Starting phenix.real_space_refine on Thu Jul 24 09:36:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m3n_23658/07_2025/7m3n_23658.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3n_23658/07_2025/7m3n_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m3n_23658/07_2025/7m3n_23658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3n_23658/07_2025/7m3n_23658.map" model { file = "/net/cci-nas-00/data/ceres_data/7m3n_23658/07_2025/7m3n_23658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3n_23658/07_2025/7m3n_23658.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.53, per 1000 atoms: 0.92 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: 1.43 Conformation dependent library (CDL) restraints added in 802.0 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: 0.72 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: 1.83 Time building geometry restraints manager: 1.72 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: 11.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.300 Find NCS groups from input model: 0.070 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:12.400 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.520 ------------------------------------------------------------------------------- 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 : 5.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP H 50 HIS 0.007 0.001 HIS L 91 PHE 0.015 0.002 PHE A 535 TYR 0.019 0.002 TYR A 342 ARG 0.012 0.001 ARG H 84 Details of bonding type rmsd hydrogen bonds : bond 0.15120 ( 143) hydrogen bonds : angle 7.68729 ( 387) SS BOND : bond 0.00583 ( 3) SS BOND : angle 0.57962 ( 6) covalent geometry : bond 0.00455 ( 6173) covalent geometry : angle 0.63043 ( 8420) *********************** 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 : 0.652 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: 0.9159 time to fit residues: 169.6765 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 : 0.707 ------------------------------------------------------------------------------- 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 62 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 72 ASN A 93 ASN A 104 GLN A 137 HIS A 143 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 296 GLN A 309 GLN 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.125658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111800 restraints weight = 7661.435| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.62 r_work: 0.3388 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6176 Z= 0.121 Angle : 0.537 8.244 8426 Z= 0.277 Chirality : 0.043 0.143 907 Planarity : 0.004 0.063 1096 Dihedral : 6.827 59.029 849 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.13 % Rotamer: Outliers : 4.28 % Allowed : 22.63 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.27), residues: 749 helix: -1.90 (0.84), residues: 16 sheet: -0.30 (0.32), residues: 241 loop : -1.59 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.004 0.001 HIS L 91 PHE 0.009 0.001 PHE A 535 TYR 0.011 0.001 TYR A 342 ARG 0.004 0.000 ARG H 84 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 143) hydrogen bonds : angle 5.62452 ( 387) SS BOND : bond 0.00451 ( 3) SS BOND : angle 0.88485 ( 6) covalent geometry : bond 0.00286 ( 6173) covalent geometry : angle 0.53673 ( 8420) *********************** 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 185 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.674 Fit side-chains REVERT: H 5 GLN cc_start: 0.8568 (tp40) cc_final: 0.8250 (tp40) REVERT: A 53 PHE cc_start: 0.8644 (m-80) cc_final: 0.8330 (m-80) REVERT: A 125 ASP cc_start: 0.7523 (m-30) cc_final: 0.7269 (m-30) REVERT: A 154 SER cc_start: 0.8333 (t) cc_final: 0.7975 (p) REVERT: A 240 ASP cc_start: 0.8314 (m-30) cc_final: 0.8114 (m-30) REVERT: A 305 ASP cc_start: 0.8286 (m-30) cc_final: 0.6333 (m-30) REVERT: A 314 ARG cc_start: 0.8451 (mtm180) cc_final: 0.7888 (mtp180) REVERT: A 475 ASP cc_start: 0.8264 (t0) cc_final: 0.8044 (t0) outliers start: 28 outliers final: 12 residues processed: 169 average time/residue: 0.9015 time to fit residues: 161.6848 Evaluate side-chains 162 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER 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 105 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 87 MET 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 66 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3655 r_free = 0.3655 target = 0.123155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109128 restraints weight = 7759.421| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.64 r_work: 0.3350 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 6176 Z= 0.270 Angle : 0.620 8.422 8426 Z= 0.321 Chirality : 0.047 0.153 907 Planarity : 0.005 0.068 1096 Dihedral : 5.845 55.389 826 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.81 % Favored : 95.06 % Rotamer: Outliers : 4.43 % Allowed : 23.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.28), residues: 749 helix: -1.23 (0.97), residues: 16 sheet: -0.14 (0.32), residues: 244 loop : -1.42 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.010 0.001 HIS L 91 PHE 0.022 0.002 PHE A 535 TYR 0.023 0.002 TYR A 342 ARG 0.005 0.001 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 143) hydrogen bonds : angle 5.79132 ( 387) SS BOND : bond 0.00775 ( 3) SS BOND : angle 0.58502 ( 6) covalent geometry : bond 0.00661 ( 6173) covalent geometry : angle 0.62033 ( 8420) *********************** 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 182 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: L 79 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7144 (mp10) REVERT: H 5 GLN cc_start: 0.8634 (tp40) cc_final: 0.8339 (tp40) REVERT: A 53 PHE cc_start: 0.8660 (m-80) cc_final: 0.8338 (m-80) REVERT: A 154 SER cc_start: 0.8287 (t) cc_final: 0.7988 (p) REVERT: A 240 ASP cc_start: 0.8325 (m-30) cc_final: 0.8078 (m-30) REVERT: A 298 GLU cc_start: 0.5430 (OUTLIER) cc_final: 0.4224 (mp0) REVERT: A 305 ASP cc_start: 0.8326 (m-30) cc_final: 0.6491 (m-30) REVERT: A 314 ARG cc_start: 0.8453 (mtm180) cc_final: 0.7867 (mtp180) REVERT: A 346 GLU cc_start: 0.6383 (tt0) cc_final: 0.4527 (tt0) REVERT: A 475 ASP cc_start: 0.8311 (t0) cc_final: 0.8086 (t0) outliers start: 29 outliers final: 19 residues processed: 168 average time/residue: 0.9569 time to fit residues: 169.8359 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 : 0.720 ------------------------------------------------------------------------------- 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 21 SER 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 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 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 49 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 35 optimal weight: 0.0980 chunk 57 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN H 81 GLN A 137 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3670 r_free = 0.3670 target = 0.124403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110385 restraints weight = 7905.331| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.65 r_work: 0.3367 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6176 Z= 0.188 Angle : 0.570 9.021 8426 Z= 0.292 Chirality : 0.045 0.145 907 Planarity : 0.004 0.069 1096 Dihedral : 5.411 50.769 823 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.54 % Favored : 95.33 % Rotamer: Outliers : 5.05 % Allowed : 23.09 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.28), residues: 749 helix: -1.18 (0.97), residues: 16 sheet: 0.03 (0.33), residues: 244 loop : -1.26 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.006 0.001 HIS L 91 PHE 0.017 0.002 PHE A 535 TYR 0.017 0.001 TYR A 342 ARG 0.003 0.001 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 143) hydrogen bonds : angle 5.56332 ( 387) SS BOND : bond 0.00663 ( 3) SS BOND : angle 1.17949 ( 6) covalent geometry : bond 0.00459 ( 6173) covalent geometry : angle 0.56962 ( 8420) *********************** 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 182 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8606 (tp40) cc_final: 0.8302 (tp40) REVERT: A 53 PHE cc_start: 0.8631 (m-80) cc_final: 0.8300 (m-80) REVERT: A 99 ASP cc_start: 0.8158 (t0) cc_final: 0.7899 (t70) REVERT: A 154 SER cc_start: 0.8294 (t) cc_final: 0.8027 (p) REVERT: A 298 GLU cc_start: 0.5309 (OUTLIER) cc_final: 0.3803 (mp0) REVERT: A 314 ARG cc_start: 0.8431 (mtm180) cc_final: 0.7882 (mtp180) REVERT: A 346 GLU cc_start: 0.6283 (tt0) cc_final: 0.4689 (tt0) REVERT: A 475 ASP cc_start: 0.8310 (t0) cc_final: 0.8085 (t0) outliers start: 33 outliers final: 27 residues processed: 165 average time/residue: 0.9386 time to fit residues: 163.8423 Evaluate side-chains 175 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 11 MET 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 78 THR Chi-restraints excluded: chain H residue 97 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 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 357 ILE Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 476 THR 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 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 1 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- 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 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 = 0.3689 r_free = 0.3689 target = 0.125692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111718 restraints weight = 7838.220| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.65 r_work: 0.3389 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6176 Z= 0.128 Angle : 0.530 9.819 8426 Z= 0.269 Chirality : 0.043 0.145 907 Planarity : 0.004 0.065 1096 Dihedral : 4.981 41.493 823 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 4.13 % Allowed : 24.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.29), residues: 749 helix: -1.53 (0.93), residues: 16 sheet: 0.24 (0.34), residues: 239 loop : -1.09 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.005 0.001 HIS L 91 PHE 0.012 0.001 PHE A 535 TYR 0.012 0.001 TYR A 342 ARG 0.003 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 143) hydrogen bonds : angle 5.31406 ( 387) SS BOND : bond 0.00518 ( 3) SS BOND : angle 1.20807 ( 6) covalent geometry : bond 0.00309 ( 6173) covalent geometry : angle 0.52960 ( 8420) *********************** 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 174 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.642 Fit side-chains REVERT: L 89 GLN cc_start: 0.8280 (tt0) cc_final: 0.8022 (tt0) REVERT: H 5 GLN cc_start: 0.8588 (tp40) cc_final: 0.8378 (tp-100) REVERT: A 53 PHE cc_start: 0.8620 (m-80) cc_final: 0.8273 (m-80) REVERT: A 99 ASP cc_start: 0.8114 (t0) cc_final: 0.7889 (t70) REVERT: A 149 VAL cc_start: 0.8551 (m) cc_final: 0.8300 (p) REVERT: A 154 SER cc_start: 0.8280 (t) cc_final: 0.8074 (p) REVERT: A 298 GLU cc_start: 0.5165 (OUTLIER) cc_final: 0.3739 (mp0) REVERT: A 314 ARG cc_start: 0.8409 (mtm180) cc_final: 0.7327 (tpt-90) REVERT: A 475 ASP cc_start: 0.8289 (t0) cc_final: 0.8063 (t0) outliers start: 27 outliers final: 18 residues processed: 159 average time/residue: 0.9980 time to fit residues: 167.5293 Evaluate side-chains 162 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 113 THR Chi-restraints excluded: chain H residue 116 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 316 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 50 optimal weight: 0.0870 chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS A 309 GLN A 404 GLN A 459 ASN A 466 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.112684 restraints weight = 7719.527| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.64 r_work: 0.3405 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6176 Z= 0.112 Angle : 0.516 9.389 8426 Z= 0.262 Chirality : 0.043 0.169 907 Planarity : 0.004 0.067 1096 Dihedral : 4.717 33.076 823 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.82 % Allowed : 24.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.29), residues: 749 helix: -1.38 (0.96), residues: 16 sheet: 0.34 (0.33), residues: 239 loop : -0.94 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.004 0.001 HIS L 91 PHE 0.011 0.001 PHE A 535 TYR 0.011 0.001 TYR A 342 ARG 0.002 0.000 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 143) hydrogen bonds : angle 5.15098 ( 387) SS BOND : bond 0.00426 ( 3) SS BOND : angle 1.17328 ( 6) covalent geometry : bond 0.00274 ( 6173) covalent geometry : angle 0.51556 ( 8420) *********************** 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 172 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8564 (tp40) cc_final: 0.8291 (tp-100) REVERT: H 8 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6298 (pp20) REVERT: A 53 PHE cc_start: 0.8628 (m-80) cc_final: 0.8292 (m-80) REVERT: A 99 ASP cc_start: 0.8090 (t0) cc_final: 0.7864 (t70) REVERT: A 149 VAL cc_start: 0.8522 (m) cc_final: 0.8277 (p) REVERT: A 298 GLU cc_start: 0.5103 (OUTLIER) cc_final: 0.3765 (mp0) REVERT: A 314 ARG cc_start: 0.8421 (mtm180) cc_final: 0.7359 (tpt-90) REVERT: A 475 ASP cc_start: 0.8294 (t0) cc_final: 0.8087 (t0) REVERT: A 551 MET cc_start: 0.8467 (ttt) cc_final: 0.8097 (ttm) outliers start: 25 outliers final: 20 residues processed: 160 average time/residue: 1.1102 time to fit residues: 187.6868 Evaluate side-chains 158 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 8 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 97 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 361 ARG Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 509 GLU 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 40 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN A 137 HIS 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 = 0.3701 r_free = 0.3701 target = 0.126440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112417 restraints weight = 7784.139| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.66 r_work: 0.3400 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6176 Z= 0.130 Angle : 0.528 9.517 8426 Z= 0.269 Chirality : 0.044 0.174 907 Planarity : 0.004 0.065 1096 Dihedral : 4.671 26.339 822 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.54 % Favored : 95.33 % Rotamer: Outliers : 4.13 % Allowed : 24.77 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.29), residues: 749 helix: -1.30 (1.00), residues: 16 sheet: 0.39 (0.33), residues: 239 loop : -0.89 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.005 0.001 HIS L 91 PHE 0.012 0.001 PHE A 535 TYR 0.014 0.001 TYR A 342 ARG 0.002 0.000 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 143) hydrogen bonds : angle 5.20106 ( 387) SS BOND : bond 0.00465 ( 3) SS BOND : angle 1.21820 ( 6) covalent geometry : bond 0.00317 ( 6173) covalent geometry : angle 0.52755 ( 8420) *********************** 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 163 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: L 89 GLN cc_start: 0.8290 (tt0) cc_final: 0.8035 (tt0) REVERT: H 5 GLN cc_start: 0.8566 (tp40) cc_final: 0.8254 (tp-100) REVERT: H 8 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6211 (pp20) REVERT: A 53 PHE cc_start: 0.8636 (m-80) cc_final: 0.8312 (m-80) REVERT: A 99 ASP cc_start: 0.8102 (t0) cc_final: 0.7855 (t70) REVERT: A 149 VAL cc_start: 0.8509 (m) cc_final: 0.8272 (p) REVERT: A 298 GLU cc_start: 0.5154 (OUTLIER) cc_final: 0.3801 (mp0) REVERT: A 314 ARG cc_start: 0.8442 (mtm180) cc_final: 0.7352 (tpt-90) outliers start: 27 outliers final: 21 residues processed: 154 average time/residue: 1.0231 time to fit residues: 166.1022 Evaluate side-chains 155 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 20 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 97 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 44 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 472 LYS Chi-restraints excluded: chain A residue 509 GLU 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 41 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 24 optimal weight: 0.0770 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 50 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3730 r_free = 0.3730 target = 0.128748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114866 restraints weight = 7841.903| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.66 r_work: 0.3437 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6176 Z= 0.091 Angle : 0.524 8.861 8426 Z= 0.266 Chirality : 0.043 0.144 907 Planarity : 0.004 0.062 1096 Dihedral : 4.361 20.562 821 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.67 % Allowed : 24.31 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.29), residues: 749 helix: -1.37 (0.97), residues: 16 sheet: 0.35 (0.33), residues: 255 loop : -0.77 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS L 91 PHE 0.010 0.001 PHE A 266 TYR 0.008 0.001 TYR A 573 ARG 0.002 0.000 ARG A 520 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 143) hydrogen bonds : angle 4.93007 ( 387) SS BOND : bond 0.00279 ( 3) SS BOND : angle 3.53049 ( 6) covalent geometry : bond 0.00214 ( 6173) covalent geometry : angle 0.51540 ( 8420) *********************** 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: 24 poor density : 138 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8516 (tp40) cc_final: 0.8164 (tp40) REVERT: H 8 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6096 (pp20) REVERT: A 53 PHE cc_start: 0.8613 (m-80) cc_final: 0.8302 (m-80) REVERT: A 99 ASP cc_start: 0.8105 (t0) cc_final: 0.7858 (t70) REVERT: A 149 VAL cc_start: 0.8459 (m) cc_final: 0.8222 (p) REVERT: A 314 ARG cc_start: 0.8430 (mtm180) cc_final: 0.7364 (tpt-90) outliers start: 24 outliers final: 19 residues processed: 153 average time/residue: 1.0098 time to fit residues: 163.1710 Evaluate side-chains 155 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 8 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 97 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 60 GLU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 555 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 0.9980 chunk 52 optimal weight: 0.0050 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3719 r_free = 0.3719 target = 0.126127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112344 restraints weight = 7867.691| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.65 r_work: 0.3433 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2244 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= 0.099 Angle : 0.529 8.618 8426 Z= 0.267 Chirality : 0.043 0.144 907 Planarity : 0.004 0.063 1096 Dihedral : 4.324 20.391 821 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.21 % Allowed : 25.54 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.30), residues: 749 helix: -1.38 (1.00), residues: 16 sheet: 0.43 (0.33), residues: 255 loop : -0.70 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.003 0.001 HIS L 91 PHE 0.008 0.001 PHE A 398 TYR 0.012 0.001 TYR A 573 ARG 0.002 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 143) hydrogen bonds : angle 4.85907 ( 387) SS BOND : bond 0.00375 ( 3) SS BOND : angle 2.96930 ( 6) covalent geometry : bond 0.00239 ( 6173) covalent geometry : angle 0.52327 ( 8420) *********************** 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 159 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: L 89 GLN cc_start: 0.8287 (tt0) cc_final: 0.8006 (tt0) REVERT: H 5 GLN cc_start: 0.8506 (tp40) cc_final: 0.8174 (tp40) REVERT: H 8 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6230 (pp20) REVERT: A 53 PHE cc_start: 0.8650 (m-80) cc_final: 0.8311 (m-80) REVERT: A 99 ASP cc_start: 0.8143 (t0) cc_final: 0.7870 (t70) REVERT: A 149 VAL cc_start: 0.8476 (m) cc_final: 0.8219 (p) REVERT: A 314 ARG cc_start: 0.8434 (mtm180) cc_final: 0.7356 (tpt-90) outliers start: 21 outliers final: 17 residues processed: 151 average time/residue: 1.0178 time to fit residues: 162.2848 Evaluate side-chains 155 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 8 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 97 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 144 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 555 VAL 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 40 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 67 optimal weight: 5.9990 chunk 63 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3720 r_free = 0.3720 target = 0.127531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113580 restraints weight = 7898.974| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.68 r_work: 0.3419 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2201 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= 0.124 Angle : 0.540 9.016 8426 Z= 0.275 Chirality : 0.044 0.145 907 Planarity : 0.004 0.065 1096 Dihedral : 4.498 21.467 821 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.21 % Allowed : 25.23 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.30), residues: 749 helix: -1.39 (0.95), residues: 16 sheet: 0.57 (0.34), residues: 239 loop : -0.67 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS L 91 PHE 0.012 0.001 PHE A 535 TYR 0.013 0.001 TYR A 573 ARG 0.002 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 143) hydrogen bonds : angle 4.99091 ( 387) SS BOND : bond 0.00353 ( 3) SS BOND : angle 2.80806 ( 6) covalent geometry : bond 0.00302 ( 6173) covalent geometry : angle 0.53484 ( 8420) ********************** 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 156 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: L 89 GLN cc_start: 0.8257 (tt0) cc_final: 0.7986 (tt0) REVERT: H 5 GLN cc_start: 0.8504 (tp40) cc_final: 0.8157 (tp40) REVERT: H 8 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6146 (pp20) REVERT: A 53 PHE cc_start: 0.8688 (m-80) cc_final: 0.8345 (m-80) REVERT: A 99 ASP cc_start: 0.8162 (t0) cc_final: 0.7904 (t70) REVERT: A 149 VAL cc_start: 0.8556 (m) cc_final: 0.8314 (p) REVERT: A 314 ARG cc_start: 0.8440 (mtm180) cc_final: 0.7337 (tpt-90) outliers start: 21 outliers final: 18 residues processed: 147 average time/residue: 1.0058 time to fit residues: 155.8257 Evaluate side-chains 155 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 8 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 97 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 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 555 VAL 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 28 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3718 r_free = 0.3718 target = 0.126014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112297 restraints weight = 8013.168| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.65 r_work: 0.3434 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6176 Z= 0.104 Angle : 0.524 8.128 8426 Z= 0.266 Chirality : 0.043 0.145 907 Planarity : 0.004 0.063 1096 Dihedral : 4.355 20.751 821 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.21 % Allowed : 25.54 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.30), residues: 749 helix: -1.20 (1.04), residues: 16 sheet: 0.44 (0.32), residues: 255 loop : -0.55 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS L 91 PHE 0.008 0.001 PHE A 398 TYR 0.019 0.001 TYR A 573 ARG 0.002 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 143) hydrogen bonds : angle 4.82807 ( 387) SS BOND : bond 0.00278 ( 3) SS BOND : angle 2.58908 ( 6) covalent geometry : bond 0.00249 ( 6173) covalent geometry : angle 0.51989 ( 8420) =============================================================================== Job complete usr+sys time: 6912.84 seconds wall clock time: 121 minutes 24.31 seconds (7284.31 seconds total)