Starting phenix.real_space_refine on Tue Aug 4 19:43:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/27ke_81217/08_2026/27ke_81217_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/27ke_81217/08_2026/27ke_81217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/27ke_81217/08_2026/27ke_81217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/27ke_81217/08_2026/27ke_81217.map" model { file = "/net/cci-nas-00/data/ceres_data/27ke_81217/08_2026/27ke_81217_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/27ke_81217/08_2026/27ke_81217_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 40 5.16 5 C 4114 2.51 5 N 1065 2.21 5 O 1215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6434 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4888 Classifications: {'peptide': 597} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 571} Chain: "B" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1546 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Time building chain proxies: 1.31, per 1000 atoms: 0.20 Number of scatterers: 6434 At special positions: 0 Unit cell: (73.44, 83.13, 120.87, 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 40 16.00 O 1215 8.00 N 1065 7.00 C 4114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 513 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 29 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 100 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 156 " 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: 0.49 Conformation dependent library (CDL) restraints added in 300.4 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 58.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 2 through 35 Processing helix chain 'A' and resid 37 through 64 Processing helix chain 'A' and resid 72 through 84 removed outlier: 3.787A pdb=" N ASP A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.700A pdb=" N SER A 88 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 112 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 139 through 176 Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 200 through 234 removed outlier: 3.642A pdb=" N VAL A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.596A pdb=" N TRP A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 369 Processing helix chain 'A' and resid 370 through 371 No H-bonds generated for 'chain 'A' and resid 370 through 371' Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 486 through 492 Processing helix chain 'A' and resid 495 through 516 removed outlier: 3.866A pdb=" N TYR A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 530 through 544 removed outlier: 4.137A pdb=" N GLY A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 557 Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.665A pdb=" N VAL B 9 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 removed outlier: 3.641A pdb=" N TRP B 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 51 through 56 removed outlier: 4.393A pdb=" N ASN B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.779A pdb=" N SER B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 246 removed outlier: 6.043A pdb=" N LEU A 245 " --> pdb=" O VAL A 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 335 removed outlier: 6.415A pdb=" N ASP A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.845A pdb=" N ASN B 22 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 67 " --> pdb=" O ASN B 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 142 339 hydrogen bonds defined for protein. 972 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: 1.08 Time building geometry restraints manager: 0.68 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: 2056 1.34 - 1.46: 1734 1.46 - 1.58: 2765 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 6619 Sorted by residual: bond pdb=" C ARG A 159 " pdb=" N PRO A 160 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.06e+00 bond pdb=" C LYS A 216 " pdb=" N PRO A 217 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.36e-02 5.41e+03 1.36e+00 bond pdb=" C GLU A 572 " pdb=" N PRO A 573 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.36e-02 5.41e+03 1.31e+00 bond pdb=" CA VAL A 347 " pdb=" CB VAL A 347 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.05e-02 9.07e+03 1.25e+00 bond pdb=" C TYR A 193 " pdb=" N PRO A 194 " ideal model delta sigma weight residual 1.335 1.344 -0.009 8.70e-03 1.32e+04 1.14e+00 ... (remaining 6614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 8652 1.34 - 2.68: 281 2.68 - 4.01: 54 4.01 - 5.35: 10 5.35 - 6.69: 5 Bond angle restraints: 9002 Sorted by residual: angle pdb=" N ASN A 188 " pdb=" CA ASN A 188 " pdb=" C ASN A 188 " ideal model delta sigma weight residual 114.56 109.10 5.46 1.27e+00 6.20e-01 1.85e+01 angle pdb=" N TYR A 596 " pdb=" CA TYR A 596 " pdb=" C TYR A 596 " ideal model delta sigma weight residual 114.16 109.82 4.34 1.48e+00 4.57e-01 8.61e+00 angle pdb=" N ASP A 592 " pdb=" CA ASP A 592 " pdb=" C ASP A 592 " ideal model delta sigma weight residual 114.56 110.84 3.72 1.27e+00 6.20e-01 8.59e+00 angle pdb=" CA TYR A 368 " pdb=" CB TYR A 368 " pdb=" CG TYR A 368 " ideal model delta sigma weight residual 113.90 119.12 -5.22 1.80e+00 3.09e-01 8.41e+00 angle pdb=" CA ASN A 188 " pdb=" C ASN A 188 " pdb=" N TYR A 189 " ideal model delta sigma weight residual 119.26 116.02 3.24 1.14e+00 7.69e-01 8.07e+00 ... (remaining 8997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 3341 18.07 - 36.14: 428 36.14 - 54.21: 109 54.21 - 72.28: 15 72.28 - 90.34: 7 Dihedral angle restraints: 3900 sinusoidal: 1561 harmonic: 2339 Sorted by residual: dihedral pdb=" CA CYS A 327 " pdb=" C CYS A 327 " pdb=" N HIS A 328 " pdb=" CA HIS A 328 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CB CYS B 59 " pdb=" SG CYS B 59 " pdb=" SG CYS B 193 " pdb=" CB CYS B 193 " ideal model delta sinusoidal sigma weight residual -86.00 -54.33 -31.67 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CA ASP A 192 " pdb=" C ASP A 192 " pdb=" N TYR A 193 " pdb=" CA TYR A 193 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 565 0.028 - 0.057: 248 0.057 - 0.085: 78 0.085 - 0.114: 46 0.114 - 0.142: 5 Chirality restraints: 942 Sorted by residual: chirality pdb=" CA ILE A 138 " pdb=" N ILE A 138 " pdb=" C ILE A 138 " pdb=" CB ILE A 138 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA VAL A 326 " pdb=" N VAL A 326 " pdb=" C VAL A 326 " pdb=" CB VAL A 326 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA TYR A 368 " pdb=" N TYR A 368 " pdb=" C TYR A 368 " pdb=" CB TYR A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 939 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 14 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C PHE A 14 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE A 14 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A 15 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 18 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C ALA A 18 " 0.026 2.00e-02 2.50e+03 pdb=" O ALA A 18 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU A 19 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 492 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C ASP A 492 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP A 492 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 493 " -0.008 2.00e-02 2.50e+03 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1144 2.77 - 3.30: 6113 3.30 - 3.83: 11008 3.83 - 4.37: 13022 4.37 - 4.90: 22484 Nonbonded interactions: 53771 Sorted by model distance: nonbonded pdb=" OH TYR A 304 " pdb=" OE2 GLU A 542 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP B 110 " pdb=" OH TYR B 119 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR A 23 " pdb=" OG1 THR B 168 " model vdw 2.244 3.040 nonbonded pdb=" O LEU A 316 " pdb=" OG1 THR A 345 " model vdw 2.314 3.040 nonbonded pdb=" O THR A 100 " pdb=" OG1 THR A 104 " model vdw 2.338 3.040 ... (remaining 53766 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: 1.960 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.570 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 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 : 0.003 0.041 6626 Z= 0.160 Angle : 0.602 6.691 9016 Z= 0.363 Chirality : 0.039 0.142 942 Planarity : 0.004 0.032 1161 Dihedral : 17.074 90.344 2381 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.14 % Allowed : 20.26 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.30), residues: 788 helix: 1.51 (0.26), residues: 405 sheet: 1.58 (0.78), residues: 49 loop : -0.20 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 25 TYR 0.018 0.001 TYR A 368 PHE 0.018 0.001 PHE A 352 TRP 0.012 0.001 TRP A 145 HIS 0.007 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 ( 6619) covalent geometry : angle 0.60197 / 0.36 ( 9002) SS BOND : bond 0.00180 / 0.08 ( 7) SS BOND : angle 0.57317 / 0.35 ( 14) hydrogen bonds : bond 0.14372 / 9.27 ( 339) hydrogen bonds : angle 5.57707 / 4.14 ( 972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.253 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.0830 time to fit residues: 10.5788 Evaluate side-chains 90 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS ** A 582 ASN ** 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 = 0.3512 r_free = 0.3512 target = 0.129908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.101423 restraints weight = 8925.690| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.86 r_work: 0.2987 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6626 Z= 0.111 Angle : 0.465 5.358 9016 Z= 0.249 Chirality : 0.039 0.145 942 Planarity : 0.003 0.030 1161 Dihedral : 3.945 38.260 878 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.46 % Allowed : 17.95 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.41 (0.30), residues: 788 helix: 1.71 (0.25), residues: 410 sheet: 1.20 (0.75), residues: 49 loop : -0.04 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.019 0.001 TYR A 368 PHE 0.014 0.001 PHE A 352 TRP 0.010 0.001 TRP A 145 HIS 0.005 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 6619) covalent geometry : angle 0.46474 / 0.25 ( 9002) SS BOND : bond 0.00248 / 0.13 ( 7) SS BOND : angle 0.61994 / 0.37 ( 14) hydrogen bonds : bond 0.05187 / 3.44 ( 339) hydrogen bonds : angle 4.66807 / 3.48 ( 972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: B 64 TYR cc_start: 0.7388 (m-80) cc_final: 0.6960 (m-80) outliers start: 17 outliers final: 9 residues processed: 113 average time/residue: 0.0691 time to fit residues: 10.8314 Evaluate side-chains 103 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.0470 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 HIS ** A 582 ASN ** 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 = 0.3509 r_free = 0.3509 target = 0.130012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.101463 restraints weight = 8935.739| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.89 r_work: 0.2993 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6626 Z= 0.110 Angle : 0.450 5.509 9016 Z= 0.238 Chirality : 0.039 0.146 942 Planarity : 0.003 0.028 1161 Dihedral : 3.644 19.109 878 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.60 % Allowed : 18.38 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.52 (0.29), residues: 788 helix: 1.83 (0.25), residues: 410 sheet: 1.23 (0.75), residues: 49 loop : -0.01 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 227 TYR 0.019 0.001 TYR A 368 PHE 0.015 0.001 PHE A 352 TRP 0.010 0.001 TRP A 145 HIS 0.004 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 6619) covalent geometry : angle 0.45005 / 0.24 ( 9002) SS BOND : bond 0.00184 / 0.09 ( 7) SS BOND : angle 0.56443 / 0.34 ( 14) hydrogen bonds : bond 0.04915 / 3.26 ( 339) hydrogen bonds : angle 4.46315 / 3.33 ( 972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 107 THR cc_start: 0.8317 (m) cc_final: 0.8031 (p) REVERT: A 501 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7624 (ttp-170) REVERT: B 64 TYR cc_start: 0.7376 (m-80) cc_final: 0.7042 (m-80) REVERT: B 126 LYS cc_start: 0.7933 (mptt) cc_final: 0.7714 (mmtm) outliers start: 18 outliers final: 16 residues processed: 115 average time/residue: 0.0782 time to fit residues: 12.3591 Evaluate side-chains 104 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** 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 = 0.3513 r_free = 0.3513 target = 0.130318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101431 restraints weight = 9022.883| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.91 r_work: 0.2995 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6626 Z= 0.105 Angle : 0.439 5.248 9016 Z= 0.232 Chirality : 0.039 0.148 942 Planarity : 0.003 0.027 1161 Dihedral : 3.471 17.474 878 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.32 % Allowed : 18.67 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.60 (0.29), residues: 788 helix: 1.92 (0.25), residues: 411 sheet: 1.20 (0.75), residues: 49 loop : -0.00 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 227 TYR 0.018 0.001 TYR A 368 PHE 0.012 0.001 PHE A 352 TRP 0.010 0.001 TRP A 145 HIS 0.003 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 ( 6619) covalent geometry : angle 0.43901 / 0.23 ( 9002) SS BOND : bond 0.00162 / 0.08 ( 7) SS BOND : angle 0.50794 / 0.30 ( 14) hydrogen bonds : bond 0.04722 / 3.13 ( 339) hydrogen bonds : angle 4.35156 / 3.25 ( 972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 399 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7524 (tp40) REVERT: A 501 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7634 (ttp-170) REVERT: B 64 TYR cc_start: 0.7367 (m-80) cc_final: 0.6999 (m-80) REVERT: B 126 LYS cc_start: 0.7911 (mptt) cc_final: 0.7703 (mmtm) outliers start: 16 outliers final: 13 residues processed: 115 average time/residue: 0.0855 time to fit residues: 13.1096 Evaluate side-chains 109 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN ** A 582 ASN ** 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 = 0.3505 r_free = 0.3505 target = 0.129465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.101772 restraints weight = 9092.566| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.83 r_work: 0.2985 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6626 Z= 0.113 Angle : 0.450 5.306 9016 Z= 0.237 Chirality : 0.039 0.145 942 Planarity : 0.003 0.026 1161 Dihedral : 3.481 17.409 878 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.18 % Allowed : 17.66 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.66 (0.29), residues: 788 helix: 1.96 (0.25), residues: 410 sheet: 1.25 (0.74), residues: 49 loop : 0.05 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 151 TYR 0.019 0.001 TYR A 368 PHE 0.014 0.001 PHE A 352 TRP 0.009 0.001 TRP A 145 HIS 0.003 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6619) covalent geometry : angle 0.44956 / 0.24 ( 9002) SS BOND : bond 0.00163 / 0.08 ( 7) SS BOND : angle 0.47943 / 0.29 ( 14) hydrogen bonds : bond 0.04805 / 3.19 ( 339) hydrogen bonds : angle 4.32454 / 3.24 ( 972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 399 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7525 (tp40) REVERT: A 501 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7594 (ttp-170) outliers start: 22 outliers final: 18 residues processed: 114 average time/residue: 0.0844 time to fit residues: 12.9629 Evaluate side-chains 114 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN ** A 582 ASN ** 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 = 0.3485 r_free = 0.3485 target = 0.128072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.099027 restraints weight = 9049.192| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.94 r_work: 0.2953 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6626 Z= 0.130 Angle : 0.468 5.629 9016 Z= 0.246 Chirality : 0.040 0.149 942 Planarity : 0.003 0.025 1161 Dihedral : 3.581 17.978 878 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.18 % Allowed : 18.38 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.60 (0.29), residues: 788 helix: 1.90 (0.25), residues: 410 sheet: 1.33 (0.74), residues: 49 loop : 0.01 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.019 0.001 TYR A 368 PHE 0.010 0.001 PHE A 291 TRP 0.010 0.001 TRP A 145 HIS 0.004 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6619) covalent geometry : angle 0.46828 / 0.25 ( 9002) SS BOND : bond 0.00185 / 0.09 ( 7) SS BOND : angle 0.48853 / 0.30 ( 14) hydrogen bonds : bond 0.05139 / 3.41 ( 339) hydrogen bonds : angle 4.35048 / 3.26 ( 972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 399 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7563 (tp40) REVERT: A 501 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7727 (ttp-170) REVERT: B 126 LYS cc_start: 0.7905 (mptt) cc_final: 0.7679 (mmtm) outliers start: 22 outliers final: 18 residues processed: 110 average time/residue: 0.0832 time to fit residues: 12.3373 Evaluate side-chains 109 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN ** A 582 ASN ** 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 = 0.3498 r_free = 0.3498 target = 0.129081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.100518 restraints weight = 8991.495| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.88 r_work: 0.2986 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6626 Z= 0.111 Angle : 0.454 5.372 9016 Z= 0.239 Chirality : 0.039 0.141 942 Planarity : 0.003 0.026 1161 Dihedral : 3.492 17.465 878 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.04 % Allowed : 18.09 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.66 (0.29), residues: 788 helix: 1.96 (0.25), residues: 410 sheet: 1.31 (0.74), residues: 49 loop : 0.04 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.019 0.001 TYR A 368 PHE 0.009 0.001 PHE A 352 TRP 0.009 0.001 TRP A 145 HIS 0.003 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 6619) covalent geometry : angle 0.45374 / 0.24 ( 9002) SS BOND : bond 0.00151 / 0.08 ( 7) SS BOND : angle 0.47359 / 0.29 ( 14) hydrogen bonds : bond 0.04789 / 3.18 ( 339) hydrogen bonds : angle 4.30747 / 3.23 ( 972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 501 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7646 (ttp-170) REVERT: A 563 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.7820 (m-40) REVERT: B 126 LYS cc_start: 0.7900 (mptt) cc_final: 0.7696 (mmtm) outliers start: 21 outliers final: 15 residues processed: 113 average time/residue: 0.0811 time to fit residues: 12.4809 Evaluate side-chains 108 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 GLN A 563 ASN A 582 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.098943 restraints weight = 8947.834| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.88 r_work: 0.2953 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6626 Z= 0.134 Angle : 0.482 5.726 9016 Z= 0.254 Chirality : 0.040 0.137 942 Planarity : 0.003 0.025 1161 Dihedral : 3.624 18.009 878 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.33 % Allowed : 18.38 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.57 (0.29), residues: 788 helix: 1.89 (0.25), residues: 410 sheet: 1.26 (0.74), residues: 49 loop : -0.02 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.020 0.001 TYR A 368 PHE 0.014 0.001 PHE A 291 TRP 0.010 0.001 TRP A 145 HIS 0.004 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6619) covalent geometry : angle 0.48182 / 0.25 ( 9002) SS BOND : bond 0.00185 / 0.09 ( 7) SS BOND : angle 0.46564 / 0.30 ( 14) hydrogen bonds : bond 0.05232 / 3.46 ( 339) hydrogen bonds : angle 4.33377 / 3.25 ( 972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 501 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7727 (ttp-170) REVERT: B 126 LYS cc_start: 0.7909 (mptt) cc_final: 0.7709 (mmtm) outliers start: 23 outliers final: 17 residues processed: 105 average time/residue: 0.0827 time to fit residues: 11.7584 Evaluate side-chains 104 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.0070 chunk 58 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 12 optimal weight: 0.0010 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 0.0270 overall best weight: 0.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN A 563 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104947 restraints weight = 9035.817| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.94 r_work: 0.3053 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6626 Z= 0.095 Angle : 0.432 6.160 9016 Z= 0.228 Chirality : 0.038 0.134 942 Planarity : 0.003 0.025 1161 Dihedral : 3.273 15.672 878 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.03 % Allowed : 19.97 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.74 (0.29), residues: 788 helix: 2.03 (0.25), residues: 411 sheet: 1.20 (0.74), residues: 49 loop : 0.08 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.018 0.001 TYR A 368 PHE 0.011 0.001 PHE A 291 TRP 0.009 0.001 TRP A 461 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 ( 6619) covalent geometry : angle 0.43242 / 0.23 ( 9002) SS BOND : bond 0.00095 / 0.05 ( 7) SS BOND : angle 0.39822 / 0.23 ( 14) hydrogen bonds : bond 0.03991 / 2.67 ( 339) hydrogen bonds : angle 4.20026 / 3.15 ( 972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 0.0873 time to fit residues: 12.4401 Evaluate side-chains 101 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 562 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 71 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102532 restraints weight = 8820.546| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.91 r_work: 0.3016 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6626 Z= 0.104 Angle : 0.452 6.501 9016 Z= 0.238 Chirality : 0.039 0.130 942 Planarity : 0.003 0.025 1161 Dihedral : 3.306 15.907 878 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.03 % Allowed : 19.83 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.83 (0.30), residues: 788 helix: 2.15 (0.25), residues: 405 sheet: 1.31 (0.75), residues: 49 loop : 0.09 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 501 TYR 0.019 0.001 TYR A 368 PHE 0.010 0.001 PHE A 291 TRP 0.009 0.001 TRP A 461 HIS 0.003 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 6619) covalent geometry : angle 0.45199 / 0.24 ( 9002) SS BOND : bond 0.00139 / 0.07 ( 7) SS BOND : angle 0.41695 / 0.25 ( 14) hydrogen bonds : bond 0.04431 / 2.95 ( 339) hydrogen bonds : angle 4.18444 / 3.14 ( 972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 GLU cc_start: 0.7293 (tp30) cc_final: 0.7069 (tp30) outliers start: 14 outliers final: 13 residues processed: 101 average time/residue: 0.0757 time to fit residues: 10.1755 Evaluate side-chains 105 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.098709 restraints weight = 8970.106| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.94 r_work: 0.2947 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6626 Z= 0.146 Angle : 0.503 6.502 9016 Z= 0.265 Chirality : 0.041 0.134 942 Planarity : 0.003 0.026 1161 Dihedral : 3.626 17.373 878 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.03 % Allowed : 19.83 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.67 (0.29), residues: 788 helix: 1.97 (0.25), residues: 405 sheet: 1.40 (0.76), residues: 49 loop : 0.05 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 501 TYR 0.020 0.001 TYR A 368 PHE 0.012 0.001 PHE A 291 TRP 0.011 0.001 TRP A 145 HIS 0.004 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 6619) covalent geometry : angle 0.50303 / 0.27 ( 9002) SS BOND : bond 0.00207 / 0.10 ( 7) SS BOND : angle 0.47940 / 0.31 ( 14) hydrogen bonds : bond 0.05345 / 3.54 ( 339) hydrogen bonds : angle 4.32386 / 3.25 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.99 seconds wall clock time: 32 minutes 15.87 seconds (1935.87 seconds total)