Starting phenix.real_space_refine on Tue Feb 3 16:24:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l07_62691/02_2026/9l07_62691.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l07_62691/02_2026/9l07_62691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l07_62691/02_2026/9l07_62691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l07_62691/02_2026/9l07_62691.map" model { file = "/net/cci-nas-00/data/ceres_data/9l07_62691/02_2026/9l07_62691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l07_62691/02_2026/9l07_62691.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 18 5.16 5 C 3030 2.51 5 N 797 2.21 5 O 937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4782 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1553 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 14, 'TRANS': 181} Chain: "L" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1620 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "H" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 1 Time building chain proxies: 1.02, per 1000 atoms: 0.21 Number of scatterers: 4782 At special positions: 0 Unit cell: (74.56, 102.52, 114.636, 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 18 16.00 O 937 8.00 N 797 7.00 C 3030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 155 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 265.1 milliseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1158 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 16 sheets defined 11.7% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.584A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.247A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.658A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'L' and resid 82 through 84 No H-bonds generated for 'chain 'L' and resid 82 through 84' Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.556A pdb=" N ASP L 98 " --> pdb=" O LYS L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 148 Processing helix chain 'L' and resid 202 through 208 Processing helix chain 'H' and resid 69 through 72 removed outlier: 3.766A pdb=" N LYS H 72 " --> pdb=" O PRO H 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 69 through 72' Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.931A pdb=" N THR H 99 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 173 removed outlier: 3.850A pdb=" N SER H 171 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.724A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.647A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.549A pdb=" N SER L 77 " --> pdb=" O THR L 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.652A pdb=" N GLU L 13 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR L 102 " --> pdb=" O THR L 122 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP L 41 " --> pdb=" O VAL L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.652A pdb=" N GLU L 13 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR L 102 " --> pdb=" O THR L 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 137 through 139 removed outlier: 4.134A pdb=" N VAL L 154 " --> pdb=" O PHE L 139 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR L 193 " --> pdb=" O ASP L 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 137 through 139 removed outlier: 4.134A pdb=" N VAL L 154 " --> pdb=" O PHE L 139 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR L 193 " --> pdb=" O ASP L 159 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA L 194 " --> pdb=" O SER L 186 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER L 186 " --> pdb=" O ALA L 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 166 through 170 removed outlier: 3.599A pdb=" N SER L 213 " --> pdb=" O LYS L 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.624A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR H 55 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TRP H 39 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG H 106 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE H 115 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.624A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR H 55 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TRP H 39 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA H 100 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL H 124 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 122 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 135 through 138 removed outlier: 3.553A pdb=" N SER H 195 " --> pdb=" O CYS H 155 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 135 through 138 removed outlier: 3.553A pdb=" N SER H 195 " --> pdb=" O CYS H 155 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER H 192 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL H 184 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 211 through 215 191 hydrogen bonds defined for protein. 462 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: 0.57 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1523 1.35 - 1.46: 1228 1.46 - 1.58: 2139 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 4910 Sorted by residual: bond pdb=" N ILE H 30 " pdb=" CA ILE H 30 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.17e+00 bond pdb=" N ASN L 85 " pdb=" CA ASN L 85 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 9.00e-01 bond pdb=" CA ASN H 34 " pdb=" C ASN H 34 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.34e-02 5.57e+03 8.91e-01 bond pdb=" CA ILE H 210 " pdb=" CB ILE H 210 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.05e-02 9.07e+03 8.69e-01 bond pdb=" CA SER H 130 " pdb=" C SER H 130 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.59e-01 ... (remaining 4905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 6303 1.08 - 2.15: 291 2.15 - 3.23: 93 3.23 - 4.31: 16 4.31 - 5.38: 4 Bond angle restraints: 6707 Sorted by residual: angle pdb=" N ALA L 171 " pdb=" CA ALA L 171 " pdb=" C ALA L 171 " ideal model delta sigma weight residual 112.41 107.48 4.93 1.30e+00 5.92e-01 1.44e+01 angle pdb=" N SER L 173 " pdb=" CA SER L 173 " pdb=" C SER L 173 " ideal model delta sigma weight residual 114.75 110.84 3.91 1.26e+00 6.30e-01 9.65e+00 angle pdb=" CA SER H 128 " pdb=" C SER H 128 " pdb=" O SER H 128 " ideal model delta sigma weight residual 122.37 119.20 3.17 1.15e+00 7.56e-01 7.61e+00 angle pdb=" N ILE L 30 " pdb=" CA ILE L 30 " pdb=" C ILE L 30 " ideal model delta sigma weight residual 113.07 109.50 3.57 1.36e+00 5.41e-01 6.90e+00 angle pdb=" CA SER H 128 " pdb=" C SER H 128 " pdb=" N ALA H 129 " ideal model delta sigma weight residual 115.10 118.33 -3.23 1.26e+00 6.30e-01 6.56e+00 ... (remaining 6702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.95: 2724 10.95 - 21.89: 132 21.89 - 32.84: 47 32.84 - 43.78: 10 43.78 - 54.73: 5 Dihedral angle restraints: 2918 sinusoidal: 1101 harmonic: 1817 Sorted by residual: dihedral pdb=" SG CYS A 391 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sinusoidal sigma weight residual 79.00 24.58 54.42 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" N ASP L 172 " pdb=" CA ASP L 172 " pdb=" CB ASP L 172 " pdb=" CG ASP L 172 " ideal model delta sinusoidal sigma weight residual 60.00 114.73 -54.73 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CA ARG H 111A" pdb=" CB ARG H 111A" pdb=" CG ARG H 111A" pdb=" CD ARG H 111A" ideal model delta sinusoidal sigma weight residual 60.00 113.14 -53.14 3 1.50e+01 4.44e-03 9.18e+00 ... (remaining 2915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 432 0.026 - 0.052: 193 0.052 - 0.078: 51 0.078 - 0.103: 51 0.103 - 0.129: 20 Chirality restraints: 747 Sorted by residual: chirality pdb=" CA ILE L 157 " pdb=" N ILE L 157 " pdb=" C ILE L 157 " pdb=" CB ILE L 157 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE L 54 " pdb=" N ILE L 54 " pdb=" C ILE L 54 " pdb=" CB ILE L 54 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA VAL L 71 " pdb=" N VAL L 71 " pdb=" C VAL L 71 " pdb=" CB VAL L 71 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.27e-01 ... (remaining 744 not shown) Planarity restraints: 864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO A 463 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 14 " -0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO H 15 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO H 15 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO H 15 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 216 " 0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO H 217 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO H 217 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 217 " 0.015 5.00e-02 4.00e+02 ... (remaining 861 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1078 2.78 - 3.31: 4292 3.31 - 3.84: 7738 3.84 - 4.37: 8911 4.37 - 4.90: 15949 Nonbonded interactions: 37968 Sorted by model distance: nonbonded pdb=" O GLU L 1 " pdb=" OG SER L 27 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.270 3.040 nonbonded pdb=" ND2 ASN L 114 " pdb=" OH TYR H 55 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASN H 68 " pdb=" OG SER H 70 " model vdw 2.316 3.040 nonbonded pdb=" NZ LYS L 187 " pdb=" OH TYR L 193 " model vdw 2.343 3.120 ... (remaining 37963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.840 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 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 : 0.002 0.040 4918 Z= 0.121 Angle : 0.590 5.384 6723 Z= 0.360 Chirality : 0.040 0.129 747 Planarity : 0.004 0.029 864 Dihedral : 7.706 54.726 1736 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.86 % Allowed : 4.28 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.31), residues: 617 helix: -3.13 (0.54), residues: 45 sheet: -0.93 (0.34), residues: 210 loop : -2.08 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.009 0.001 TYR H 37 PHE 0.011 0.001 PHE H 115 TRP 0.005 0.001 TRP H 118 HIS 0.002 0.000 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 4910) covalent geometry : angle 0.59081 ( 6707) SS BOND : bond 0.00119 ( 8) SS BOND : angle 0.39696 ( 16) hydrogen bonds : bond 0.26394 ( 153) hydrogen bonds : angle 9.88054 ( 462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7205 (m-40) cc_final: 0.6904 (m-40) REVERT: A 405 ASN cc_start: 0.7211 (t0) cc_final: 0.6960 (t0) REVERT: A 406 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7245 (mt-10) REVERT: A 439 ASN cc_start: 0.8171 (t0) cc_final: 0.7647 (t0) REVERT: A 514 SER cc_start: 0.7972 (t) cc_final: 0.7697 (m) REVERT: A 528 LYS cc_start: 0.7277 (mmtt) cc_final: 0.6836 (mtmt) REVERT: L 106 SER cc_start: 0.7835 (t) cc_final: 0.7560 (m) REVERT: L 145 GLU cc_start: 0.7098 (tt0) cc_final: 0.6876 (tt0) REVERT: L 169 TRP cc_start: 0.7022 (m100) cc_final: 0.6538 (m100) REVERT: L 183 THR cc_start: 0.6857 (p) cc_final: 0.6563 (p) REVERT: L 204 GLU cc_start: 0.7397 (tp30) cc_final: 0.6717 (tp30) REVERT: H 92 ASN cc_start: 0.8717 (p0) cc_final: 0.8391 (p0) REVERT: H 108 SER cc_start: 0.8121 (m) cc_final: 0.7796 (p) REVERT: H 117 TYR cc_start: 0.7654 (m-80) cc_final: 0.7439 (m-80) REVERT: H 122 THR cc_start: 0.8232 (t) cc_final: 0.7913 (p) REVERT: H 167 VAL cc_start: 0.8346 (m) cc_final: 0.7943 (t) REVERT: H 179 HIS cc_start: 0.7788 (t-170) cc_final: 0.7561 (t-90) REVERT: H 181 PHE cc_start: 0.8302 (m-80) cc_final: 0.7901 (m-10) outliers start: 10 outliers final: 3 residues processed: 179 average time/residue: 0.0473 time to fit residues: 11.5004 Evaluate side-chains 145 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain H residue 111 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.0020 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.4866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN L 188 GLN L 191 ASN H 3 GLN H 34 ASN H 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.144277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118588 restraints weight = 7567.068| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.41 r_work: 0.3390 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4918 Z= 0.141 Angle : 0.604 9.164 6723 Z= 0.312 Chirality : 0.046 0.206 747 Planarity : 0.004 0.035 864 Dihedral : 5.010 54.600 687 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.66 % Allowed : 13.78 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.32), residues: 617 helix: -2.08 (0.67), residues: 40 sheet: -0.37 (0.33), residues: 223 loop : -1.63 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 355 TYR 0.035 0.002 TYR H 55 PHE 0.020 0.002 PHE H 115 TRP 0.012 0.001 TRP L 206 HIS 0.005 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4910) covalent geometry : angle 0.60243 ( 6707) SS BOND : bond 0.00312 ( 8) SS BOND : angle 1.00441 ( 16) hydrogen bonds : bond 0.04264 ( 153) hydrogen bonds : angle 6.53455 ( 462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 ASN cc_start: 0.8545 (t0) cc_final: 0.8135 (t0) REVERT: A 394 ASN cc_start: 0.7969 (m-40) cc_final: 0.7630 (m-40) REVERT: A 405 ASN cc_start: 0.8114 (t0) cc_final: 0.7860 (t0) REVERT: A 468 ILE cc_start: 0.8498 (mt) cc_final: 0.8225 (tt) REVERT: A 497 PHE cc_start: 0.7812 (m-10) cc_final: 0.7509 (m-10) REVERT: A 514 SER cc_start: 0.8364 (t) cc_final: 0.8055 (p) REVERT: A 528 LYS cc_start: 0.7789 (mmtt) cc_final: 0.7035 (mtmt) REVERT: L 106 SER cc_start: 0.8243 (t) cc_final: 0.7930 (m) REVERT: L 145 GLU cc_start: 0.7688 (tt0) cc_final: 0.7324 (tt0) REVERT: L 169 TRP cc_start: 0.7403 (m100) cc_final: 0.6908 (m100) REVERT: L 204 GLU cc_start: 0.7784 (tp30) cc_final: 0.7095 (tp30) REVERT: L 206 TRP cc_start: 0.8305 (OUTLIER) cc_final: 0.8008 (t-100) REVERT: H 36 VAL cc_start: 0.4851 (m) cc_final: 0.3703 (p) REVERT: H 92 ASN cc_start: 0.8734 (p0) cc_final: 0.8429 (p0) REVERT: H 122 THR cc_start: 0.8541 (t) cc_final: 0.8192 (p) REVERT: H 181 PHE cc_start: 0.8654 (m-80) cc_final: 0.8340 (m-10) REVERT: H 186 GLN cc_start: 0.7155 (mt0) cc_final: 0.6903 (mt0) outliers start: 25 outliers final: 16 residues processed: 153 average time/residue: 0.0405 time to fit residues: 8.4049 Evaluate side-chains 154 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 150 LYS Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 206 TRP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 111 ARG Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115109 restraints weight = 7641.208| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.39 r_work: 0.3328 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4918 Z= 0.168 Angle : 0.601 8.158 6723 Z= 0.312 Chirality : 0.046 0.163 747 Planarity : 0.004 0.031 864 Dihedral : 5.293 55.682 687 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.84 % Allowed : 13.59 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.32), residues: 617 helix: -1.82 (0.74), residues: 40 sheet: -0.22 (0.33), residues: 222 loop : -1.47 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.037 0.002 TYR H 55 PHE 0.023 0.002 PHE H 115 TRP 0.011 0.002 TRP L 206 HIS 0.005 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 4910) covalent geometry : angle 0.60017 ( 6707) SS BOND : bond 0.00294 ( 8) SS BOND : angle 0.99224 ( 16) hydrogen bonds : bond 0.03744 ( 153) hydrogen bonds : angle 6.01182 ( 462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.141 Fit side-chains REVERT: A 367 VAL cc_start: 0.7947 (m) cc_final: 0.7734 (t) REVERT: A 394 ASN cc_start: 0.7946 (m-40) cc_final: 0.7556 (m-40) REVERT: A 405 ASN cc_start: 0.8254 (t0) cc_final: 0.7987 (t0) REVERT: A 438 SER cc_start: 0.8541 (p) cc_final: 0.8253 (p) REVERT: A 514 SER cc_start: 0.8340 (t) cc_final: 0.8018 (p) REVERT: A 528 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7246 (mtmt) REVERT: L 106 SER cc_start: 0.8462 (t) cc_final: 0.8084 (m) REVERT: L 145 GLU cc_start: 0.7706 (tt0) cc_final: 0.7362 (tt0) REVERT: L 169 TRP cc_start: 0.7484 (m100) cc_final: 0.7021 (m100) REVERT: L 204 GLU cc_start: 0.7739 (tp30) cc_final: 0.7112 (tp30) REVERT: L 206 TRP cc_start: 0.8279 (OUTLIER) cc_final: 0.7984 (t-100) REVERT: H 92 ASN cc_start: 0.8836 (p0) cc_final: 0.8473 (p0) REVERT: H 122 THR cc_start: 0.8625 (t) cc_final: 0.8277 (p) REVERT: H 181 PHE cc_start: 0.8781 (m-80) cc_final: 0.8433 (m-10) REVERT: H 186 GLN cc_start: 0.7131 (mt0) cc_final: 0.6922 (mt0) outliers start: 26 outliers final: 18 residues processed: 152 average time/residue: 0.0428 time to fit residues: 8.8409 Evaluate side-chains 153 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 206 TRP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 131 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114467 restraints weight = 7598.717| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.37 r_work: 0.3316 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4918 Z= 0.150 Angle : 0.586 7.191 6723 Z= 0.301 Chirality : 0.046 0.163 747 Planarity : 0.004 0.030 864 Dihedral : 4.923 46.772 683 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.10 % Allowed : 15.27 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.33), residues: 617 helix: -1.83 (0.74), residues: 40 sheet: -0.05 (0.33), residues: 222 loop : -1.36 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.038 0.002 TYR H 55 PHE 0.017 0.002 PHE H 115 TRP 0.010 0.002 TRP L 206 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4910) covalent geometry : angle 0.58546 ( 6707) SS BOND : bond 0.00358 ( 8) SS BOND : angle 0.74702 ( 16) hydrogen bonds : bond 0.03384 ( 153) hydrogen bonds : angle 5.67590 ( 462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.148 Fit side-chains REVERT: A 343 ASN cc_start: 0.8486 (t0) cc_final: 0.8179 (t0) REVERT: A 388 ASN cc_start: 0.8493 (p0) cc_final: 0.8225 (p0) REVERT: A 394 ASN cc_start: 0.7954 (m-40) cc_final: 0.7564 (m-40) REVERT: A 405 ASN cc_start: 0.8249 (t0) cc_final: 0.7955 (t0) REVERT: A 497 PHE cc_start: 0.7691 (m-10) cc_final: 0.7285 (m-10) REVERT: A 514 SER cc_start: 0.8334 (t) cc_final: 0.8020 (p) REVERT: A 528 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7242 (mtmt) REVERT: L 14 SER cc_start: 0.8431 (m) cc_final: 0.7561 (t) REVERT: L 17 MET cc_start: 0.5836 (mtp) cc_final: 0.5588 (mtp) REVERT: L 106 SER cc_start: 0.8451 (t) cc_final: 0.8097 (m) REVERT: L 145 GLU cc_start: 0.7673 (tt0) cc_final: 0.7322 (tt0) REVERT: L 169 TRP cc_start: 0.7418 (m100) cc_final: 0.6971 (m100) REVERT: L 204 GLU cc_start: 0.7756 (tp30) cc_final: 0.7122 (tp30) REVERT: L 206 TRP cc_start: 0.8300 (OUTLIER) cc_final: 0.7993 (t-100) REVERT: H 76 VAL cc_start: 0.8458 (t) cc_final: 0.7991 (m) REVERT: H 92 ASN cc_start: 0.8826 (p0) cc_final: 0.8458 (p0) REVERT: H 122 THR cc_start: 0.8602 (t) cc_final: 0.8258 (p) REVERT: H 181 PHE cc_start: 0.8799 (m-80) cc_final: 0.8509 (m-10) outliers start: 22 outliers final: 18 residues processed: 152 average time/residue: 0.0419 time to fit residues: 8.8125 Evaluate side-chains 156 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 206 TRP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 190 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113552 restraints weight = 7603.618| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.36 r_work: 0.3309 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4918 Z= 0.149 Angle : 0.583 7.609 6723 Z= 0.300 Chirality : 0.046 0.158 747 Planarity : 0.004 0.032 864 Dihedral : 4.925 46.010 683 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.03 % Allowed : 16.76 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.33), residues: 617 helix: -1.85 (0.74), residues: 40 sheet: 0.17 (0.34), residues: 216 loop : -1.33 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.041 0.002 TYR H 55 PHE 0.010 0.002 PHE H 115 TRP 0.011 0.002 TRP H 52 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4910) covalent geometry : angle 0.58254 ( 6707) SS BOND : bond 0.00258 ( 8) SS BOND : angle 0.87712 ( 16) hydrogen bonds : bond 0.03289 ( 153) hydrogen bonds : angle 5.56084 ( 462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.112 Fit side-chains REVERT: A 343 ASN cc_start: 0.8509 (t0) cc_final: 0.8198 (t0) REVERT: A 388 ASN cc_start: 0.8499 (p0) cc_final: 0.8249 (p0) REVERT: A 394 ASN cc_start: 0.7935 (m-40) cc_final: 0.7550 (m-40) REVERT: A 405 ASN cc_start: 0.8252 (t0) cc_final: 0.7958 (t0) REVERT: A 497 PHE cc_start: 0.7628 (m-10) cc_final: 0.7191 (m-10) REVERT: A 514 SER cc_start: 0.8358 (t) cc_final: 0.8038 (p) REVERT: A 528 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7245 (mtmt) REVERT: L 14 SER cc_start: 0.8468 (m) cc_final: 0.7539 (t) REVERT: L 17 MET cc_start: 0.5932 (mtp) cc_final: 0.5620 (mtp) REVERT: L 106 SER cc_start: 0.8455 (t) cc_final: 0.8170 (m) REVERT: L 145 GLU cc_start: 0.7685 (tt0) cc_final: 0.7337 (tt0) REVERT: L 169 TRP cc_start: 0.7426 (m100) cc_final: 0.6993 (m100) REVERT: L 204 GLU cc_start: 0.7775 (tp30) cc_final: 0.7134 (tp30) REVERT: L 206 TRP cc_start: 0.8310 (OUTLIER) cc_final: 0.8001 (t-100) REVERT: H 76 VAL cc_start: 0.8495 (t) cc_final: 0.8041 (m) REVERT: H 92 ASN cc_start: 0.8837 (p0) cc_final: 0.8441 (p0) REVERT: H 115 PHE cc_start: 0.8236 (m-10) cc_final: 0.7983 (m-80) REVERT: H 122 THR cc_start: 0.8587 (t) cc_final: 0.8266 (p) REVERT: H 181 PHE cc_start: 0.8809 (m-80) cc_final: 0.8490 (m-80) outliers start: 27 outliers final: 20 residues processed: 153 average time/residue: 0.0408 time to fit residues: 8.7619 Evaluate side-chains 157 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 206 TRP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.0070 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113656 restraints weight = 7749.378| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.43 r_work: 0.3317 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4918 Z= 0.121 Angle : 0.588 10.091 6723 Z= 0.295 Chirality : 0.045 0.177 747 Planarity : 0.004 0.032 864 Dihedral : 4.528 36.440 681 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.47 % Allowed : 17.88 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.33), residues: 617 helix: -1.78 (0.74), residues: 40 sheet: 0.20 (0.34), residues: 216 loop : -1.34 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.040 0.001 TYR H 55 PHE 0.012 0.001 PHE H 87 TRP 0.010 0.001 TRP H 52 HIS 0.003 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4910) covalent geometry : angle 0.58638 ( 6707) SS BOND : bond 0.00245 ( 8) SS BOND : angle 1.04081 ( 16) hydrogen bonds : bond 0.03104 ( 153) hydrogen bonds : angle 5.35220 ( 462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.121 Fit side-chains REVERT: A 343 ASN cc_start: 0.8522 (t0) cc_final: 0.8210 (t0) REVERT: A 388 ASN cc_start: 0.8482 (p0) cc_final: 0.8238 (p0) REVERT: A 394 ASN cc_start: 0.7947 (m-40) cc_final: 0.7530 (m-40) REVERT: A 405 ASN cc_start: 0.8275 (t0) cc_final: 0.7990 (t0) REVERT: A 514 SER cc_start: 0.8360 (t) cc_final: 0.8056 (p) REVERT: A 528 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7230 (mtmt) REVERT: L 14 SER cc_start: 0.8473 (m) cc_final: 0.7568 (t) REVERT: L 17 MET cc_start: 0.6045 (mtp) cc_final: 0.5713 (mtp) REVERT: L 106 SER cc_start: 0.8398 (t) cc_final: 0.8130 (m) REVERT: L 169 TRP cc_start: 0.7398 (m100) cc_final: 0.7068 (m100) REVERT: L 204 GLU cc_start: 0.7817 (tp30) cc_final: 0.7179 (tp30) REVERT: L 206 TRP cc_start: 0.8288 (t-100) cc_final: 0.7987 (t-100) REVERT: H 19 LEU cc_start: 0.7727 (tp) cc_final: 0.7319 (tt) REVERT: H 76 VAL cc_start: 0.8514 (t) cc_final: 0.8045 (m) REVERT: H 92 ASN cc_start: 0.8821 (p0) cc_final: 0.8379 (p0) REVERT: H 122 THR cc_start: 0.8619 (t) cc_final: 0.8307 (p) REVERT: H 181 PHE cc_start: 0.8820 (m-80) cc_final: 0.8533 (m-80) outliers start: 24 outliers final: 19 residues processed: 151 average time/residue: 0.0507 time to fit residues: 10.5182 Evaluate side-chains 153 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 190 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.137895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112941 restraints weight = 7590.538| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.34 r_work: 0.3291 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4918 Z= 0.177 Angle : 0.616 9.138 6723 Z= 0.312 Chirality : 0.046 0.156 747 Planarity : 0.004 0.031 864 Dihedral : 4.725 36.615 681 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.84 % Allowed : 18.44 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.33), residues: 617 helix: -1.88 (0.74), residues: 40 sheet: 0.25 (0.34), residues: 221 loop : -1.44 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.041 0.002 TYR H 55 PHE 0.012 0.002 PHE A 392 TRP 0.012 0.002 TRP A 353 HIS 0.005 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 4910) covalent geometry : angle 0.61418 ( 6707) SS BOND : bond 0.00259 ( 8) SS BOND : angle 1.07051 ( 16) hydrogen bonds : bond 0.03329 ( 153) hydrogen bonds : angle 5.47041 ( 462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.134 Fit side-chains REVERT: A 343 ASN cc_start: 0.8532 (t0) cc_final: 0.8260 (t0) REVERT: A 388 ASN cc_start: 0.8461 (p0) cc_final: 0.8253 (p0) REVERT: A 394 ASN cc_start: 0.7940 (m-40) cc_final: 0.7532 (m-40) REVERT: A 405 ASN cc_start: 0.8290 (t0) cc_final: 0.7991 (t0) REVERT: A 497 PHE cc_start: 0.7580 (m-10) cc_final: 0.7170 (m-10) REVERT: A 514 SER cc_start: 0.8367 (t) cc_final: 0.8027 (p) REVERT: A 528 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7290 (mtmt) REVERT: L 14 SER cc_start: 0.8559 (m) cc_final: 0.7599 (t) REVERT: L 17 MET cc_start: 0.5945 (mtp) cc_final: 0.5611 (mtp) REVERT: L 106 SER cc_start: 0.8508 (t) cc_final: 0.8161 (m) REVERT: L 145 GLU cc_start: 0.7844 (tt0) cc_final: 0.7576 (tt0) REVERT: L 169 TRP cc_start: 0.7473 (m100) cc_final: 0.7110 (m100) REVERT: L 204 GLU cc_start: 0.7779 (tp30) cc_final: 0.7134 (tp30) REVERT: L 206 TRP cc_start: 0.8317 (OUTLIER) cc_final: 0.8001 (t-100) REVERT: H 19 LEU cc_start: 0.7741 (tp) cc_final: 0.7326 (tt) REVERT: H 76 VAL cc_start: 0.8522 (t) cc_final: 0.8053 (m) REVERT: H 92 ASN cc_start: 0.8847 (p0) cc_final: 0.8479 (p0) REVERT: H 122 THR cc_start: 0.8567 (t) cc_final: 0.8225 (p) REVERT: H 167 VAL cc_start: 0.8449 (m) cc_final: 0.8209 (t) REVERT: H 181 PHE cc_start: 0.8829 (m-80) cc_final: 0.8487 (m-80) outliers start: 26 outliers final: 22 residues processed: 146 average time/residue: 0.0406 time to fit residues: 8.2015 Evaluate side-chains 152 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 206 TRP Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 190 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.0050 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.138835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113540 restraints weight = 7745.697| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.38 r_work: 0.3303 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4918 Z= 0.130 Angle : 0.630 17.932 6723 Z= 0.306 Chirality : 0.046 0.233 747 Planarity : 0.004 0.032 864 Dihedral : 4.601 36.808 681 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.28 % Allowed : 18.81 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.32), residues: 617 helix: -1.85 (0.74), residues: 40 sheet: 0.30 (0.34), residues: 217 loop : -1.42 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.039 0.002 TYR H 55 PHE 0.012 0.001 PHE H 87 TRP 0.015 0.001 TRP H 52 HIS 0.003 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4910) covalent geometry : angle 0.62927 ( 6707) SS BOND : bond 0.00190 ( 8) SS BOND : angle 0.87552 ( 16) hydrogen bonds : bond 0.03082 ( 153) hydrogen bonds : angle 5.31297 ( 462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.173 Fit side-chains REVERT: A 343 ASN cc_start: 0.8503 (t0) cc_final: 0.8236 (t0) REVERT: A 394 ASN cc_start: 0.7900 (m-40) cc_final: 0.7461 (m-40) REVERT: A 405 ASN cc_start: 0.8253 (t0) cc_final: 0.7958 (t0) REVERT: A 514 SER cc_start: 0.8335 (t) cc_final: 0.8014 (p) REVERT: A 528 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7231 (mtmt) REVERT: L 14 SER cc_start: 0.8547 (m) cc_final: 0.7553 (t) REVERT: L 17 MET cc_start: 0.5962 (mtp) cc_final: 0.5633 (mtp) REVERT: L 106 SER cc_start: 0.8453 (t) cc_final: 0.8152 (m) REVERT: L 145 GLU cc_start: 0.7837 (tt0) cc_final: 0.7527 (tt0) REVERT: L 169 TRP cc_start: 0.7467 (m100) cc_final: 0.7208 (m100) REVERT: L 204 GLU cc_start: 0.7724 (tp30) cc_final: 0.7083 (tp30) REVERT: L 206 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.8015 (t-100) REVERT: H 19 LEU cc_start: 0.7743 (tp) cc_final: 0.7325 (tt) REVERT: H 76 VAL cc_start: 0.8519 (t) cc_final: 0.8020 (m) REVERT: H 92 ASN cc_start: 0.8831 (p0) cc_final: 0.8423 (p0) REVERT: H 122 THR cc_start: 0.8590 (t) cc_final: 0.8253 (p) REVERT: H 181 PHE cc_start: 0.8835 (m-80) cc_final: 0.8550 (m-80) outliers start: 23 outliers final: 22 residues processed: 144 average time/residue: 0.0443 time to fit residues: 8.7432 Evaluate side-chains 151 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 206 TRP Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 190 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110840 restraints weight = 7668.426| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.36 r_work: 0.3249 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4918 Z= 0.240 Angle : 0.689 15.681 6723 Z= 0.344 Chirality : 0.049 0.237 747 Planarity : 0.004 0.044 864 Dihedral : 5.079 37.769 681 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 5.21 % Allowed : 18.44 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.33), residues: 617 helix: -2.17 (0.73), residues: 40 sheet: 0.25 (0.34), residues: 223 loop : -1.47 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.042 0.002 TYR H 55 PHE 0.015 0.002 PHE A 338 TRP 0.018 0.002 TRP A 353 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 4910) covalent geometry : angle 0.68736 ( 6707) SS BOND : bond 0.00384 ( 8) SS BOND : angle 1.22385 ( 16) hydrogen bonds : bond 0.03649 ( 153) hydrogen bonds : angle 5.66104 ( 462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 343 ASN cc_start: 0.8534 (t0) cc_final: 0.8305 (t0) REVERT: A 394 ASN cc_start: 0.8007 (m-40) cc_final: 0.7568 (m-40) REVERT: A 405 ASN cc_start: 0.8279 (t0) cc_final: 0.7979 (t0) REVERT: A 497 PHE cc_start: 0.7602 (m-10) cc_final: 0.7215 (m-10) REVERT: A 514 SER cc_start: 0.8340 (t) cc_final: 0.7925 (p) REVERT: A 528 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7305 (mtmt) REVERT: L 14 SER cc_start: 0.8675 (m) cc_final: 0.7704 (t) REVERT: L 17 MET cc_start: 0.6090 (mtp) cc_final: 0.5761 (mtp) REVERT: L 106 SER cc_start: 0.8535 (t) cc_final: 0.8235 (m) REVERT: L 145 GLU cc_start: 0.7869 (tt0) cc_final: 0.7535 (tt0) REVERT: L 169 TRP cc_start: 0.7521 (m100) cc_final: 0.7168 (m100) REVERT: L 196 SER cc_start: 0.8169 (p) cc_final: 0.7948 (p) REVERT: L 204 GLU cc_start: 0.7915 (tp30) cc_final: 0.7271 (tp30) REVERT: L 206 TRP cc_start: 0.8339 (OUTLIER) cc_final: 0.8067 (t-100) REVERT: H 19 LEU cc_start: 0.7769 (tp) cc_final: 0.7337 (tt) REVERT: H 76 VAL cc_start: 0.8559 (t) cc_final: 0.8061 (m) REVERT: H 92 ASN cc_start: 0.8858 (p0) cc_final: 0.8542 (p0) REVERT: H 122 THR cc_start: 0.8560 (t) cc_final: 0.8187 (p) REVERT: H 167 VAL cc_start: 0.8433 (m) cc_final: 0.8174 (t) REVERT: H 181 PHE cc_start: 0.8835 (m-80) cc_final: 0.8498 (m-80) outliers start: 28 outliers final: 23 residues processed: 148 average time/residue: 0.0472 time to fit residues: 9.4843 Evaluate side-chains 155 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 206 TRP Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 46 optimal weight: 0.4980 chunk 57 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.137977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113001 restraints weight = 7705.617| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.48 r_work: 0.3293 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4918 Z= 0.116 Angle : 0.633 16.855 6723 Z= 0.308 Chirality : 0.046 0.226 747 Planarity : 0.004 0.032 864 Dihedral : 4.701 37.441 681 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.72 % Allowed : 20.11 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.33), residues: 617 helix: -2.01 (0.74), residues: 40 sheet: 0.32 (0.34), residues: 221 loop : -1.39 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.037 0.001 TYR H 55 PHE 0.013 0.002 PHE A 338 TRP 0.017 0.001 TRP H 52 HIS 0.003 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4910) covalent geometry : angle 0.63217 ( 6707) SS BOND : bond 0.00104 ( 8) SS BOND : angle 0.76949 ( 16) hydrogen bonds : bond 0.03022 ( 153) hydrogen bonds : angle 5.35436 ( 462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 343 ASN cc_start: 0.8467 (t0) cc_final: 0.8046 (t0) REVERT: A 387 LEU cc_start: 0.8430 (mt) cc_final: 0.8182 (mt) REVERT: A 394 ASN cc_start: 0.7972 (m-40) cc_final: 0.7556 (m-40) REVERT: A 405 ASN cc_start: 0.8221 (t0) cc_final: 0.7911 (t0) REVERT: A 497 PHE cc_start: 0.7532 (m-10) cc_final: 0.6685 (m-10) REVERT: A 514 SER cc_start: 0.8327 (t) cc_final: 0.7974 (p) REVERT: A 528 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7228 (mtmt) REVERT: L 14 SER cc_start: 0.8542 (m) cc_final: 0.7554 (t) REVERT: L 17 MET cc_start: 0.6071 (mtp) cc_final: 0.5738 (mtp) REVERT: L 145 GLU cc_start: 0.7846 (tt0) cc_final: 0.7523 (tt0) REVERT: L 169 TRP cc_start: 0.7513 (m100) cc_final: 0.7206 (m100) REVERT: L 204 GLU cc_start: 0.7787 (tp30) cc_final: 0.7130 (tp30) REVERT: L 206 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.8020 (t-100) REVERT: H 19 LEU cc_start: 0.7729 (tp) cc_final: 0.7299 (tt) REVERT: H 36 VAL cc_start: 0.5118 (m) cc_final: 0.3814 (p) REVERT: H 76 VAL cc_start: 0.8543 (t) cc_final: 0.8057 (m) REVERT: H 92 ASN cc_start: 0.8829 (p0) cc_final: 0.8401 (p0) REVERT: H 122 THR cc_start: 0.8604 (t) cc_final: 0.8259 (p) REVERT: H 181 PHE cc_start: 0.8838 (m-80) cc_final: 0.8566 (m-80) outliers start: 20 outliers final: 19 residues processed: 144 average time/residue: 0.0406 time to fit residues: 8.1505 Evaluate side-chains 153 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 206 TRP Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.0030 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.137502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112462 restraints weight = 7732.721| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.50 r_work: 0.3280 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4918 Z= 0.138 Angle : 0.635 16.043 6723 Z= 0.310 Chirality : 0.046 0.229 747 Planarity : 0.004 0.032 864 Dihedral : 4.693 37.460 681 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.91 % Allowed : 19.93 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.33), residues: 617 helix: -2.00 (0.74), residues: 40 sheet: 0.35 (0.34), residues: 221 loop : -1.38 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.038 0.002 TYR H 55 PHE 0.011 0.002 PHE A 392 TRP 0.014 0.001 TRP H 52 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4910) covalent geometry : angle 0.63465 ( 6707) SS BOND : bond 0.00162 ( 8) SS BOND : angle 0.82358 ( 16) hydrogen bonds : bond 0.03077 ( 153) hydrogen bonds : angle 5.35611 ( 462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1312.99 seconds wall clock time: 23 minutes 7.99 seconds (1387.99 seconds total)