 1.10e-02 8.26e+03 4.15e+00 bond pdb=" C3' DG b 15 " pdb=" C2' DG b 15 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.11e+00 ... (remaining 6924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 9089 1.22 - 2.43: 379 2.43 - 3.65: 66 3.65 - 4.86: 9 4.86 - 6.08: 6 Bond angle restraints: 9549 Sorted by residual: angle pdb=" O4' DG b 4 " pdb=" C4' DG b 4 " pdb=" C3' DG b 4 " ideal model delta sigma weight residual 106.00 103.45 2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT b 9 " pdb=" C4 DT b 9 " pdb=" O4 DT b 9 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT b 14 " pdb=" C4 DT b 14 " pdb=" O4 DT b 14 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT b 13 " pdb=" C4 DT b 13 " pdb=" O4 DT b 13 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.59e+01 angle pdb=" N3 DT b 16 " pdb=" C4 DT b 16 " pdb=" O4 DT b 16 " ideal model delta sigma weight residual 119.90 122.27 -2.37 6.00e-01 2.78e+00 1.56e+01 ... (remaining 9544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.30: 3894 27.30 - 54.60: 203 54.60 - 81.90: 34 81.90 - 109.20: 3 109.20 - 136.50: 1 Dihedral angle restraints: 4135 sinusoidal: 1943 harmonic: 2192 Sorted by residual: dihedral pdb=" CA ASN a 223 " pdb=" C ASN a 223 " pdb=" N GLY a 224 " pdb=" CA GLY a 224 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C4' DT b 13 " pdb=" C3' DT b 13 " pdb=" O3' DT b 13 " pdb=" P DT b 14 " ideal model delta sinusoidal sigma weight residual 220.00 83.50 136.50 1 3.50e+01 8.16e-04 1.35e+01 dihedral pdb=" CA PRO a 372 " pdb=" C PRO a 372 " pdb=" N ILE a 373 " pdb=" CA ILE a 373 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 613 0.028 - 0.057: 282 0.057 - 0.085: 101 0.085 - 0.113: 52 0.113 - 0.141: 20 Chirality restraints: 1068 Sorted by residual: chirality pdb=" CA ILE a 94 " pdb=" N ILE a 94 " pdb=" C ILE a 94 " pdb=" CB ILE a 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL a 561 " pdb=" N VAL a 561 " pdb=" C VAL a 561 " pdb=" CB VAL a 561 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE a 689 " pdb=" N ILE a 689 " pdb=" C ILE a 689 " pdb=" CB ILE a 689 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1065 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS a 174 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO a 175 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO a 175 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO a 175 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL a 266 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO a 267 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO a 267 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO a 267 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN a 716 " -0.024 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO a 717 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO a 717 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO a 717 " -0.021 5.00e-02 4.00e+02 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 574 2.74 - 3.28: 5973 3.28 - 3.82: 10861 3.82 - 4.36: 13755 4.36 - 4.90: 22764 Nonbonded interactions: 53927 Sorted by model distance: nonbonded pdb=" OP1 U c 7 " pdb="MG MG a 802 " model vdw 2.201 2.170 nonbonded pdb=" NE2 GLN a 85 " pdb=" O ARG a 90 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS a 654 " pdb=" OP2 U c 7 " model vdw 2.276 3.120 nonbonded pdb=" OE1 GLU a 651 " pdb=" OG1 THR a 714 " model vdw 2.295 3.040 nonbonded pdb=" NZ LYS a 596 " pdb=" OE1 GLU a 634 " model vdw 2.335 3.120 ... (remaining 53922 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: 1.120 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.100 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 0.026 6929 Z= 0.239 Angle : 0.589 6.081 9549 Z= 0.390 Chirality : 0.042 0.141 1068 Planarity : 0.005 0.044 1138 Dihedral : 15.762 136.504 2723 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.66 (0.30), residues: 758 helix: 1.47 (0.34), residues: 231 sheet: 0.56 (0.39), residues: 181 loop : -0.27 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 490 TYR 0.013 0.001 TYR a 380 PHE 0.019 0.002 PHE a 232 TRP 0.017 0.002 TRP a 65 HIS 0.006 0.001 HIS a 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.24 ( 6929) covalent geometry : angle 0.58946 / 0.39 ( 9549) hydrogen bonds : bond 0.17209 / 12.14 ( 296) hydrogen bonds : angle 7.03880 / 4.83 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.147 Fit side-chains REVERT: a 361 ASN cc_start: 0.7386 (m-40) cc_final: 0.7181 (t0) REVERT: a 646 GLN cc_start: 0.7700 (mt0) cc_final: 0.7411 (mt0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4053 time to fit residues: 38.4610 Evaluate side-chains 67 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 341 HIS ** a 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.175484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137171 restraints weight = 7108.749| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.56 r_work: 0.3267 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6929 Z= 0.142 Angle : 0.540 5.954 9549 Z= 0.305 Chirality : 0.043 0.236 1068 Planarity : 0.005 0.047 1138 Dihedral : 15.073 145.634 1249 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.24 % Allowed : 6.80 % Favored : 91.96 % 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: 0.95 (0.30), residues: 758 helix: 1.89 (0.34), residues: 232 sheet: 0.60 (0.39), residues: 182 loop : -0.17 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 415 TYR 0.013 0.001 TYR a 380 PHE 0.013 0.002 PHE a 159 TRP 0.010 0.001 TRP a 136 HIS 0.004 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 6929) covalent geometry : angle 0.54021 / 0.30 ( 9549) hydrogen bonds : bond 0.05164 / 3.61 ( 296) hydrogen bonds : angle 5.36522 / 3.71 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.172 Fit side-chains REVERT: a 54 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7166 (mptp) REVERT: a 361 ASN cc_start: 0.7828 (m-40) cc_final: 0.7278 (t0) REVERT: a 390 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7985 (tm-30) outliers start: 8 outliers final: 3 residues processed: 69 average time/residue: 0.4425 time to fit residues: 32.2354 Evaluate side-chains 66 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 547 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.173046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133116 restraints weight = 7035.061| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.07 r_work: 0.3228 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6929 Z= 0.187 Angle : 0.585 6.146 9549 Z= 0.322 Chirality : 0.045 0.193 1068 Planarity : 0.005 0.058 1138 Dihedral : 15.187 145.297 1249 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.47 % Allowed : 7.26 % Favored : 90.26 % 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: 0.89 (0.30), residues: 758 helix: 1.83 (0.34), residues: 234 sheet: 0.68 (0.40), residues: 179 loop : -0.28 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 290 TYR 0.016 0.002 TYR a 406 PHE 0.018 0.002 PHE a 545 TRP 0.012 0.002 TRP a 620 HIS 0.006 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 6929) covalent geometry : angle 0.58459 / 0.32 ( 9549) hydrogen bonds : bond 0.05189 / 3.60 ( 296) hydrogen bonds : angle 5.09252 / 3.53 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.173 Fit side-chains REVERT: a 54 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7277 (mptp) REVERT: a 361 ASN cc_start: 0.7975 (m-40) cc_final: 0.7312 (t0) REVERT: a 373 ILE cc_start: 0.7800 (mp) cc_final: 0.7575 (mm) REVERT: a 390 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: a 415 ARG cc_start: 0.6916 (ttp80) cc_final: 0.6693 (ttp-170) REVERT: a 417 LYS cc_start: 0.7586 (mppt) cc_final: 0.6948 (mtmt) REVERT: a 424 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7733 (tp30) REVERT: a 555 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7932 (tp40) outliers start: 16 outliers final: 5 residues processed: 76 average time/residue: 0.5094 time to fit residues: 40.5065 Evaluate side-chains 70 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 528 THR Chi-restraints excluded: chain a residue 555 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.0010 chunk 8 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.173178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131284 restraints weight = 7142.611| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.15 r_work: 0.3244 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6929 Z= 0.120 Angle : 0.484 4.728 9549 Z= 0.276 Chirality : 0.042 0.197 1068 Planarity : 0.004 0.041 1138 Dihedral : 15.113 144.607 1249 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.70 % Allowed : 8.96 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.30), residues: 758 helix: 2.17 (0.34), residues: 233 sheet: 0.77 (0.41), residues: 173 loop : -0.22 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 290 TYR 0.015 0.001 TYR a 380 PHE 0.014 0.001 PHE a 232 TRP 0.010 0.001 TRP a 570 HIS 0.003 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 6929) covalent geometry : angle 0.48355 / 0.28 ( 9549) hydrogen bonds : bond 0.03885 / 2.68 ( 296) hydrogen bonds : angle 4.75548 / 3.31 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.216 Fit side-chains REVERT: a 54 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7162 (mptp) REVERT: a 99 GLU cc_start: 0.7055 (mp0) cc_final: 0.6813 (mp0) REVERT: a 276 ARG cc_start: 0.6364 (tpt90) cc_final: 0.6081 (tpt170) REVERT: a 361 ASN cc_start: 0.7959 (m-40) cc_final: 0.7231 (t0) REVERT: a 373 ILE cc_start: 0.7568 (mp) cc_final: 0.7330 (mm) REVERT: a 390 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: a 417 LYS cc_start: 0.7518 (mppt) cc_final: 0.6996 (mtmt) REVERT: a 424 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7648 (tp30) REVERT: a 427 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8112 (tptp) REVERT: a 745 GLU cc_start: 0.8182 (mp0) cc_final: 0.7831 (mp0) outliers start: 11 outliers final: 4 residues processed: 73 average time/residue: 0.5195 time to fit residues: 39.7780 Evaluate side-chains 72 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.0570 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.172537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131927 restraints weight = 7172.823| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.30 r_work: 0.3233 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6929 Z= 0.125 Angle : 0.486 4.722 9549 Z= 0.275 Chirality : 0.042 0.181 1068 Planarity : 0.004 0.040 1138 Dihedral : 15.042 144.130 1249 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.55 % Allowed : 10.20 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.31), residues: 758 helix: 2.22 (0.34), residues: 234 sheet: 0.74 (0.41), residues: 176 loop : -0.11 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 290 TYR 0.015 0.001 TYR a 380 PHE 0.013 0.001 PHE a 545 TRP 0.009 0.001 TRP a 136 HIS 0.003 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6929) covalent geometry : angle 0.48602 / 0.27 ( 9549) hydrogen bonds : bond 0.03880 / 2.69 ( 296) hydrogen bonds : angle 4.66904 / 3.25 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7157 (mptp) REVERT: a 99 GLU cc_start: 0.7071 (mp0) cc_final: 0.6848 (mp0) REVERT: a 276 ARG cc_start: 0.6351 (tpt90) cc_final: 0.6057 (tpt170) REVERT: a 325 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8554 (t0) REVERT: a 328 ARG cc_start: 0.7624 (mmt180) cc_final: 0.7375 (mpt-90) REVERT: a 361 ASN cc_start: 0.7915 (m-40) cc_final: 0.7173 (t0) REVERT: a 390 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: a 417 LYS cc_start: 0.7564 (mppt) cc_final: 0.7028 (mtmt) REVERT: a 424 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7644 (tp30) REVERT: a 427 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8113 (tptp) REVERT: a 745 GLU cc_start: 0.8177 (mp0) cc_final: 0.7823 (mp0) outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.5333 time to fit residues: 42.4976 Evaluate side-chains 75 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 325 ASN Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 586 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 47 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.172837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.133144 restraints weight = 7167.395| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.05 r_work: 0.3261 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6929 Z= 0.121 Angle : 0.476 4.718 9549 Z= 0.270 Chirality : 0.041 0.182 1068 Planarity : 0.004 0.039 1138 Dihedral : 15.024 144.053 1249 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.55 % Allowed : 11.28 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.31), residues: 758 helix: 2.29 (0.34), residues: 235 sheet: 0.78 (0.41), residues: 176 loop : -0.12 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 290 TYR 0.013 0.001 TYR a 380 PHE 0.014 0.001 PHE a 232 TRP 0.009 0.001 TRP a 570 HIS 0.003 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 6929) covalent geometry : angle 0.47597 / 0.27 ( 9549) hydrogen bonds : bond 0.03768 / 2.61 ( 296) hydrogen bonds : angle 4.56915 / 3.18 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7209 (mptp) REVERT: a 276 ARG cc_start: 0.6421 (tpt90) cc_final: 0.6177 (tpt170) REVERT: a 325 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8564 (t0) REVERT: a 361 ASN cc_start: 0.7869 (m-40) cc_final: 0.7173 (t0) REVERT: a 390 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: a 417 LYS cc_start: 0.7599 (mppt) cc_final: 0.7109 (mtmt) REVERT: a 424 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7610 (tp30) REVERT: a 427 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8099 (tptp) REVERT: a 745 GLU cc_start: 0.8155 (mp0) cc_final: 0.7812 (mp0) REVERT: a 761 GLU cc_start: 0.6038 (mt-10) cc_final: 0.5672 (mm-30) outliers start: 10 outliers final: 4 residues processed: 76 average time/residue: 0.5201 time to fit residues: 41.3454 Evaluate side-chains 75 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 325 ASN Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.172261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132941 restraints weight = 7072.733| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.04 r_work: 0.3267 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6929 Z= 0.130 Angle : 0.487 4.726 9549 Z= 0.275 Chirality : 0.042 0.181 1068 Planarity : 0.004 0.040 1138 Dihedral : 15.005 144.250 1249 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.01 % Allowed : 11.28 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.30), residues: 758 helix: 2.31 (0.34), residues: 235 sheet: 0.89 (0.41), residues: 173 loop : -0.17 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 290 TYR 0.014 0.001 TYR a 380 PHE 0.013 0.001 PHE a 545 TRP 0.009 0.001 TRP a 570 HIS 0.003 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 6929) covalent geometry : angle 0.48743 / 0.28 ( 9549) hydrogen bonds : bond 0.03872 / 2.69 ( 296) hydrogen bonds : angle 4.54806 / 3.16 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7207 (mptp) REVERT: a 276 ARG cc_start: 0.6447 (tpt90) cc_final: 0.6197 (tpt170) REVERT: a 361 ASN cc_start: 0.7896 (m-40) cc_final: 0.7223 (t0) REVERT: a 390 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: a 417 LYS cc_start: 0.7626 (mppt) cc_final: 0.7391 (mtmt) REVERT: a 424 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7606 (tp30) REVERT: a 427 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8099 (tptp) REVERT: a 745 GLU cc_start: 0.8152 (mp0) cc_final: 0.7811 (mp0) REVERT: a 761 GLU cc_start: 0.6049 (mt-10) cc_final: 0.5682 (mm-30) outliers start: 13 outliers final: 5 residues processed: 77 average time/residue: 0.5037 time to fit residues: 40.6149 Evaluate side-chains 74 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 684 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.169864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129970 restraints weight = 7096.741| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.12 r_work: 0.3205 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6929 Z= 0.183 Angle : 0.554 5.718 9549 Z= 0.306 Chirality : 0.045 0.194 1068 Planarity : 0.005 0.056 1138 Dihedral : 15.100 146.240 1249 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.85 % Allowed : 11.44 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.30), residues: 758 helix: 2.14 (0.34), residues: 234 sheet: 0.75 (0.40), residues: 173 loop : -0.33 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 290 TYR 0.014 0.002 TYR a 380 PHE 0.016 0.002 PHE a 545 TRP 0.011 0.002 TRP a 620 HIS 0.004 0.001 HIS a 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 6929) covalent geometry : angle 0.55391 / 0.31 ( 9549) hydrogen bonds : bond 0.04723 / 3.28 ( 296) hydrogen bonds : angle 4.72441 / 3.28 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7183 (mptp) REVERT: a 276 ARG cc_start: 0.6543 (tpt90) cc_final: 0.6321 (tpt90) REVERT: a 325 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8573 (t0) REVERT: a 361 ASN cc_start: 0.7913 (m-40) cc_final: 0.7228 (t0) REVERT: a 390 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: a 412 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6602 (tmm160) REVERT: a 415 ARG cc_start: 0.6961 (ttp80) cc_final: 0.6711 (ttp-170) REVERT: a 417 LYS cc_start: 0.7683 (mppt) cc_final: 0.7428 (mppt) REVERT: a 424 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7626 (tp30) outliers start: 12 outliers final: 6 residues processed: 79 average time/residue: 0.5169 time to fit residues: 42.8366 Evaluate side-chains 81 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 325 ASN Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 412 ARG Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 684 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 684 ASN a 685 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.173045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133602 restraints weight = 7155.668| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.04 r_work: 0.3277 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6929 Z= 0.117 Angle : 0.471 4.688 9549 Z= 0.269 Chirality : 0.041 0.188 1068 Planarity : 0.004 0.038 1138 Dihedral : 15.023 144.038 1249 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.16 % Allowed : 11.75 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.30), residues: 758 helix: 2.35 (0.34), residues: 235 sheet: 0.73 (0.40), residues: 176 loop : -0.19 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 290 TYR 0.015 0.001 TYR a 380 PHE 0.011 0.001 PHE a 545 TRP 0.011 0.001 TRP a 570 HIS 0.002 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 6929) covalent geometry : angle 0.47139 / 0.27 ( 9549) hydrogen bonds : bond 0.03681 / 2.55 ( 296) hydrogen bonds : angle 4.49203 / 3.12 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: a 52 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6319 (mp0) REVERT: a 54 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7184 (mptp) REVERT: a 276 ARG cc_start: 0.6494 (tpt90) cc_final: 0.6281 (tpt90) REVERT: a 328 ARG cc_start: 0.7785 (mmt180) cc_final: 0.7571 (mmt180) REVERT: a 361 ASN cc_start: 0.7862 (m-40) cc_final: 0.7201 (t0) REVERT: a 390 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: a 412 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6564 (tmm160) REVERT: a 417 LYS cc_start: 0.7655 (mppt) cc_final: 0.7245 (mtmt) REVERT: a 424 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7600 (tp30) REVERT: a 427 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8100 (tptp) REVERT: a 745 GLU cc_start: 0.8132 (mp0) cc_final: 0.7781 (mp0) REVERT: a 761 GLU cc_start: 0.6003 (mt-10) cc_final: 0.5620 (mm-30) outliers start: 14 outliers final: 5 residues processed: 74 average time/residue: 0.5319 time to fit residues: 41.1574 Evaluate side-chains 72 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 412 ARG Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 684 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 0.0470 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.164994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125143 restraints weight = 7070.719| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.05 r_work: 0.3188 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6929 Z= 0.217 Angle : 0.580 5.859 9549 Z= 0.318 Chirality : 0.046 0.189 1068 Planarity : 0.006 0.067 1138 Dihedral : 15.077 145.112 1249 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.70 % Allowed : 12.36 % Favored : 85.94 % 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: 0.95 (0.30), residues: 758 helix: 2.08 (0.34), residues: 234 sheet: 0.73 (0.40), residues: 173 loop : -0.40 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 419 TYR 0.014 0.002 TYR a 380 PHE 0.018 0.002 PHE a 545 TRP 0.011 0.002 TRP a 136 HIS 0.005 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 6929) covalent geometry : angle 0.58039 / 0.32 ( 9549) hydrogen bonds : bond 0.04882 / 3.40 ( 296) hydrogen bonds : angle 4.72647 / 3.28 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7147 (mptp) REVERT: a 276 ARG cc_start: 0.6507 (tpt90) cc_final: 0.6281 (tpt90) REVERT: a 328 ARG cc_start: 0.7816 (mmt180) cc_final: 0.7601 (mmt180) REVERT: a 361 ASN cc_start: 0.7869 (m-40) cc_final: 0.7180 (t0) REVERT: a 390 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: a 412 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6529 (tmm160) REVERT: a 415 ARG cc_start: 0.6963 (ttp80) cc_final: 0.6710 (ttp-170) REVERT: a 417 LYS cc_start: 0.7708 (mppt) cc_final: 0.7448 (mtmt) REVERT: a 424 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7529 (tp30) REVERT: a 745 GLU cc_start: 0.8161 (mp0) cc_final: 0.7764 (mp0) REVERT: a 761 GLU cc_start: 0.6078 (mt-10) cc_final: 0.5723 (mm-30) outliers start: 11 outliers final: 6 residues processed: 77 average time/residue: 0.5583 time to fit residues: 45.0322 Evaluate side-chains 78 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 412 ARG Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 684 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 684 ASN a 685 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.173643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.134188 restraints weight = 7112.994| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.02 r_work: 0.3292 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6929 Z= 0.111 Angle : 0.466 4.630 9549 Z= 0.267 Chirality : 0.041 0.185 1068 Planarity : 0.004 0.037 1138 Dihedral : 15.022 143.971 1249 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.85 % Allowed : 12.36 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.30), residues: 758 helix: 2.35 (0.34), residues: 235 sheet: 0.72 (0.40), residues: 176 loop : -0.22 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 290 TYR 0.014 0.001 TYR a 380 PHE 0.011 0.001 PHE a 545 TRP 0.012 0.001 TRP a 570 HIS 0.003 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 6929) covalent geometry : angle 0.46613 / 0.27 ( 9549) hydrogen bonds : bond 0.03569 / 2.48 ( 296) hydrogen bonds : angle 4.45313 / 3.09 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1931.03 seconds wall clock time: 33 minutes 28.92 seconds (2008.92 seconds total)