Starting phenix.real_space_refine on Wed Sep 17 04:17:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1o_44086/09_2025/9b1o_44086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1o_44086/09_2025/9b1o_44086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b1o_44086/09_2025/9b1o_44086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1o_44086/09_2025/9b1o_44086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b1o_44086/09_2025/9b1o_44086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1o_44086/09_2025/9b1o_44086.map" } resolution = 3.1 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= 0.014 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 30 5.16 5 C 2570 2.51 5 N 664 2.21 5 O 681 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3945 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3922 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'NAG': 1, 'VGL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.05, per 1000 atoms: 0.27 Number of scatterers: 3945 At special positions: 0 Unit cell: (56.463, 88.913, 101.893, 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 30 16.00 O 681 8.00 N 664 7.00 C 2570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " 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 A 601 " - " ASN A 56 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 178.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 83.1% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.785A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 37 removed outlier: 3.752A pdb=" N SER A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.838A pdb=" N TRP A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.784A pdb=" N GLY A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.627A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 220 removed outlier: 3.657A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 222 No H-bonds generated for 'chain 'A' and resid 221 through 222' Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.152A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 264 through 273 removed outlier: 4.163A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 304 removed outlier: 3.680A pdb=" N GLN A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 326 through 329 removed outlier: 3.569A pdb=" N GLU A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 332 through 339 removed outlier: 4.033A pdb=" N LEU A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 364 removed outlier: 4.435A pdb=" N ARG A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.799A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.896A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.511A pdb=" N SER A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 419 removed outlier: 3.780A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 3.701A pdb=" N SER A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 482 removed outlier: 4.623A pdb=" N MET A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.679A pdb=" N VAL A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.704A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Proline residue: A 501 - end of helix removed outlier: 3.599A pdb=" N LEU A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 88 267 hydrogen bonds defined for protein. 762 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: 0.52 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1245 1.35 - 1.46: 953 1.46 - 1.58: 1799 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4044 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" N PHE A 3 " pdb=" CA PHE A 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 bond pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 1.520 1.531 -0.011 8.80e-03 1.29e+04 1.68e+00 bond pdb=" C VAL A 320 " pdb=" O VAL A 320 " ideal model delta sigma weight residual 1.236 1.255 -0.019 1.47e-02 4.63e+03 1.65e+00 bond pdb=" C TRP A 353 " pdb=" O TRP A 353 " ideal model delta sigma weight residual 1.236 1.250 -0.013 1.15e-02 7.56e+03 1.37e+00 ... (remaining 4039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 5154 1.37 - 2.73: 280 2.73 - 4.09: 67 4.09 - 5.46: 12 5.46 - 6.82: 2 Bond angle restraints: 5515 Sorted by residual: angle pdb=" CA TYR A 272 " pdb=" CB TYR A 272 " pdb=" CG TYR A 272 " ideal model delta sigma weight residual 113.90 120.72 -6.82 1.80e+00 3.09e-01 1.44e+01 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 118.90 -5.00 1.80e+00 3.09e-01 7.71e+00 angle pdb=" C VAL A 264 " pdb=" CA VAL A 264 " pdb=" CB VAL A 264 " ideal model delta sigma weight residual 114.35 111.44 2.91 1.06e+00 8.90e-01 7.55e+00 angle pdb=" N PHE A 356 " pdb=" CA PHE A 356 " pdb=" CB PHE A 356 " ideal model delta sigma weight residual 109.82 113.91 -4.09 1.52e+00 4.33e-01 7.26e+00 angle pdb=" C LEU A 271 " pdb=" N TYR A 272 " pdb=" CA TYR A 272 " ideal model delta sigma weight residual 121.58 116.48 5.10 1.95e+00 2.63e-01 6.85e+00 ... (remaining 5510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 2246 16.47 - 32.94: 115 32.94 - 49.41: 22 49.41 - 65.88: 6 65.88 - 82.34: 3 Dihedral angle restraints: 2392 sinusoidal: 920 harmonic: 1472 Sorted by residual: dihedral pdb=" CA GLU A 38 " pdb=" C GLU A 38 " pdb=" N ASN A 39 " pdb=" CA ASN A 39 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PRO A 457 " pdb=" C PRO A 457 " pdb=" N THR A 458 " pdb=" CA THR A 458 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LYS A 328 " pdb=" C LYS A 328 " pdb=" N GLU A 329 " pdb=" CA GLU A 329 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 397 0.032 - 0.063: 180 0.063 - 0.095: 39 0.095 - 0.127: 31 0.127 - 0.159: 4 Chirality restraints: 651 Sorted by residual: chirality pdb=" CA TYR A 272 " pdb=" N TYR A 272 " pdb=" C TYR A 272 " pdb=" CB TYR A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA PRO A 501 " pdb=" N PRO A 501 " pdb=" C PRO A 501 " pdb=" CB PRO A 501 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA VAL A 118 " pdb=" N VAL A 118 " pdb=" C VAL A 118 " pdb=" CB VAL A 118 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 648 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 354 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C PHE A 354 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE A 354 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 355 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 272 " -0.019 2.00e-02 2.50e+03 1.30e-02 3.38e+00 pdb=" CG TYR A 272 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 272 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 272 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 272 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 272 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 272 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 272 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 264 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 265 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.022 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1687 2.92 - 3.41: 4028 3.41 - 3.91: 6454 3.91 - 4.40: 7489 4.40 - 4.90: 12247 Nonbonded interactions: 31905 Sorted by model distance: nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 385 " model vdw 2.424 3.040 nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.487 3.040 nonbonded pdb=" N ASP A 290 " pdb=" OD1 ASP A 290 " model vdw 2.513 3.120 nonbonded pdb=" O LEU A 417 " pdb=" OG1 THR A 420 " model vdw 2.526 3.040 nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.531 3.040 ... (remaining 31900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.730 Find NCS groups from input model: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 0.044 4047 Z= 0.215 Angle : 0.766 6.825 5522 Z= 0.422 Chirality : 0.042 0.159 651 Planarity : 0.006 0.052 686 Dihedral : 11.209 82.344 1436 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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 aren not related in a simple way. whole: -0.17 (0.36), residues: 513 helix: -0.34 (0.24), residues: 372 sheet: None (None), residues: 0 loop : 1.13 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 401 TYR 0.031 0.002 TYR A 272 PHE 0.023 0.002 PHE A 344 TRP 0.013 0.002 TRP A 50 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 4044) covalent geometry : angle 0.76373 ( 5515) SS BOND : bond 0.00051 ( 2) SS BOND : angle 2.11335 ( 4) hydrogen bonds : bond 0.12818 ( 267) hydrogen bonds : angle 5.72788 ( 762) link_NAG-ASN : bond 0.00926 ( 1) link_NAG-ASN : angle 1.79066 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 10 VAL cc_start: 0.7776 (t) cc_final: 0.7556 (p) REVERT: A 15 ARG cc_start: 0.7177 (ttm110) cc_final: 0.6680 (ttt180) REVERT: A 301 ARG cc_start: 0.8252 (ttp80) cc_final: 0.8029 (ttt90) REVERT: A 343 ARG cc_start: 0.5709 (ttp80) cc_final: 0.5345 (ttm170) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1104 time to fit residues: 8.7382 Evaluate side-chains 50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.164720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116718 restraints weight = 4428.737| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.58 r_work: 0.3208 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4047 Z= 0.153 Angle : 0.579 7.236 5522 Z= 0.296 Chirality : 0.040 0.131 651 Planarity : 0.005 0.048 686 Dihedral : 4.284 19.742 570 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.48 % Allowed : 5.53 % Favored : 93.99 % 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 aren not related in a simple way. whole: 1.29 (0.37), residues: 513 helix: 0.81 (0.26), residues: 368 sheet: None (None), residues: 0 loop : 1.39 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 281 TYR 0.021 0.002 TYR A 272 PHE 0.015 0.002 PHE A 356 TRP 0.014 0.001 TRP A 353 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4044) covalent geometry : angle 0.57711 ( 5515) SS BOND : bond 0.00224 ( 2) SS BOND : angle 1.72001 ( 4) hydrogen bonds : bond 0.05489 ( 267) hydrogen bonds : angle 4.33816 ( 762) link_NAG-ASN : bond 0.00255 ( 1) link_NAG-ASN : angle 1.34058 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.098 Fit side-chains REVERT: A 6 LEU cc_start: 0.7911 (mm) cc_final: 0.7691 (mt) REVERT: A 10 VAL cc_start: 0.7886 (t) cc_final: 0.7657 (p) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.0640 time to fit residues: 4.4766 Evaluate side-chains 45 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.166313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118424 restraints weight = 4373.927| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.56 r_work: 0.3231 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4047 Z= 0.132 Angle : 0.541 6.594 5522 Z= 0.270 Chirality : 0.038 0.125 651 Planarity : 0.005 0.042 686 Dihedral : 3.867 18.050 570 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.24 % Allowed : 7.21 % Favored : 92.55 % 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 aren not related in a simple way. whole: 1.99 (0.38), residues: 513 helix: 1.47 (0.27), residues: 355 sheet: -1.91 (1.33), residues: 10 loop : 1.51 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.019 0.002 TYR A 272 PHE 0.013 0.001 PHE A 358 TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4044) covalent geometry : angle 0.53885 ( 5515) SS BOND : bond 0.00155 ( 2) SS BOND : angle 1.57998 ( 4) hydrogen bonds : bond 0.04973 ( 267) hydrogen bonds : angle 4.13751 ( 762) link_NAG-ASN : bond 0.00280 ( 1) link_NAG-ASN : angle 0.98393 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.143 Fit side-chains REVERT: A 6 LEU cc_start: 0.7862 (mm) cc_final: 0.7625 (mt) REVERT: A 10 VAL cc_start: 0.7913 (t) cc_final: 0.7690 (p) REVERT: A 272 TYR cc_start: 0.6899 (p90) cc_final: 0.5482 (m-10) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.0594 time to fit residues: 3.9958 Evaluate side-chains 47 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117292 restraints weight = 4386.574| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.59 r_work: 0.3233 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4047 Z= 0.134 Angle : 0.526 6.396 5522 Z= 0.262 Chirality : 0.038 0.134 651 Planarity : 0.005 0.043 686 Dihedral : 3.679 15.334 570 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.96 % Allowed : 8.89 % Favored : 90.14 % 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 aren not related in a simple way. whole: 2.02 (0.37), residues: 513 helix: 1.66 (0.27), residues: 355 sheet: -2.33 (1.31), residues: 10 loop : 1.05 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.019 0.002 TYR A 272 PHE 0.014 0.001 PHE A 358 TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4044) covalent geometry : angle 0.52395 ( 5515) SS BOND : bond 0.00181 ( 2) SS BOND : angle 1.47390 ( 4) hydrogen bonds : bond 0.04749 ( 267) hydrogen bonds : angle 4.03063 ( 762) link_NAG-ASN : bond 0.00202 ( 1) link_NAG-ASN : angle 1.02716 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.148 Fit side-chains REVERT: A 10 VAL cc_start: 0.7887 (t) cc_final: 0.7650 (p) REVERT: A 272 TYR cc_start: 0.6883 (p90) cc_final: 0.5423 (m-10) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.0433 time to fit residues: 3.2616 Evaluate side-chains 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116304 restraints weight = 4447.960| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.59 r_work: 0.3220 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4047 Z= 0.144 Angle : 0.542 9.974 5522 Z= 0.266 Chirality : 0.038 0.136 651 Planarity : 0.004 0.043 686 Dihedral : 3.617 14.804 570 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.44 % Allowed : 8.41 % Favored : 90.14 % 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 aren not related in a simple way. whole: 2.02 (0.37), residues: 513 helix: 1.70 (0.27), residues: 355 sheet: -2.50 (1.31), residues: 10 loop : 0.98 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.019 0.002 TYR A 272 PHE 0.016 0.001 PHE A 358 TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4044) covalent geometry : angle 0.53983 ( 5515) SS BOND : bond 0.00195 ( 2) SS BOND : angle 1.49727 ( 4) hydrogen bonds : bond 0.04826 ( 267) hydrogen bonds : angle 4.00305 ( 762) link_NAG-ASN : bond 0.00180 ( 1) link_NAG-ASN : angle 1.04087 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.206 Fit side-chains REVERT: A 10 VAL cc_start: 0.7876 (t) cc_final: 0.7648 (p) REVERT: A 272 TYR cc_start: 0.6940 (p90) cc_final: 0.5426 (m-10) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.0409 time to fit residues: 3.0656 Evaluate side-chains 53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118583 restraints weight = 4488.015| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.62 r_work: 0.3220 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4047 Z= 0.140 Angle : 0.549 10.232 5522 Z= 0.266 Chirality : 0.038 0.137 651 Planarity : 0.004 0.043 686 Dihedral : 3.571 14.588 570 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.96 % Allowed : 9.86 % Favored : 89.18 % 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 aren not related in a simple way. whole: 2.03 (0.37), residues: 513 helix: 1.71 (0.27), residues: 357 sheet: -2.49 (1.40), residues: 10 loop : 0.96 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.018 0.002 TYR A 272 PHE 0.015 0.001 PHE A 358 TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4044) covalent geometry : angle 0.54754 ( 5515) SS BOND : bond 0.00206 ( 2) SS BOND : angle 1.41722 ( 4) hydrogen bonds : bond 0.04734 ( 267) hydrogen bonds : angle 3.96991 ( 762) link_NAG-ASN : bond 0.00178 ( 1) link_NAG-ASN : angle 0.96731 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.143 Fit side-chains REVERT: A 272 TYR cc_start: 0.6847 (p90) cc_final: 0.5427 (m-10) outliers start: 4 outliers final: 4 residues processed: 52 average time/residue: 0.0421 time to fit residues: 3.1981 Evaluate side-chains 50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.0370 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.164887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119381 restraints weight = 4482.509| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.59 r_work: 0.3257 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4047 Z= 0.114 Angle : 0.522 10.755 5522 Z= 0.250 Chirality : 0.037 0.140 651 Planarity : 0.004 0.040 686 Dihedral : 3.440 12.896 570 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.72 % Allowed : 10.34 % Favored : 88.94 % 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 aren not related in a simple way. whole: 2.28 (0.37), residues: 513 helix: 1.93 (0.27), residues: 357 sheet: -2.64 (1.36), residues: 10 loop : 0.98 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.017 0.001 TYR A 272 PHE 0.012 0.001 PHE A 358 TRP 0.011 0.001 TRP A 353 HIS 0.002 0.000 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4044) covalent geometry : angle 0.52057 ( 5515) SS BOND : bond 0.00152 ( 2) SS BOND : angle 1.25286 ( 4) hydrogen bonds : bond 0.04195 ( 267) hydrogen bonds : angle 3.85049 ( 762) link_NAG-ASN : bond 0.00273 ( 1) link_NAG-ASN : angle 0.87715 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.158 Fit side-chains REVERT: A 425 GLU cc_start: 0.7316 (tt0) cc_final: 0.7030 (tm-30) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.0440 time to fit residues: 3.4913 Evaluate side-chains 53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.162842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116967 restraints weight = 4484.590| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.58 r_work: 0.3231 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4047 Z= 0.137 Angle : 0.546 10.679 5522 Z= 0.263 Chirality : 0.038 0.140 651 Planarity : 0.004 0.043 686 Dihedral : 3.443 13.748 570 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.44 % Allowed : 9.62 % Favored : 88.94 % 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 aren not related in a simple way. whole: 2.27 (0.37), residues: 513 helix: 1.93 (0.27), residues: 357 sheet: -2.83 (1.32), residues: 10 loop : 0.95 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.012 0.001 TYR A 272 PHE 0.016 0.001 PHE A 358 TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4044) covalent geometry : angle 0.54437 ( 5515) SS BOND : bond 0.00202 ( 2) SS BOND : angle 1.34528 ( 4) hydrogen bonds : bond 0.04591 ( 267) hydrogen bonds : angle 3.88989 ( 762) link_NAG-ASN : bond 0.00121 ( 1) link_NAG-ASN : angle 1.15998 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.148 Fit side-chains REVERT: A 425 GLU cc_start: 0.7343 (tt0) cc_final: 0.7055 (tm-30) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.0436 time to fit residues: 3.3239 Evaluate side-chains 54 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117292 restraints weight = 4473.014| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.59 r_work: 0.3238 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4047 Z= 0.130 Angle : 0.540 11.050 5522 Z= 0.260 Chirality : 0.038 0.144 651 Planarity : 0.004 0.041 686 Dihedral : 3.428 13.541 570 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.44 % Allowed : 9.38 % Favored : 89.18 % 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 aren not related in a simple way. whole: 2.35 (0.37), residues: 513 helix: 1.98 (0.27), residues: 357 sheet: -2.80 (1.33), residues: 10 loop : 1.02 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.012 0.001 TYR A 272 PHE 0.014 0.001 PHE A 358 TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4044) covalent geometry : angle 0.53846 ( 5515) SS BOND : bond 0.00189 ( 2) SS BOND : angle 1.28334 ( 4) hydrogen bonds : bond 0.04449 ( 267) hydrogen bonds : angle 3.87879 ( 762) link_NAG-ASN : bond 0.00224 ( 1) link_NAG-ASN : angle 0.97640 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.144 Fit side-chains REVERT: A 272 TYR cc_start: 0.7290 (p90) cc_final: 0.5548 (m-10) REVERT: A 425 GLU cc_start: 0.7292 (tt0) cc_final: 0.7036 (tm-30) outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.0417 time to fit residues: 3.2463 Evaluate side-chains 57 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 9 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118604 restraints weight = 4435.564| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.57 r_work: 0.3252 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4047 Z= 0.123 Angle : 0.539 11.595 5522 Z= 0.259 Chirality : 0.038 0.144 651 Planarity : 0.004 0.040 686 Dihedral : 3.388 12.992 570 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.44 % Allowed : 10.34 % Favored : 88.22 % 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 aren not related in a simple way. whole: 2.39 (0.37), residues: 513 helix: 2.03 (0.27), residues: 357 sheet: -2.77 (1.34), residues: 10 loop : 0.99 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.012 0.001 TYR A 272 PHE 0.013 0.001 PHE A 358 TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4044) covalent geometry : angle 0.53828 ( 5515) SS BOND : bond 0.00176 ( 2) SS BOND : angle 1.23767 ( 4) hydrogen bonds : bond 0.04304 ( 267) hydrogen bonds : angle 3.85770 ( 762) link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 0.96778 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.158 Fit side-chains REVERT: A 272 TYR cc_start: 0.7258 (p90) cc_final: 0.5536 (m-10) REVERT: A 425 GLU cc_start: 0.7274 (tt0) cc_final: 0.7030 (tm-30) outliers start: 6 outliers final: 6 residues processed: 55 average time/residue: 0.0415 time to fit residues: 3.3824 Evaluate side-chains 59 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 1 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118896 restraints weight = 4460.945| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.49 r_work: 0.3255 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4047 Z= 0.119 Angle : 0.530 11.586 5522 Z= 0.253 Chirality : 0.037 0.141 651 Planarity : 0.004 0.039 686 Dihedral : 3.336 12.526 570 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.44 % Allowed : 10.34 % Favored : 88.22 % 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 aren not related in a simple way. whole: 2.45 (0.37), residues: 513 helix: 2.07 (0.27), residues: 357 sheet: -2.62 (1.46), residues: 10 loop : 0.99 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.012 0.001 TYR A 272 PHE 0.013 0.001 PHE A 358 TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4044) covalent geometry : angle 0.52921 ( 5515) SS BOND : bond 0.00165 ( 2) SS BOND : angle 1.18449 ( 4) hydrogen bonds : bond 0.04178 ( 267) hydrogen bonds : angle 3.82915 ( 762) link_NAG-ASN : bond 0.00215 ( 1) link_NAG-ASN : angle 0.96462 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1316.14 seconds wall clock time: 23 minutes 13.66 seconds (1393.66 seconds total)