Starting phenix.real_space_refine on Tue Aug 4 19:45:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/27kf_81218/08_2026/27kf_81218_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/27kf_81218/08_2026/27kf_81218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/27kf_81218/08_2026/27kf_81218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/27kf_81218/08_2026/27kf_81218.map" model { file = "/net/cci-nas-00/data/ceres_data/27kf_81218/08_2026/27kf_81218_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/27kf_81218/08_2026/27kf_81218_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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 39 5.16 5 C 4115 2.51 5 N 1064 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 3 residue(s): 0.01s 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: 6433 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4887 Classifications: {'peptide': 597} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, '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: 1.18, per 1000 atoms: 0.18 Number of scatterers: 6433 At special positions: 0 Unit cell: (75.04, 87.77, 122.61, 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 39 16.00 O 1215 8.00 N 1064 7.00 C 4115 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=2.01 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: 0.29 Conformation dependent library (CDL) restraints added in 223.3 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 4 sheets defined 58.6% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 34 Processing helix chain 'A' and resid 37 through 64 Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.542A pdb=" N SER A 88 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.785A pdb=" N CYS A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 139 through 176 removed outlier: 3.590A pdb=" N ARG A 151 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 200 through 235 removed outlier: 3.834A pdb=" N LEU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.701A 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 257 through 260 removed outlier: 4.534A pdb=" N ASN A 260 " --> pdb=" O PHE A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 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 302 removed outlier: 3.558A pdb=" N GLY A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 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 removed outlier: 3.512A pdb=" N ARG A 376 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 395 Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 414 through 429 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 468 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 495 through 517 removed outlier: 4.425A pdb=" N TYR A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 530 through 544 removed outlier: 4.141A 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: 3.641A pdb=" N PHE B 10 " --> pdb=" O PHE B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 39 removed outlier: 3.837A pdb=" N SER B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 removed outlier: 3.630A pdb=" N LEU B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASN B 56 " --> pdb=" O THR B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 52 through 56' Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 170 through 174 Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 246 removed outlier: 5.772A pdb=" N LEU A 245 " --> pdb=" O VAL A 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 333 Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.509A pdb=" N SER B 67 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 182 " --> pdb=" O TYR B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 122 327 hydrogen bonds defined for protein. 936 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: 0.68 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2089 1.36 - 1.50: 1957 1.50 - 1.64: 2510 1.64 - 1.77: 3 1.77 - 1.91: 59 Bond restraints: 6618 Sorted by residual: bond pdb=" CB CYS A 115 " pdb=" SG CYS A 115 " ideal model delta sigma weight residual 1.808 1.912 -0.104 3.30e-02 9.18e+02 9.85e+00 bond pdb=" CG LEU A 422 " pdb=" CD2 LEU A 422 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.39e+00 bond pdb=" N ASP B 95 " pdb=" CA ASP B 95 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.85e+00 bond pdb=" N PRO B 94 " pdb=" CA PRO B 94 " ideal model delta sigma weight residual 1.466 1.496 -0.029 1.24e-02 6.50e+03 5.64e+00 bond pdb=" C GLU A 127 " pdb=" N PRO A 128 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.90e+00 ... (remaining 6613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8879 1.97 - 3.94: 98 3.94 - 5.91: 20 5.91 - 7.88: 2 7.88 - 9.85: 3 Bond angle restraints: 9002 Sorted by residual: angle pdb=" C LEU A 126 " pdb=" N GLU A 127 " pdb=" CA GLU A 127 " ideal model delta sigma weight residual 120.60 126.38 -5.78 1.53e+00 4.27e-01 1.43e+01 angle pdb=" CA CYS A 123 " pdb=" CB CYS A 123 " pdb=" SG CYS A 123 " ideal model delta sigma weight residual 114.40 122.73 -8.33 2.30e+00 1.89e-01 1.31e+01 angle pdb=" CB LEU A 422 " pdb=" CG LEU A 422 " pdb=" CD2 LEU A 422 " ideal model delta sigma weight residual 110.70 100.85 9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C TRP A 444 " pdb=" N MET A 445 " pdb=" CA MET A 445 " ideal model delta sigma weight residual 122.65 117.51 5.14 1.60e+00 3.91e-01 1.03e+01 angle pdb=" CA GLY A 335 " pdb=" C GLY A 335 " pdb=" O GLY A 335 " ideal model delta sigma weight residual 122.37 120.23 2.14 7.30e-01 1.88e+00 8.61e+00 ... (remaining 8997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3268 17.91 - 35.82: 460 35.82 - 53.73: 142 53.73 - 71.64: 21 71.64 - 89.55: 7 Dihedral angle restraints: 3898 sinusoidal: 1559 harmonic: 2339 Sorted by residual: dihedral pdb=" CB CYS A 115 " pdb=" SG CYS A 115 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual 93.00 35.76 57.24 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CA PRO A 128 " pdb=" C PRO A 128 " pdb=" N GLY A 129 " pdb=" CA GLY A 129 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CB CYS B 4 " pdb=" SG CYS B 4 " pdb=" SG CYS B 29 " pdb=" CB CYS B 29 " ideal model delta sinusoidal sigma weight residual 93.00 51.72 41.28 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 3895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 734 0.045 - 0.089: 160 0.089 - 0.133: 45 0.133 - 0.177: 3 0.177 - 0.222: 2 Chirality restraints: 944 Sorted by residual: chirality pdb=" CA CYS A 123 " pdb=" N CYS A 123 " pdb=" C CYS A 123 " pdb=" CB CYS A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LEU B 93 " pdb=" N LEU B 93 " pdb=" C LEU B 93 " pdb=" CB LEU B 93 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PRO A 128 " pdb=" N PRO A 128 " pdb=" C PRO A 128 " pdb=" CB PRO A 128 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 941 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 127 " -0.058 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO A 128 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 128 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 128 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 418 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" CD GLU A 418 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU A 418 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A 418 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 10 " -0.010 2.00e-02 2.50e+03 1.42e-02 3.53e+00 pdb=" CG PHE B 10 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 10 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 10 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 10 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 10 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 10 " 0.001 2.00e-02 2.50e+03 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 586 2.74 - 3.28: 6426 3.28 - 3.82: 10947 3.82 - 4.36: 12476 4.36 - 4.90: 21648 Nonbonded interactions: 52083 Sorted by model distance: nonbonded pdb=" OG1 THR A 117 " pdb=" OD2 ASP A 122 " model vdw 2.203 3.040 nonbonded pdb=" O ILE A 138 " pdb=" OH TYR A 234 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP A 84 " pdb=" OH TYR A 184 " model vdw 2.229 3.040 nonbonded pdb=" O ASN A 61 " pdb=" OG SER A 64 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 199 " pdb=" OD2 ASP A 207 " model vdw 2.244 3.040 ... (remaining 52078 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 6625 Z= 0.161 Angle : 0.568 9.851 9016 Z= 0.305 Chirality : 0.040 0.222 944 Planarity : 0.004 0.089 1160 Dihedral : 18.048 89.555 2379 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.81 % Rotamer: Outliers : 0.58 % Allowed : 27.17 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.30), residues: 788 helix: 1.54 (0.26), residues: 407 sheet: -0.32 (0.80), residues: 49 loop : -0.99 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 159 TYR 0.017 0.001 TYR A 32 PHE 0.025 0.001 PHE B 10 TRP 0.015 0.001 TRP A 577 HIS 0.006 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 6618) covalent geometry : angle 0.56105 / 0.30 ( 9002) SS BOND : bond 0.00845 / 0.44 ( 7) SS BOND : angle 2.28521 / 1.53 ( 14) hydrogen bonds : bond 0.16361 / 10.74 ( 327) hydrogen bonds : angle 5.92528 / 4.34 ( 936) *********************** 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 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 522 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7412 (tp) outliers start: 4 outliers final: 1 residues processed: 90 average time/residue: 0.0585 time to fit residues: 7.2712 Evaluate side-chains 92 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 58 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.0010 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.152742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122483 restraints weight = 10601.380| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.36 r_work: 0.3451 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6625 Z= 0.126 Angle : 0.503 6.704 9016 Z= 0.268 Chirality : 0.041 0.151 944 Planarity : 0.005 0.088 1160 Dihedral : 4.802 47.939 881 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.55 % Favored : 96.32 % Rotamer: Outliers : 2.02 % Allowed : 25.14 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.30), residues: 788 helix: 1.49 (0.25), residues: 415 sheet: -0.17 (0.75), residues: 50 loop : -0.76 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.019 0.001 TYR A 32 PHE 0.014 0.001 PHE B 10 TRP 0.012 0.001 TRP A 577 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6618) covalent geometry : angle 0.50230 / 0.27 ( 9002) SS BOND : bond 0.00420 / 0.22 ( 7) SS BOND : angle 0.99370 / 0.54 ( 14) hydrogen bonds : bond 0.05212 / 3.46 ( 327) hydrogen bonds : angle 4.73002 / 3.44 ( 936) *********************** 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 112 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7785 (mtp) REVERT: A 184 TYR cc_start: 0.7463 (t80) cc_final: 0.7025 (t80) REVERT: A 478 GLU cc_start: 0.5703 (tp30) cc_final: 0.5361 (tp30) REVERT: B 142 GLN cc_start: 0.5667 (OUTLIER) cc_final: 0.4685 (pp30) outliers start: 14 outliers final: 5 residues processed: 107 average time/residue: 0.0573 time to fit residues: 8.2047 Evaluate side-chains 98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 142 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.153600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123201 restraints weight = 10542.323| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.39 r_work: 0.3452 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6625 Z= 0.116 Angle : 0.483 6.137 9016 Z= 0.256 Chirality : 0.040 0.148 944 Planarity : 0.004 0.091 1160 Dihedral : 4.404 44.513 879 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 2.46 % Allowed : 24.86 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.30), residues: 788 helix: 1.58 (0.25), residues: 415 sheet: -0.12 (0.74), residues: 49 loop : -0.71 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.018 0.001 TYR A 368 PHE 0.011 0.001 PHE A 506 TRP 0.010 0.001 TRP B 21 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 6618) covalent geometry : angle 0.48230 / 0.26 ( 9002) SS BOND : bond 0.00397 / 0.21 ( 7) SS BOND : angle 0.92801 / 0.57 ( 14) hydrogen bonds : bond 0.04913 / 3.25 ( 327) hydrogen bonds : angle 4.52724 / 3.30 ( 936) *********************** 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 125 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 ARG cc_start: 0.6487 (ttm-80) cc_final: 0.6275 (ttm-80) REVERT: A 184 TYR cc_start: 0.7512 (t80) cc_final: 0.7098 (t80) REVERT: A 478 GLU cc_start: 0.5557 (tp30) cc_final: 0.5276 (tp30) REVERT: B 119 TYR cc_start: 0.7262 (m-80) cc_final: 0.7025 (m-80) outliers start: 17 outliers final: 7 residues processed: 121 average time/residue: 0.0562 time to fit residues: 9.3028 Evaluate side-chains 105 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.151461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121140 restraints weight = 10557.613| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.37 r_work: 0.3421 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6625 Z= 0.144 Angle : 0.529 7.817 9016 Z= 0.276 Chirality : 0.041 0.155 944 Planarity : 0.005 0.096 1160 Dihedral : 4.518 45.632 879 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.07 % Rotamer: Outliers : 3.47 % Allowed : 24.42 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.30), residues: 788 helix: 1.48 (0.26), residues: 415 sheet: 0.04 (0.72), residues: 50 loop : -0.69 (0.36), residues: 323 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 0.015 0.001 PHE A 506 TRP 0.018 0.001 TRP B 21 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 6618) covalent geometry : angle 0.52804 / 0.28 ( 9002) SS BOND : bond 0.00348 / 0.18 ( 7) SS BOND : angle 0.83289 / 0.55 ( 14) hydrogen bonds : bond 0.05363 / 3.57 ( 327) hydrogen bonds : angle 4.61424 / 3.37 ( 936) *********************** 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 124 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.7558 (t80) cc_final: 0.7130 (t80) REVERT: A 399 GLN cc_start: 0.7133 (tp40) cc_final: 0.6924 (tp40) REVERT: A 522 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7240 (tp) REVERT: B 142 GLN cc_start: 0.5691 (OUTLIER) cc_final: 0.5195 (pp30) REVERT: B 160 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7789 (tp) outliers start: 24 outliers final: 13 residues processed: 118 average time/residue: 0.0613 time to fit residues: 9.7503 Evaluate side-chains 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 160 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 0.0060 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122829 restraints weight = 10576.072| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.37 r_work: 0.3442 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 6625 Z= 0.113 Angle : 0.500 7.181 9016 Z= 0.259 Chirality : 0.039 0.151 944 Planarity : 0.005 0.098 1160 Dihedral : 4.340 44.196 879 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.94 % Rotamer: Outliers : 3.03 % Allowed : 24.71 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.30), residues: 788 helix: 1.67 (0.26), residues: 406 sheet: -0.09 (0.73), residues: 49 loop : -0.83 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 159 TYR 0.017 0.001 TYR A 368 PHE 0.014 0.001 PHE A 506 TRP 0.020 0.001 TRP B 21 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 6618) covalent geometry : angle 0.50003 / 0.26 ( 9002) SS BOND : bond 0.00364 / 0.19 ( 7) SS BOND : angle 0.70867 / 0.48 ( 14) hydrogen bonds : bond 0.04768 / 3.15 ( 327) hydrogen bonds : angle 4.52531 / 3.30 ( 936) *********************** 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 118 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.7569 (t80) cc_final: 0.7130 (t80) REVERT: A 446 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8653 (t) REVERT: A 540 LEU cc_start: 0.8220 (tp) cc_final: 0.7961 (tt) REVERT: A 569 HIS cc_start: 0.7432 (m90) cc_final: 0.7184 (m170) REVERT: B 142 GLN cc_start: 0.5757 (OUTLIER) cc_final: 0.5315 (pt0) REVERT: B 160 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7760 (tp) outliers start: 21 outliers final: 14 residues processed: 116 average time/residue: 0.0600 time to fit residues: 9.3305 Evaluate side-chains 112 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 160 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.150918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120660 restraints weight = 10546.824| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.36 r_work: 0.3413 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6625 Z= 0.145 Angle : 0.529 8.053 9016 Z= 0.277 Chirality : 0.041 0.153 944 Planarity : 0.005 0.099 1160 Dihedral : 4.484 45.999 879 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.69 % Rotamer: Outliers : 3.32 % Allowed : 25.00 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.30), residues: 788 helix: 1.57 (0.26), residues: 407 sheet: -0.03 (0.72), residues: 50 loop : -0.84 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 159 TYR 0.018 0.001 TYR A 368 PHE 0.019 0.001 PHE A 506 TRP 0.016 0.001 TRP B 21 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 6618) covalent geometry : angle 0.52894 / 0.28 ( 9002) SS BOND : bond 0.00316 / 0.16 ( 7) SS BOND : angle 0.79669 / 0.57 ( 14) hydrogen bonds : bond 0.05375 / 3.58 ( 327) hydrogen bonds : angle 4.58877 / 3.35 ( 936) *********************** 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 115 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.7585 (t80) cc_final: 0.7137 (t80) REVERT: A 200 SER cc_start: 0.8092 (t) cc_final: 0.7788 (m) REVERT: A 522 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7189 (tp) REVERT: B 142 GLN cc_start: 0.5615 (OUTLIER) cc_final: 0.5155 (pt0) REVERT: B 160 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7769 (tp) outliers start: 23 outliers final: 15 residues processed: 110 average time/residue: 0.0581 time to fit residues: 8.7622 Evaluate side-chains 109 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 160 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 0.0370 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS A 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123874 restraints weight = 10513.972| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.34 r_work: 0.3461 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 6625 Z= 0.107 Angle : 0.490 7.221 9016 Z= 0.253 Chirality : 0.039 0.153 944 Planarity : 0.005 0.101 1160 Dihedral : 4.201 43.640 879 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.55 % Favored : 96.32 % Rotamer: Outliers : 2.46 % Allowed : 25.58 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.30), residues: 788 helix: 1.70 (0.26), residues: 406 sheet: -0.10 (0.73), residues: 49 loop : -0.77 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 159 TYR 0.017 0.001 TYR A 368 PHE 0.013 0.001 PHE A 506 TRP 0.012 0.001 TRP B 21 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 6618) covalent geometry : angle 0.48997 / 0.25 ( 9002) SS BOND : bond 0.00282 / 0.15 ( 7) SS BOND : angle 0.74697 / 0.49 ( 14) hydrogen bonds : bond 0.04513 / 2.97 ( 327) hydrogen bonds : angle 4.45751 / 3.26 ( 936) *********************** 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 113 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.7545 (t80) cc_final: 0.7113 (t80) REVERT: A 540 LEU cc_start: 0.8199 (tp) cc_final: 0.7960 (tt) REVERT: B 142 GLN cc_start: 0.5735 (OUTLIER) cc_final: 0.5351 (pt0) outliers start: 17 outliers final: 12 residues processed: 111 average time/residue: 0.0726 time to fit residues: 10.7308 Evaluate side-chains 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 142 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.153401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123543 restraints weight = 10460.226| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.34 r_work: 0.3458 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 6625 Z= 0.112 Angle : 0.502 7.922 9016 Z= 0.259 Chirality : 0.040 0.152 944 Planarity : 0.005 0.102 1160 Dihedral : 3.886 28.867 877 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.94 % Rotamer: Outliers : 2.89 % Allowed : 25.29 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.30), residues: 788 helix: 1.72 (0.26), residues: 406 sheet: -0.06 (0.73), residues: 49 loop : -0.78 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 159 TYR 0.018 0.001 TYR A 368 PHE 0.016 0.001 PHE A 506 TRP 0.011 0.001 TRP B 21 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6618) covalent geometry : angle 0.50178 / 0.26 ( 9002) SS BOND : bond 0.00277 / 0.14 ( 7) SS BOND : angle 0.65765 / 0.37 ( 14) hydrogen bonds : bond 0.04635 / 3.07 ( 327) hydrogen bonds : angle 4.42471 / 3.24 ( 936) *********************** 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 109 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.7546 (t80) cc_final: 0.7119 (t80) REVERT: A 522 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7060 (tp) REVERT: B 142 GLN cc_start: 0.5724 (OUTLIER) cc_final: 0.5350 (pt0) REVERT: B 160 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7752 (tp) outliers start: 20 outliers final: 16 residues processed: 107 average time/residue: 0.0582 time to fit residues: 8.5379 Evaluate side-chains 106 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 160 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 0.0050 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124857 restraints weight = 10672.531| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.37 r_work: 0.3474 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 6625 Z= 0.105 Angle : 0.501 9.498 9016 Z= 0.256 Chirality : 0.039 0.152 944 Planarity : 0.005 0.104 1160 Dihedral : 3.799 24.911 877 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.70 % Rotamer: Outliers : 2.75 % Allowed : 25.58 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.30), residues: 788 helix: 1.74 (0.26), residues: 406 sheet: -0.02 (0.73), residues: 49 loop : -0.73 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 159 TYR 0.018 0.001 TYR A 368 PHE 0.014 0.001 PHE A 506 TRP 0.022 0.001 TRP B 21 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 6618) covalent geometry : angle 0.50070 / 0.26 ( 9002) SS BOND : bond 0.00268 / 0.14 ( 7) SS BOND : angle 0.66530 / 0.42 ( 14) hydrogen bonds : bond 0.04417 / 2.92 ( 327) hydrogen bonds : angle 4.40905 / 3.23 ( 936) *********************** 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 120 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.7543 (t80) cc_final: 0.7104 (t80) REVERT: A 540 LEU cc_start: 0.8189 (tp) cc_final: 0.7915 (tt) REVERT: A 586 TYR cc_start: 0.7326 (t80) cc_final: 0.7100 (t80) REVERT: A 594 THR cc_start: 0.7444 (t) cc_final: 0.6781 (m) REVERT: B 142 GLN cc_start: 0.5682 (OUTLIER) cc_final: 0.5004 (pp30) REVERT: B 160 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7763 (tp) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.0586 time to fit residues: 9.1742 Evaluate side-chains 104 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125047 restraints weight = 10399.903| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.33 r_work: 0.3476 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 6625 Z= 0.105 Angle : 0.502 8.359 9016 Z= 0.254 Chirality : 0.039 0.152 944 Planarity : 0.005 0.106 1160 Dihedral : 3.748 23.282 877 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.07 % Rotamer: Outliers : 2.60 % Allowed : 25.58 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.30), residues: 788 helix: 1.76 (0.26), residues: 406 sheet: -0.04 (0.73), residues: 49 loop : -0.72 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 159 TYR 0.018 0.001 TYR A 368 PHE 0.015 0.001 PHE A 506 TRP 0.020 0.001 TRP B 21 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 6618) covalent geometry : angle 0.50214 / 0.25 ( 9002) SS BOND : bond 0.00313 / 0.16 ( 7) SS BOND : angle 0.66459 / 0.42 ( 14) hydrogen bonds : bond 0.04401 / 2.90 ( 327) hydrogen bonds : angle 4.38005 / 3.20 ( 936) ********************** 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 111 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.7535 (t80) cc_final: 0.7107 (t80) REVERT: A 540 LEU cc_start: 0.8177 (tp) cc_final: 0.7900 (tt) REVERT: A 594 THR cc_start: 0.7474 (t) cc_final: 0.6796 (m) REVERT: B 119 TYR cc_start: 0.7071 (m-80) cc_final: 0.6851 (m-80) REVERT: B 142 GLN cc_start: 0.5703 (OUTLIER) cc_final: 0.5025 (pp30) REVERT: B 149 ASN cc_start: 0.6645 (m-40) cc_final: 0.6145 (p0) REVERT: B 160 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7744 (tp) outliers start: 18 outliers final: 13 residues processed: 108 average time/residue: 0.0601 time to fit residues: 8.9009 Evaluate side-chains 105 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.152933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122695 restraints weight = 10416.912| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.34 r_work: 0.3442 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6625 Z= 0.128 Angle : 0.533 8.740 9016 Z= 0.272 Chirality : 0.040 0.160 944 Planarity : 0.005 0.108 1160 Dihedral : 3.898 23.735 877 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.94 % Rotamer: Outliers : 2.60 % Allowed : 25.29 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 788 helix: 1.67 (0.26), residues: 406 sheet: -0.06 (0.72), residues: 49 loop : -0.76 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 159 TYR 0.018 0.001 TYR A 368 PHE 0.017 0.001 PHE A 506 TRP 0.021 0.001 TRP B 21 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6618) covalent geometry : angle 0.53242 / 0.27 ( 9002) SS BOND : bond 0.00266 / 0.14 ( 7) SS BOND : angle 0.75817 / 0.54 ( 14) hydrogen bonds : bond 0.04975 / 3.30 ( 327) hydrogen bonds : angle 4.46901 / 3.26 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1399.68 seconds wall clock time: 24 minutes 31.23 seconds (1471.23 seconds total)