Starting phenix.real_space_refine on Tue Mar 3 14:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m3n_23658/03_2026/7m3n_23658.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3n_23658/03_2026/7m3n_23658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m3n_23658/03_2026/7m3n_23658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3n_23658/03_2026/7m3n_23658.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m3n_23658/03_2026/7m3n_23658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3n_23658/03_2026/7m3n_23658.map" } resolution = 2.4 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3813 2.51 5 N 1024 2.21 5 O 1144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6004 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Time building chain proxies: 1.39, per 1000 atoms: 0.23 Number of scatterers: 6004 At special positions: 0 Unit cell: (82.5, 113.3, 105.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1144 8.00 N 1024 7.00 C 3813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.04 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: 0.45 Conformation dependent library (CDL) restraints added in 368.4 milliseconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 17 sheets defined 9.6% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.611A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.533A pdb=" N VAL A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.979A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.853A pdb=" N VAL A 241 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.037A pdb=" N LEU A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 4.099A pdb=" N ARG A 313 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.192A pdb=" N GLY A 385 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.556A pdb=" N ASP A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.722A pdb=" N PHE A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.692A pdb=" N ASN A 560 " --> pdb=" O ASN A 557 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 561 " --> pdb=" O GLN A 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 561' Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.687A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.685A pdb=" N VAL L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N SER L 65 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.443A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.979A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 49 through 53 removed outlier: 6.761A pdb=" N TYR A 524 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 149 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP A 526 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN A 147 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP A 528 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 145 " --> pdb=" O TRP A 528 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS A 530 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN A 143 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS A 532 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 141 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 534 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 538 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 135 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLN A 143 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLY A 264 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 145 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA A 262 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA9, first strand: chain 'A' and resid 80 through 84 removed outlier: 4.235A pdb=" N ALA A 103 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP A 208 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TRP A 109 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR A 206 " --> pdb=" O TRP A 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 80 through 84 removed outlier: 5.963A pdb=" N VAL A 502 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 497 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 215 through 218 removed outlier: 6.336A pdb=" N ASP A 215 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AB4, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.357A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AB6, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AB7, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AB8, first strand: chain 'A' and resid 470 through 472 removed outlier: 6.555A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 167 hydrogen bonds defined for protein. 387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.69 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: 1.23 - 1.34: 1949 1.34 - 1.46: 1564 1.46 - 1.58: 2622 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 6173 Sorted by residual: bond pdb=" CA ILE A 219 " pdb=" CB ILE A 219 " ideal model delta sigma weight residual 1.537 1.522 0.015 1.29e-02 6.01e+03 1.36e+00 bond pdb=" CG1 ILE A 101 " pdb=" CD1 ILE A 101 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.09e+00 bond pdb=" CA ASP A 269 " pdb=" C ASP A 269 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.08e-02 8.57e+03 1.04e+00 bond pdb=" CB THR A 230 " pdb=" CG2 THR A 230 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.49e-01 bond pdb=" CB GLN A 143 " pdb=" CG GLN A 143 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.83e-01 ... (remaining 6168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8195 1.61 - 3.22: 192 3.22 - 4.83: 26 4.83 - 6.43: 6 6.43 - 8.04: 1 Bond angle restraints: 8420 Sorted by residual: angle pdb=" C GLY H 54 " pdb=" N ASP H 55 " pdb=" CA ASP H 55 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.48e+00 angle pdb=" N ALA L 32 " pdb=" CA ALA L 32 " pdb=" C ALA L 32 " ideal model delta sigma weight residual 111.30 114.69 -3.39 1.36e+00 5.41e-01 6.21e+00 angle pdb=" N PRO A 423 " pdb=" CA PRO A 423 " pdb=" C PRO A 423 " ideal model delta sigma weight residual 112.47 107.54 4.93 2.06e+00 2.36e-01 5.73e+00 angle pdb=" C LYS H 74 " pdb=" N SER H 75 " pdb=" CA SER H 75 " ideal model delta sigma weight residual 121.54 125.91 -4.37 1.91e+00 2.74e-01 5.23e+00 angle pdb=" CA ASN H 83 " pdb=" C ASN H 83 " pdb=" N ARG H 84 " ideal model delta sigma weight residual 114.17 117.47 -3.30 1.45e+00 4.76e-01 5.18e+00 ... (remaining 8415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 3131 16.94 - 33.88: 353 33.88 - 50.82: 86 50.82 - 67.76: 30 67.76 - 84.70: 6 Dihedral angle restraints: 3606 sinusoidal: 1417 harmonic: 2189 Sorted by residual: dihedral pdb=" CB CYS A 490 " pdb=" SG CYS A 490 " pdb=" SG CYS A 494 " pdb=" CB CYS A 494 " ideal model delta sinusoidal sigma weight residual 93.00 37.65 55.35 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CA THR L 31 " pdb=" C THR L 31 " pdb=" N ALA L 32 " pdb=" CA ALA L 32 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N LEU A 422 " pdb=" CA LEU A 422 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 3603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 483 0.028 - 0.057: 256 0.057 - 0.085: 99 0.085 - 0.113: 52 0.113 - 0.141: 17 Chirality restraints: 907 Sorted by residual: chirality pdb=" CA ILE L 39 " pdb=" N ILE L 39 " pdb=" C ILE L 39 " pdb=" CB ILE L 39 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 306 " pdb=" N ILE A 306 " pdb=" C ILE A 306 " pdb=" CB ILE A 306 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 904 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 122 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO A 123 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 464 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 465 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 465 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 465 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 55 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C ASP H 55 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP H 55 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY H 56 " 0.010 2.00e-02 2.50e+03 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 259 2.71 - 3.26: 5360 3.26 - 3.81: 9281 3.81 - 4.35: 11759 4.35 - 4.90: 20009 Nonbonded interactions: 46668 Sorted by model distance: nonbonded pdb=" OG SER L 43 " pdb=" O GLY H 110 " model vdw 2.168 3.040 nonbonded pdb=" NH2 ARG A 382 " pdb=" O GLY A 392 " model vdw 2.220 3.120 nonbonded pdb=" OG SER A 65 " pdb=" O VAL A 119 " model vdw 2.287 3.040 nonbonded pdb=" O THR A 301 " pdb=" OG1 THR A 301 " model vdw 2.324 3.040 nonbonded pdb=" ND2 ASN A 443 " pdb=" OG1 THR A 445 " model vdw 2.346 3.120 ... (remaining 46663 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: 6.160 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.070 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6176 Z= 0.204 Angle : 0.630 8.042 8426 Z= 0.358 Chirality : 0.044 0.141 907 Planarity : 0.005 0.060 1096 Dihedral : 15.949 84.702 2197 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.59 % Rotamer: Outliers : 4.28 % Allowed : 22.48 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.53 (0.26), residues: 749 helix: -2.08 (1.08), residues: 10 sheet: -1.02 (0.30), residues: 248 loop : -2.14 (0.22), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 84 TYR 0.019 0.002 TYR A 342 PHE 0.015 0.002 PHE A 535 TRP 0.013 0.001 TRP H 50 HIS 0.007 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 6173) covalent geometry : angle 0.63043 ( 8420) SS BOND : bond 0.00583 ( 3) SS BOND : angle 0.57962 ( 6) hydrogen bonds : bond 0.15120 ( 143) hydrogen bonds : angle 7.68729 ( 387) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.234 Fit side-chains REVERT: L 72 THR cc_start: 0.8624 (m) cc_final: 0.8411 (t) REVERT: L 86 TYR cc_start: 0.8534 (m-80) cc_final: 0.8178 (m-80) REVERT: L 89 GLN cc_start: 0.8053 (tt0) cc_final: 0.7769 (tt0) REVERT: L 97 THR cc_start: 0.8446 (m) cc_final: 0.8226 (p) REVERT: H 5 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7975 (tp40) REVERT: H 8 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5830 (pp20) REVERT: A 53 PHE cc_start: 0.8535 (m-80) cc_final: 0.8193 (m-80) REVERT: A 125 ASP cc_start: 0.6873 (m-30) cc_final: 0.6624 (m-30) REVERT: A 154 SER cc_start: 0.8050 (t) cc_final: 0.7696 (p) REVERT: A 305 ASP cc_start: 0.8063 (m-30) cc_final: 0.7189 (m-30) REVERT: A 314 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7055 (tpt-90) REVERT: A 319 MET cc_start: 0.7868 (mtp) cc_final: 0.7587 (mtp) REVERT: A 346 GLU cc_start: 0.5765 (tt0) cc_final: 0.4426 (tt0) REVERT: A 475 ASP cc_start: 0.7852 (t0) cc_final: 0.7631 (t0) outliers start: 28 outliers final: 13 residues processed: 175 average time/residue: 0.4367 time to fit residues: 80.6874 Evaluate side-chains 165 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 526 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 27 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 42 GLN L 53 ASN H 5 GLN H 39 GLN H 43 GLN H 81 GLN A 93 ASN A 104 GLN A 137 HIS A 143 GLN A 222 HIS A 280 GLN A 296 GLN A 309 GLN A 384 HIS A 404 GLN A 417 ASN A 428 ASN A 443 ASN A 446 ASN A 459 ASN A 468 GLN A 560 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112730 restraints weight = 7796.672| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.65 r_work: 0.3400 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6176 Z= 0.101 Angle : 0.522 7.991 8426 Z= 0.269 Chirality : 0.043 0.143 907 Planarity : 0.004 0.062 1096 Dihedral : 6.688 59.916 849 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.82 % Allowed : 23.24 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.70 (0.27), residues: 749 helix: -1.81 (0.85), residues: 16 sheet: -0.49 (0.31), residues: 257 loop : -1.52 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 84 TYR 0.008 0.001 TYR A 342 PHE 0.008 0.001 PHE A 268 TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 6173) covalent geometry : angle 0.52127 ( 8420) SS BOND : bond 0.00406 ( 3) SS BOND : angle 0.79594 ( 6) hydrogen bonds : bond 0.03435 ( 143) hydrogen bonds : angle 5.54230 ( 387) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.262 Fit side-chains REVERT: H 5 GLN cc_start: 0.8573 (tp40) cc_final: 0.8264 (tp40) REVERT: A 53 PHE cc_start: 0.8645 (m-80) cc_final: 0.8320 (m-80) REVERT: A 125 ASP cc_start: 0.7488 (m-30) cc_final: 0.7231 (m-30) REVERT: A 154 SER cc_start: 0.8331 (t) cc_final: 0.7993 (p) REVERT: A 305 ASP cc_start: 0.8206 (m-30) cc_final: 0.6278 (m-30) REVERT: A 314 ARG cc_start: 0.8474 (mtm180) cc_final: 0.7922 (mtp180) REVERT: A 475 ASP cc_start: 0.8296 (t0) cc_final: 0.8073 (t0) outliers start: 25 outliers final: 10 residues processed: 169 average time/residue: 0.4275 time to fit residues: 76.4090 Evaluate side-chains 161 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 555 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 8 HIS L 89 GLN A 137 HIS A 404 GLN A 459 ASN A 483 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.123267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109310 restraints weight = 7727.724| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.63 r_work: 0.3352 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 6176 Z= 0.270 Angle : 0.611 8.487 8426 Z= 0.317 Chirality : 0.047 0.147 907 Planarity : 0.005 0.067 1096 Dihedral : 5.790 54.394 826 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.41 % Favored : 95.46 % Rotamer: Outliers : 4.59 % Allowed : 23.09 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.40 (0.28), residues: 749 helix: -1.17 (0.99), residues: 16 sheet: -0.12 (0.32), residues: 244 loop : -1.42 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 581 TYR 0.024 0.002 TYR A 342 PHE 0.016 0.002 PHE A 535 TRP 0.011 0.002 TRP H 50 HIS 0.011 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00657 ( 6173) covalent geometry : angle 0.60975 ( 8420) SS BOND : bond 0.00639 ( 3) SS BOND : angle 1.43486 ( 6) hydrogen bonds : bond 0.04063 ( 143) hydrogen bonds : angle 5.75249 ( 387) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: L 79 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: L 89 GLN cc_start: 0.8283 (tt0) cc_final: 0.7994 (tt0) REVERT: H 5 GLN cc_start: 0.8627 (tp40) cc_final: 0.8384 (tp-100) REVERT: H 59 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7732 (ttp-170) REVERT: A 53 PHE cc_start: 0.8663 (m-80) cc_final: 0.8343 (m-80) REVERT: A 154 SER cc_start: 0.8305 (t) cc_final: 0.8017 (p) REVERT: A 240 ASP cc_start: 0.8278 (m-30) cc_final: 0.8027 (m-30) REVERT: A 298 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.4179 (mp0) REVERT: A 305 ASP cc_start: 0.8315 (m-30) cc_final: 0.6470 (m-30) REVERT: A 314 ARG cc_start: 0.8462 (mtm180) cc_final: 0.7860 (mtp180) REVERT: A 346 GLU cc_start: 0.6364 (tt0) cc_final: 0.4521 (tt0) REVERT: A 475 ASP cc_start: 0.8294 (t0) cc_final: 0.8070 (t0) outliers start: 30 outliers final: 18 residues processed: 166 average time/residue: 0.4551 time to fit residues: 79.6708 Evaluate side-chains 172 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 583 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 48 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN A 137 HIS A 404 GLN A 458 ASN A 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111188 restraints weight = 7846.564| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.65 r_work: 0.3382 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6176 Z= 0.153 Angle : 0.568 9.296 8426 Z= 0.290 Chirality : 0.044 0.146 907 Planarity : 0.004 0.067 1096 Dihedral : 5.322 48.289 823 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 4.43 % Allowed : 23.85 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.28), residues: 749 helix: -1.15 (0.96), residues: 16 sheet: 0.08 (0.33), residues: 241 loop : -1.20 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 581 TYR 0.015 0.001 TYR A 342 PHE 0.018 0.002 PHE A 535 TRP 0.011 0.001 TRP H 50 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6173) covalent geometry : angle 0.56180 ( 8420) SS BOND : bond 0.00363 ( 3) SS BOND : angle 3.27002 ( 6) hydrogen bonds : bond 0.03444 ( 143) hydrogen bonds : angle 5.44269 ( 387) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.164 Fit side-chains REVERT: H 40 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6931 (mtp-110) REVERT: H 59 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7715 (ttp-170) REVERT: A 50 GLU cc_start: 0.7356 (mp0) cc_final: 0.7139 (mp0) REVERT: A 53 PHE cc_start: 0.8636 (m-80) cc_final: 0.8331 (m-80) REVERT: A 99 ASP cc_start: 0.8151 (t0) cc_final: 0.7906 (t70) REVERT: A 154 SER cc_start: 0.8271 (t) cc_final: 0.8043 (p) REVERT: A 298 GLU cc_start: 0.5137 (OUTLIER) cc_final: 0.3711 (mp0) REVERT: A 314 ARG cc_start: 0.8420 (mtm180) cc_final: 0.7880 (mtp180) REVERT: A 346 GLU cc_start: 0.6229 (tt0) cc_final: 0.4668 (tt0) REVERT: A 475 ASP cc_start: 0.8306 (t0) cc_final: 0.8078 (t0) outliers start: 29 outliers final: 19 residues processed: 163 average time/residue: 0.4680 time to fit residues: 80.1101 Evaluate side-chains 170 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 72 optimal weight: 0.0470 chunk 59 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN H 5 GLN A 137 HIS A 309 GLN A 404 GLN A 459 ASN A 466 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114221 restraints weight = 7978.644| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.67 r_work: 0.3427 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6176 Z= 0.089 Angle : 0.502 8.664 8426 Z= 0.254 Chirality : 0.042 0.145 907 Planarity : 0.004 0.064 1096 Dihedral : 4.658 35.254 823 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.82 % Allowed : 24.01 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.85 (0.29), residues: 749 helix: -1.35 (0.98), residues: 16 sheet: 0.09 (0.32), residues: 253 loop : -0.92 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.008 0.001 TYR A 244 PHE 0.012 0.001 PHE A 266 TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 6173) covalent geometry : angle 0.49996 ( 8420) SS BOND : bond 0.00480 ( 3) SS BOND : angle 1.76136 ( 6) hydrogen bonds : bond 0.02955 ( 143) hydrogen bonds : angle 5.03049 ( 387) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8482 (tp40) cc_final: 0.8245 (tp40) REVERT: H 59 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7761 (ttp-170) REVERT: A 50 GLU cc_start: 0.7344 (mp0) cc_final: 0.7139 (mp0) REVERT: A 53 PHE cc_start: 0.8624 (m-80) cc_final: 0.8292 (m-80) REVERT: A 99 ASP cc_start: 0.8053 (t0) cc_final: 0.7838 (t70) REVERT: A 149 VAL cc_start: 0.8443 (m) cc_final: 0.8198 (p) REVERT: A 314 ARG cc_start: 0.8400 (mtm180) cc_final: 0.7867 (mtp180) outliers start: 25 outliers final: 12 residues processed: 166 average time/residue: 0.4483 time to fit residues: 78.5028 Evaluate side-chains 158 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 555 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 34 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 70 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 137 HIS A 302 ASN A 404 GLN A 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.126679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.112741 restraints weight = 7853.847| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.63 r_work: 0.3402 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6176 Z= 0.139 Angle : 0.537 9.584 8426 Z= 0.274 Chirality : 0.044 0.167 907 Planarity : 0.004 0.064 1096 Dihedral : 4.784 30.232 822 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.41 % Favored : 95.46 % Rotamer: Outliers : 3.21 % Allowed : 24.16 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.29), residues: 749 helix: -1.46 (0.99), residues: 16 sheet: 0.18 (0.32), residues: 253 loop : -0.83 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 40 TYR 0.015 0.001 TYR A 342 PHE 0.024 0.001 PHE A 266 TRP 0.010 0.001 TRP H 50 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6173) covalent geometry : angle 0.53354 ( 8420) SS BOND : bond 0.00516 ( 3) SS BOND : angle 2.36982 ( 6) hydrogen bonds : bond 0.03259 ( 143) hydrogen bonds : angle 5.18549 ( 387) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.141 Fit side-chains REVERT: L 89 GLN cc_start: 0.8268 (tt0) cc_final: 0.8014 (tt0) REVERT: H 8 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6314 (pp20) REVERT: H 59 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7691 (ttp-170) REVERT: A 50 GLU cc_start: 0.7342 (mp0) cc_final: 0.7128 (mp0) REVERT: A 53 PHE cc_start: 0.8642 (m-80) cc_final: 0.8294 (m-80) REVERT: A 99 ASP cc_start: 0.8077 (t0) cc_final: 0.7832 (t70) REVERT: A 149 VAL cc_start: 0.8490 (m) cc_final: 0.8243 (p) REVERT: A 240 ASP cc_start: 0.8192 (m-30) cc_final: 0.7960 (m-30) REVERT: A 314 ARG cc_start: 0.8422 (mtm180) cc_final: 0.7902 (mtp180) REVERT: A 551 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7768 (ttt) outliers start: 21 outliers final: 13 residues processed: 159 average time/residue: 0.4654 time to fit residues: 77.8637 Evaluate side-chains 156 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 0.0060 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 0.0170 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 302 ASN A 404 GLN A 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111349 restraints weight = 7874.286| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.67 r_work: 0.3375 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6176 Z= 0.186 Angle : 0.578 9.943 8426 Z= 0.294 Chirality : 0.045 0.175 907 Planarity : 0.004 0.067 1096 Dihedral : 4.913 30.971 821 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.81 % Favored : 95.06 % Rotamer: Outliers : 3.82 % Allowed : 23.85 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -0.70 (0.29), residues: 749 helix: -1.60 (0.95), residues: 16 sheet: 0.36 (0.33), residues: 238 loop : -0.87 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 581 TYR 0.018 0.001 TYR A 342 PHE 0.015 0.002 PHE A 535 TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 6173) covalent geometry : angle 0.57484 ( 8420) SS BOND : bond 0.00501 ( 3) SS BOND : angle 2.45908 ( 6) hydrogen bonds : bond 0.03499 ( 143) hydrogen bonds : angle 5.33781 ( 387) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.226 Fit side-chains REVERT: H 5 GLN cc_start: 0.8508 (tp40) cc_final: 0.8295 (tp40) REVERT: H 8 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6316 (pp20) REVERT: H 59 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7686 (ttp-170) REVERT: A 50 GLU cc_start: 0.7368 (mp0) cc_final: 0.7142 (mp0) REVERT: A 53 PHE cc_start: 0.8643 (m-80) cc_final: 0.8321 (m-80) REVERT: A 99 ASP cc_start: 0.8110 (t0) cc_final: 0.7861 (t70) REVERT: A 149 VAL cc_start: 0.8570 (m) cc_final: 0.8346 (p) REVERT: A 298 GLU cc_start: 0.5245 (OUTLIER) cc_final: 0.3817 (mp0) REVERT: A 314 ARG cc_start: 0.8453 (mtm180) cc_final: 0.7869 (mtp180) REVERT: A 551 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8013 (ttt) outliers start: 25 outliers final: 18 residues processed: 154 average time/residue: 0.5101 time to fit residues: 82.3785 Evaluate side-chains 159 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 137 HIS A 302 ASN A 309 GLN A 404 GLN A 459 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113320 restraints weight = 7921.570| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.68 r_work: 0.3406 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6176 Z= 0.114 Angle : 0.529 9.238 8426 Z= 0.269 Chirality : 0.043 0.165 907 Planarity : 0.004 0.065 1096 Dihedral : 4.623 29.526 821 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.21 % Allowed : 24.46 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.57 (0.29), residues: 749 helix: -1.82 (0.88), residues: 16 sheet: 0.34 (0.32), residues: 253 loop : -0.73 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 581 TYR 0.010 0.001 TYR A 342 PHE 0.013 0.001 PHE A 266 TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6173) covalent geometry : angle 0.52757 ( 8420) SS BOND : bond 0.00310 ( 3) SS BOND : angle 1.71167 ( 6) hydrogen bonds : bond 0.03120 ( 143) hydrogen bonds : angle 5.12289 ( 387) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.232 Fit side-chains REVERT: L 89 GLN cc_start: 0.8294 (tt0) cc_final: 0.8062 (tt0) REVERT: H 5 GLN cc_start: 0.8511 (tp40) cc_final: 0.8258 (tp40) REVERT: H 8 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6140 (pp20) REVERT: H 59 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7716 (ttp-170) REVERT: A 50 GLU cc_start: 0.7355 (mp0) cc_final: 0.7136 (mp0) REVERT: A 53 PHE cc_start: 0.8642 (m-80) cc_final: 0.8328 (m-80) REVERT: A 99 ASP cc_start: 0.8071 (t0) cc_final: 0.7823 (t70) REVERT: A 149 VAL cc_start: 0.8516 (m) cc_final: 0.8266 (p) REVERT: A 314 ARG cc_start: 0.8450 (mtm180) cc_final: 0.7361 (tpt-90) outliers start: 21 outliers final: 14 residues processed: 153 average time/residue: 0.4957 time to fit residues: 79.5896 Evaluate side-chains 153 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 583 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 53 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 302 ASN A 309 GLN A 404 GLN A 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111104 restraints weight = 7835.824| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.68 r_work: 0.3374 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6176 Z= 0.195 Angle : 0.585 10.059 8426 Z= 0.300 Chirality : 0.046 0.165 907 Planarity : 0.004 0.066 1096 Dihedral : 4.998 31.417 821 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.94 % Favored : 94.93 % Rotamer: Outliers : 3.06 % Allowed : 24.31 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -0.61 (0.29), residues: 749 helix: -1.58 (0.98), residues: 16 sheet: 0.34 (0.33), residues: 242 loop : -0.76 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 581 TYR 0.020 0.001 TYR A 342 PHE 0.015 0.002 PHE A 535 TRP 0.012 0.001 TRP H 50 HIS 0.007 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6173) covalent geometry : angle 0.58198 ( 8420) SS BOND : bond 0.00465 ( 3) SS BOND : angle 2.41810 ( 6) hydrogen bonds : bond 0.03688 ( 143) hydrogen bonds : angle 5.32139 ( 387) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.228 Fit side-chains REVERT: L 89 GLN cc_start: 0.8281 (tt0) cc_final: 0.8039 (tt0) REVERT: H 5 GLN cc_start: 0.8540 (tp40) cc_final: 0.8301 (tp40) REVERT: H 8 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6272 (pp20) REVERT: H 59 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7617 (ttp-170) REVERT: A 53 PHE cc_start: 0.8659 (m-80) cc_final: 0.8329 (m-80) REVERT: A 99 ASP cc_start: 0.8142 (t0) cc_final: 0.7897 (t70) REVERT: A 149 VAL cc_start: 0.8664 (m) cc_final: 0.8424 (p) REVERT: A 298 GLU cc_start: 0.5251 (OUTLIER) cc_final: 0.3829 (mp0) REVERT: A 314 ARG cc_start: 0.8470 (mtm180) cc_final: 0.7339 (tpt-90) outliers start: 20 outliers final: 17 residues processed: 155 average time/residue: 0.5099 time to fit residues: 82.9388 Evaluate side-chains 160 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 583 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 302 ASN A 404 GLN A 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113385 restraints weight = 7906.951| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.67 r_work: 0.3411 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6176 Z= 0.112 Angle : 0.527 9.077 8426 Z= 0.268 Chirality : 0.044 0.145 907 Planarity : 0.004 0.063 1096 Dihedral : 4.653 29.711 821 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.45 % Allowed : 25.38 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.49 (0.29), residues: 749 helix: -1.49 (0.99), residues: 16 sheet: 0.35 (0.32), residues: 253 loop : -0.66 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.015 0.001 TYR A 573 PHE 0.013 0.001 PHE A 266 TRP 0.011 0.001 TRP H 50 HIS 0.003 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6173) covalent geometry : angle 0.52561 ( 8420) SS BOND : bond 0.00278 ( 3) SS BOND : angle 1.64254 ( 6) hydrogen bonds : bond 0.03130 ( 143) hydrogen bonds : angle 5.08505 ( 387) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.216 Fit side-chains REVERT: H 5 GLN cc_start: 0.8503 (tp40) cc_final: 0.8252 (tp40) REVERT: H 59 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7654 (ttp-170) REVERT: A 53 PHE cc_start: 0.8630 (m-80) cc_final: 0.8285 (m-80) REVERT: A 99 ASP cc_start: 0.8133 (t0) cc_final: 0.7878 (t70) REVERT: A 149 VAL cc_start: 0.8574 (m) cc_final: 0.8343 (p) REVERT: A 314 ARG cc_start: 0.8440 (mtm180) cc_final: 0.7364 (tpt-90) outliers start: 16 outliers final: 12 residues processed: 147 average time/residue: 0.4944 time to fit residues: 76.2877 Evaluate side-chains 149 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 583 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 72 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 137 HIS A 302 ASN A 404 GLN A 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114033 restraints weight = 7883.117| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.67 r_work: 0.3420 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6176 Z= 0.107 Angle : 0.525 8.773 8426 Z= 0.267 Chirality : 0.043 0.144 907 Planarity : 0.004 0.063 1096 Dihedral : 4.531 28.206 821 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.99 % Allowed : 26.30 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.39 (0.29), residues: 749 helix: -1.52 (0.95), residues: 16 sheet: 0.45 (0.32), residues: 253 loop : -0.60 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.017 0.001 TYR A 573 PHE 0.011 0.001 PHE A 266 TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6173) covalent geometry : angle 0.52391 ( 8420) SS BOND : bond 0.00289 ( 3) SS BOND : angle 1.58408 ( 6) hydrogen bonds : bond 0.03122 ( 143) hydrogen bonds : angle 4.96985 ( 387) =============================================================================== Job complete usr+sys time: 3033.11 seconds wall clock time: 52 minutes 9.29 seconds (3129.29 seconds total)