Starting phenix.real_space_refine on Tue Aug 4 14:14:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yxx_73619/08_2026/9yxx_73619.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yxx_73619/08_2026/9yxx_73619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yxx_73619/08_2026/9yxx_73619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yxx_73619/08_2026/9yxx_73619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yxx_73619/08_2026/9yxx_73619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yxx_73619/08_2026/9yxx_73619.map" } resolution = 3.01 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= 0.012 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 12 5.16 5 C 2379 2.51 5 N 598 2.21 5 O 685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3674 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain breaks: 4 Chain: "B" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1829 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain breaks: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.08, per 1000 atoms: 0.29 Number of scatterers: 3674 At special positions: 0 Unit cell: (81.536, 74.048, 84.864, 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 12 16.00 O 685 8.00 N 598 7.00 C 2379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 99 " " NAG A1304 " - " ASN A 234 " " NAG B1301 " - " ASN B 529 " " NAG B1302 " - " ASN B 343 " Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 153.9 milliseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 838 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.1% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.735A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.713A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.982A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.808A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.992A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.527A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 120 hydrogen bonds defined for protein. 309 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: 0.62 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: 1.22 - 1.34: 1101 1.34 - 1.46: 791 1.46 - 1.57: 1872 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 3776 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.10e-02 8.26e+03 9.35e+00 bond pdb=" N VAL A 130 " pdb=" CA VAL A 130 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.58e+00 bond pdb=" N VAL B 407 " pdb=" CA VAL B 407 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.09e+00 bond pdb=" N CYS A 131 " pdb=" CA CYS A 131 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.94e+00 ... (remaining 3771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 4807 1.32 - 2.63: 247 2.63 - 3.95: 67 3.95 - 5.27: 11 5.27 - 6.58: 3 Bond angle restraints: 5135 Sorted by residual: angle pdb=" CA PRO B 337 " pdb=" C PRO B 337 " pdb=" O PRO B 337 " ideal model delta sigma weight residual 121.31 118.40 2.91 7.40e-01 1.83e+00 1.55e+01 angle pdb=" CA GLU A 169 " pdb=" C GLU A 169 " pdb=" O GLU A 169 " ideal model delta sigma weight residual 121.58 117.61 3.97 1.16e+00 7.43e-01 1.17e+01 angle pdb=" N THR B 523 " pdb=" CA THR B 523 " pdb=" C THR B 523 " ideal model delta sigma weight residual 113.55 109.28 4.27 1.26e+00 6.30e-01 1.15e+01 angle pdb=" CA GLU B 465 " pdb=" CB GLU B 465 " pdb=" CG GLU B 465 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA SER A 162 " pdb=" C SER A 162 " pdb=" O SER A 162 " ideal model delta sigma weight residual 120.90 117.52 3.38 1.03e+00 9.43e-01 1.08e+01 ... (remaining 5130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 1998 15.98 - 31.96: 202 31.96 - 47.94: 57 47.94 - 63.92: 16 63.92 - 79.90: 4 Dihedral angle restraints: 2277 sinusoidal: 971 harmonic: 1306 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 53.20 39.80 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 125.22 -32.22 1 1.00e+01 1.00e-02 1.48e+01 dihedral pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sinusoidal sigma weight residual -60.00 -115.37 55.37 3 1.50e+01 4.44e-03 9.34e+00 ... (remaining 2274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 454 0.061 - 0.122: 99 0.122 - 0.183: 15 0.183 - 0.245: 3 0.245 - 0.306: 1 Chirality restraints: 572 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL A 130 " pdb=" CA VAL A 130 " pdb=" CG1 VAL A 130 " pdb=" CG2 VAL A 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.92e-01 ... (remaining 569 not shown) Planarity restraints: 658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.260 2.00e-02 2.50e+03 2.26e-01 6.37e+02 pdb=" C7 NAG A1304 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " -0.005 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.387 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 357 " -0.264 9.50e-02 1.11e+02 1.18e-01 8.61e+00 pdb=" NE ARG B 357 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 357 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 357 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 357 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 172 " -0.010 2.00e-02 2.50e+03 1.20e-02 2.52e+00 pdb=" CG PHE A 172 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 172 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 172 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 172 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 172 " -0.002 2.00e-02 2.50e+03 ... (remaining 655 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.02: 2087 3.02 - 3.49: 3266 3.49 - 3.96: 5643 3.96 - 4.43: 6662 4.43 - 4.90: 10959 Nonbonded interactions: 28617 Sorted by model distance: nonbonded pdb=" O GLY B 413 " pdb=" OE1 GLN B 414 " model vdw 2.544 3.040 nonbonded pdb=" O ASN B 334 " pdb=" N VAL B 362 " model vdw 2.556 3.120 nonbonded pdb=" N GLU A 281 " pdb=" OE1 GLU A 281 " model vdw 2.570 3.120 nonbonded pdb=" N GLU A 169 " pdb=" O GLU A 169 " model vdw 2.596 2.496 nonbonded pdb=" N ASP B 398 " pdb=" OD1 ASP B 398 " model vdw 2.599 3.120 ... (remaining 28612 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: 7.930 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: 0.080 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 5.580 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3786 Z= 0.312 Angle : 0.714 6.584 5161 Z= 0.444 Chirality : 0.055 0.306 572 Planarity : 0.011 0.226 652 Dihedral : 14.184 79.896 1427 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.01 % Allowed : 19.90 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.40), residues: 432 helix: -3.19 (0.72), residues: 34 sheet: -0.23 (0.42), residues: 150 loop : -1.12 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 466 TYR 0.008 0.001 TYR A 269 PHE 0.027 0.001 PHE A 172 TRP 0.008 0.001 TRP B 353 HIS 0.001 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.31 ( 3776) covalent geometry : angle 0.71086 / 0.44 ( 5135) SS BOND : bond 0.00238 / 0.13 ( 4) SS BOND : angle 0.28977 / 0.13 ( 8) hydrogen bonds : bond 0.10471 / 6.79 ( 120) hydrogen bonds : angle 7.05782 / 4.92 ( 309) link_NAG-ASN : bond 0.00197 / 0.13 ( 6) link_NAG-ASN : angle 1.46865 / 0.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.165 Fit side-chains REVERT: A 41 LYS cc_start: 0.9287 (mmtm) cc_final: 0.7657 (tptt) REVERT: B 369 TYR cc_start: 0.7916 (m-10) cc_final: 0.7311 (t80) REVERT: B 498 ARG cc_start: 0.8709 (mtt180) cc_final: 0.8479 (mpt180) outliers start: 4 outliers final: 4 residues processed: 61 average time/residue: 0.1492 time to fit residues: 10.3459 Evaluate side-chains 46 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.108574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078354 restraints weight = 7038.469| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.45 r_work: 0.3039 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3786 Z= 0.135 Angle : 0.522 6.180 5161 Z= 0.269 Chirality : 0.047 0.184 572 Planarity : 0.003 0.031 652 Dihedral : 6.804 54.258 620 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.02 % Allowed : 18.89 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.39), residues: 432 helix: -2.39 (0.76), residues: 34 sheet: -0.16 (0.41), residues: 150 loop : -1.01 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.008 0.001 TYR A 269 PHE 0.017 0.001 PHE A 65 TRP 0.006 0.001 TRP B 353 HIS 0.001 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 3776) covalent geometry : angle 0.51734 / 0.27 ( 5135) SS BOND : bond 0.00092 / 0.06 ( 4) SS BOND : angle 0.97443 / 0.66 ( 8) hydrogen bonds : bond 0.02656 / 1.69 ( 120) hydrogen bonds : angle 6.11353 / 4.25 ( 309) link_NAG-ASN : bond 0.00333 / 0.19 ( 6) link_NAG-ASN : angle 1.21934 / 0.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9236 (mmtm) cc_final: 0.7557 (tptt) REVERT: B 472 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8091 (mm) outliers start: 12 outliers final: 7 residues processed: 49 average time/residue: 0.1289 time to fit residues: 7.2967 Evaluate side-chains 49 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 10 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.108809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.077571 restraints weight = 7024.673| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.55 r_work: 0.3050 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3786 Z= 0.111 Angle : 0.495 5.957 5161 Z= 0.255 Chirality : 0.046 0.168 572 Planarity : 0.003 0.032 652 Dihedral : 6.525 55.067 615 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.77 % Allowed : 19.90 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.40), residues: 432 helix: -2.49 (0.75), residues: 34 sheet: -0.12 (0.42), residues: 147 loop : -0.94 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.007 0.001 TYR B 453 PHE 0.017 0.001 PHE A 172 TRP 0.005 0.001 TRP B 353 HIS 0.001 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 3776) covalent geometry : angle 0.48995 / 0.25 ( 5135) SS BOND : bond 0.00138 / 0.09 ( 4) SS BOND : angle 0.96890 / 0.65 ( 8) hydrogen bonds : bond 0.02449 / 1.56 ( 120) hydrogen bonds : angle 5.93726 / 4.13 ( 309) link_NAG-ASN : bond 0.00294 / 0.18 ( 6) link_NAG-ASN : angle 1.10626 / 0.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9246 (mmtm) cc_final: 0.7586 (tptt) REVERT: B 472 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8062 (mm) outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 0.1391 time to fit residues: 7.8022 Evaluate side-chains 46 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.106696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075576 restraints weight = 6971.437| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.52 r_work: 0.2976 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3786 Z= 0.164 Angle : 0.522 5.961 5161 Z= 0.270 Chirality : 0.047 0.169 572 Planarity : 0.003 0.030 652 Dihedral : 6.635 53.803 615 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.53 % Allowed : 19.14 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.40), residues: 432 helix: -2.62 (0.73), residues: 34 sheet: -0.09 (0.41), residues: 150 loop : -0.92 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.009 0.001 TYR A 269 PHE 0.018 0.001 PHE A 172 TRP 0.007 0.001 TRP B 353 HIS 0.001 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 3776) covalent geometry : angle 0.51664 / 0.27 ( 5135) SS BOND : bond 0.00129 / 0.08 ( 4) SS BOND : angle 1.07987 / 0.73 ( 8) hydrogen bonds : bond 0.02701 / 1.74 ( 120) hydrogen bonds : angle 5.99376 / 4.15 ( 309) link_NAG-ASN : bond 0.00253 / 0.15 ( 6) link_NAG-ASN : angle 1.15452 / 0.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.144 Fit side-chains REVERT: A 41 LYS cc_start: 0.9268 (mmtm) cc_final: 0.7571 (tptt) REVERT: A 169 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8114 (tm-30) REVERT: A 293 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8850 (mp) REVERT: B 446 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7341 (t70) REVERT: B 472 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7951 (mm) REVERT: B 498 ARG cc_start: 0.8815 (mtt180) cc_final: 0.8396 (mtt90) outliers start: 14 outliers final: 9 residues processed: 52 average time/residue: 0.1257 time to fit residues: 7.4810 Evaluate side-chains 51 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 16 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.108716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077369 restraints weight = 6955.379| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.57 r_work: 0.3008 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3786 Z= 0.116 Angle : 0.496 5.874 5161 Z= 0.255 Chirality : 0.046 0.163 572 Planarity : 0.003 0.030 652 Dihedral : 6.543 55.207 615 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.77 % Allowed : 19.40 % Favored : 77.83 % 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: -1.15 (0.40), residues: 432 helix: -2.65 (0.73), residues: 34 sheet: -0.04 (0.42), residues: 147 loop : -0.90 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.008 0.001 TYR B 453 PHE 0.020 0.001 PHE A 172 TRP 0.005 0.001 TRP A 64 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 3776) covalent geometry : angle 0.49131 / 0.25 ( 5135) SS BOND : bond 0.00136 / 0.09 ( 4) SS BOND : angle 1.02225 / 0.68 ( 8) hydrogen bonds : bond 0.02433 / 1.56 ( 120) hydrogen bonds : angle 5.85293 / 4.05 ( 309) link_NAG-ASN : bond 0.00277 / 0.17 ( 6) link_NAG-ASN : angle 1.12295 / 0.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9249 (mmtm) cc_final: 0.7550 (tptt) REVERT: A 169 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 218 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8968 (mm110) REVERT: B 472 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7960 (mm) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.1310 time to fit residues: 7.4866 Evaluate side-chains 46 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.107686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.076534 restraints weight = 6993.101| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.55 r_work: 0.3003 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3786 Z= 0.125 Angle : 0.503 5.757 5161 Z= 0.260 Chirality : 0.046 0.161 572 Planarity : 0.003 0.030 652 Dihedral : 6.529 54.602 615 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.53 % Allowed : 18.39 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.40), residues: 432 helix: -2.62 (0.74), residues: 34 sheet: -0.01 (0.42), residues: 147 loop : -0.85 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.008 0.001 TYR B 453 PHE 0.021 0.001 PHE A 172 TRP 0.006 0.001 TRP B 353 HIS 0.001 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 3776) covalent geometry : angle 0.49831 / 0.26 ( 5135) SS BOND : bond 0.00226 / 0.15 ( 4) SS BOND : angle 1.13974 / 0.76 ( 8) hydrogen bonds : bond 0.02495 / 1.61 ( 120) hydrogen bonds : angle 5.83045 / 4.02 ( 309) link_NAG-ASN : bond 0.00265 / 0.16 ( 6) link_NAG-ASN : angle 1.10463 / 0.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.143 Fit side-chains REVERT: A 41 LYS cc_start: 0.9259 (mmtm) cc_final: 0.7596 (tptt) REVERT: A 169 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 218 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8957 (mm110) REVERT: B 446 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7342 (t70) REVERT: B 498 ARG cc_start: 0.8822 (mtt180) cc_final: 0.8403 (mtt90) outliers start: 14 outliers final: 9 residues processed: 51 average time/residue: 0.0998 time to fit residues: 5.9279 Evaluate side-chains 50 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.0050 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.107583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.076376 restraints weight = 7106.605| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.58 r_work: 0.2999 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3786 Z= 0.130 Angle : 0.511 5.686 5161 Z= 0.263 Chirality : 0.046 0.160 572 Planarity : 0.003 0.031 652 Dihedral : 6.532 54.655 615 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.52 % Allowed : 19.14 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.40), residues: 432 helix: -2.68 (0.71), residues: 35 sheet: -0.01 (0.42), residues: 147 loop : -0.81 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.008 0.001 TYR B 453 PHE 0.021 0.001 PHE A 172 TRP 0.008 0.001 TRP B 353 HIS 0.001 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 3776) covalent geometry : angle 0.50655 / 0.26 ( 5135) SS BOND : bond 0.00219 / 0.15 ( 4) SS BOND : angle 1.10231 / 0.73 ( 8) hydrogen bonds : bond 0.02476 / 1.60 ( 120) hydrogen bonds : angle 5.82834 / 4.03 ( 309) link_NAG-ASN : bond 0.00264 / 0.16 ( 6) link_NAG-ASN : angle 1.10675 / 0.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9262 (mmtm) cc_final: 0.7595 (tptt) REVERT: A 169 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 218 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8946 (mm110) REVERT: B 358 ILE cc_start: 0.8907 (mm) cc_final: 0.8619 (mt) REVERT: B 446 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7331 (t70) REVERT: B 498 ARG cc_start: 0.8821 (mtt180) cc_final: 0.8386 (mtt90) outliers start: 10 outliers final: 8 residues processed: 50 average time/residue: 0.1014 time to fit residues: 5.8884 Evaluate side-chains 51 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.107240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.076096 restraints weight = 7039.433| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.57 r_work: 0.2985 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3786 Z= 0.138 Angle : 0.516 5.686 5161 Z= 0.266 Chirality : 0.046 0.158 572 Planarity : 0.003 0.030 652 Dihedral : 6.546 54.400 615 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.27 % Allowed : 18.64 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.40), residues: 432 helix: -2.61 (0.72), residues: 35 sheet: -0.02 (0.42), residues: 147 loop : -0.83 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.008 0.001 TYR B 453 PHE 0.022 0.001 PHE A 172 TRP 0.005 0.001 TRP B 353 HIS 0.001 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 3776) covalent geometry : angle 0.51038 / 0.27 ( 5135) SS BOND : bond 0.00207 / 0.14 ( 4) SS BOND : angle 1.21779 / 0.81 ( 8) hydrogen bonds : bond 0.02531 / 1.64 ( 120) hydrogen bonds : angle 5.84449 / 4.03 ( 309) link_NAG-ASN : bond 0.00246 / 0.15 ( 6) link_NAG-ASN : angle 1.12932 / 0.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9264 (mmtm) cc_final: 0.7602 (tptt) REVERT: A 169 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8072 (tm-30) REVERT: A 218 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8933 (mm110) REVERT: A 293 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8927 (mp) REVERT: B 358 ILE cc_start: 0.8940 (mm) cc_final: 0.8673 (mt) REVERT: B 446 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7357 (t70) REVERT: B 498 ARG cc_start: 0.8825 (mtt180) cc_final: 0.8403 (mpt90) outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 0.1211 time to fit residues: 7.4072 Evaluate side-chains 53 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.105858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.074647 restraints weight = 6983.931| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.54 r_work: 0.2965 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3786 Z= 0.187 Angle : 0.553 5.802 5161 Z= 0.286 Chirality : 0.047 0.159 572 Planarity : 0.003 0.030 652 Dihedral : 6.681 54.317 615 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.77 % Allowed : 18.64 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.40), residues: 432 helix: -2.73 (0.69), residues: 35 sheet: 0.22 (0.42), residues: 144 loop : -0.94 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.009 0.001 TYR A 269 PHE 0.024 0.002 PHE A 172 TRP 0.010 0.002 TRP B 353 HIS 0.001 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 3776) covalent geometry : angle 0.54658 / 0.28 ( 5135) SS BOND : bond 0.00188 / 0.12 ( 4) SS BOND : angle 1.39108 / 0.92 ( 8) hydrogen bonds : bond 0.02752 / 1.78 ( 120) hydrogen bonds : angle 6.00556 / 4.15 ( 309) link_NAG-ASN : bond 0.00226 / 0.14 ( 6) link_NAG-ASN : angle 1.22167 / 0.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9308 (mmtm) cc_final: 0.7567 (tptt) REVERT: A 169 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8139 (tm-30) REVERT: A 218 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8920 (mm110) REVERT: A 293 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8835 (mp) REVERT: B 358 ILE cc_start: 0.8945 (mm) cc_final: 0.8675 (mt) REVERT: B 414 GLN cc_start: 0.8298 (mm110) cc_final: 0.7997 (mm110) REVERT: B 446 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7425 (t70) REVERT: B 498 ARG cc_start: 0.8837 (mtt180) cc_final: 0.8451 (mtt90) outliers start: 11 outliers final: 9 residues processed: 50 average time/residue: 0.1267 time to fit residues: 7.3729 Evaluate side-chains 51 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.107295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076121 restraints weight = 7178.699| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.57 r_work: 0.2986 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3786 Z= 0.130 Angle : 0.532 5.777 5161 Z= 0.274 Chirality : 0.046 0.159 572 Planarity : 0.003 0.030 652 Dihedral : 6.580 54.894 615 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.52 % Allowed : 19.65 % Favored : 77.83 % 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: -1.07 (0.40), residues: 432 helix: -2.72 (0.69), residues: 35 sheet: 0.23 (0.43), residues: 141 loop : -0.96 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.007 0.001 TYR A 269 PHE 0.023 0.001 PHE A 172 TRP 0.006 0.001 TRP A 64 HIS 0.001 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 3776) covalent geometry : angle 0.52625 / 0.27 ( 5135) SS BOND : bond 0.00213 / 0.14 ( 4) SS BOND : angle 1.30052 / 0.86 ( 8) hydrogen bonds : bond 0.02503 / 1.63 ( 120) hydrogen bonds : angle 5.88970 / 4.06 ( 309) link_NAG-ASN : bond 0.00247 / 0.16 ( 6) link_NAG-ASN : angle 1.17367 / 0.67 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9267 (mmtm) cc_final: 0.7602 (tptt) REVERT: A 169 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 218 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8926 (mm110) REVERT: B 358 ILE cc_start: 0.8944 (mm) cc_final: 0.8678 (mt) REVERT: B 446 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7356 (t70) REVERT: B 498 ARG cc_start: 0.8802 (mtt180) cc_final: 0.8376 (mpt90) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.1303 time to fit residues: 7.2329 Evaluate side-chains 50 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.106159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075035 restraints weight = 7002.910| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.53 r_work: 0.2971 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3786 Z= 0.171 Angle : 0.551 6.083 5161 Z= 0.284 Chirality : 0.046 0.158 572 Planarity : 0.003 0.031 652 Dihedral : 6.649 54.847 615 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.02 % Allowed : 19.40 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.40), residues: 432 helix: -2.72 (0.69), residues: 35 sheet: 0.24 (0.42), residues: 144 loop : -0.95 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.008 0.001 TYR A 269 PHE 0.024 0.001 PHE A 172 TRP 0.009 0.002 TRP B 353 HIS 0.001 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 3776) covalent geometry : angle 0.54453 / 0.28 ( 5135) SS BOND : bond 0.00226 / 0.15 ( 4) SS BOND : angle 1.36679 / 0.91 ( 8) hydrogen bonds : bond 0.02663 / 1.73 ( 120) hydrogen bonds : angle 5.96275 / 4.12 ( 309) link_NAG-ASN : bond 0.00227 / 0.14 ( 6) link_NAG-ASN : angle 1.22071 / 0.72 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1268.32 seconds wall clock time: 22 minutes 23.76 seconds (1343.76 seconds total)