Starting phenix.real_space_refine on Fri May 9 21:54:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1o_44086/05_2025/9b1o_44086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1o_44086/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b1o_44086/05_2025/9b1o_44086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1o_44086/05_2025/9b1o_44086.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1o_44086/05_2025/9b1o_44086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1o_44086/05_2025/9b1o_44086.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.77, per 1000 atoms: 0.96 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: 1.11 Conformation dependent library (CDL) restraints added in 501.0 milliseconds 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: 0.44 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: 1.11 Time building geometry restraints manager: 1.25 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: 3.370 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.002 TRP A 50 HIS 0.002 0.001 HIS A 47 PHE 0.023 0.002 PHE A 344 TYR 0.031 0.002 TYR A 272 ARG 0.004 0.001 ARG A 401 Details of bonding type rmsd link_NAG-ASN : bond 0.00926 ( 1) link_NAG-ASN : angle 1.79066 ( 3) hydrogen bonds : bond 0.12818 ( 267) hydrogen bonds : angle 5.72788 ( 762) SS BOND : bond 0.00051 ( 2) SS BOND : angle 2.11335 ( 4) covalent geometry : bond 0.00441 ( 4044) covalent geometry : angle 0.76373 ( 5515) *********************** 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 : 0.396 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: 0.2334 time to fit residues: 18.7054 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.164786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116760 restraints weight = 4391.101| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.59 r_work: 0.3228 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1850 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= 0.152 Angle : 0.582 7.246 5522 Z= 0.295 Chirality : 0.040 0.129 651 Planarity : 0.005 0.048 686 Dihedral : 4.292 19.412 570 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.48 % Allowed : 5.29 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.37), residues: 513 helix: 0.83 (0.26), residues: 368 sheet: None (None), residues: 0 loop : 1.40 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.003 0.001 HIS A 83 PHE 0.014 0.002 PHE A 356 TYR 0.021 0.002 TYR A 272 ARG 0.006 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 1) link_NAG-ASN : angle 1.35818 ( 3) hydrogen bonds : bond 0.05468 ( 267) hydrogen bonds : angle 4.32813 ( 762) SS BOND : bond 0.00228 ( 2) SS BOND : angle 1.75230 ( 4) covalent geometry : bond 0.00343 ( 4044) covalent geometry : angle 0.57953 ( 5515) *********************** 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 : 0.438 Fit side-chains REVERT: A 6 LEU cc_start: 0.7923 (mm) cc_final: 0.7692 (mt) REVERT: A 10 VAL cc_start: 0.7879 (t) cc_final: 0.7658 (p) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.1541 time to fit residues: 10.7849 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 : 0.398 ------------------------------------------------------------------------------- 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 13 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.164334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117489 restraints weight = 4388.048| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.51 r_work: 0.3252 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4047 Z= 0.121 Angle : 0.528 6.595 5522 Z= 0.263 Chirality : 0.038 0.124 651 Planarity : 0.005 0.036 686 Dihedral : 3.829 18.554 570 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.37), residues: 513 helix: 1.56 (0.27), residues: 355 sheet: -1.98 (1.31), residues: 10 loop : 1.54 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.012 0.001 PHE A 356 TYR 0.019 0.002 TYR A 272 ARG 0.004 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 0.96196 ( 3) hydrogen bonds : bond 0.04753 ( 267) hydrogen bonds : angle 4.08803 ( 762) SS BOND : bond 0.00128 ( 2) SS BOND : angle 1.50939 ( 4) covalent geometry : bond 0.00260 ( 4044) covalent geometry : angle 0.52661 ( 5515) *********************** 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 52 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.399 Fit side-chains REVERT: A 6 LEU cc_start: 0.7896 (mm) cc_final: 0.7648 (mt) REVERT: A 10 VAL cc_start: 0.7965 (t) cc_final: 0.7740 (p) REVERT: A 272 TYR cc_start: 0.6935 (p90) cc_final: 0.5579 (m-10) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1440 time to fit residues: 10.2105 Evaluate side-chains 46 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.165296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118220 restraints weight = 4351.342| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.62 r_work: 0.3212 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2486 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= 0.146 Angle : 0.541 6.349 5522 Z= 0.269 Chirality : 0.039 0.133 651 Planarity : 0.004 0.036 686 Dihedral : 3.697 14.919 570 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.72 % Allowed : 8.17 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.37), residues: 513 helix: 1.62 (0.27), residues: 356 sheet: -2.19 (1.36), residues: 10 loop : 1.01 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 50 HIS 0.002 0.001 HIS A 83 PHE 0.016 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.003 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 1) link_NAG-ASN : angle 1.04683 ( 3) hydrogen bonds : bond 0.04953 ( 267) hydrogen bonds : angle 4.05651 ( 762) SS BOND : bond 0.00195 ( 2) SS BOND : angle 1.53488 ( 4) covalent geometry : bond 0.00340 ( 4044) covalent geometry : angle 0.53905 ( 5515) *********************** 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 52 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.575 Fit side-chains REVERT: A 10 VAL cc_start: 0.7833 (t) cc_final: 0.7617 (p) REVERT: A 272 TYR cc_start: 0.6746 (p90) cc_final: 0.5353 (m-10) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.1065 time to fit residues: 7.8592 Evaluate side-chains 50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 449 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.166180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118901 restraints weight = 4529.564| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.66 r_work: 0.3222 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2694 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= 0.132 Angle : 0.524 6.923 5522 Z= 0.257 Chirality : 0.038 0.134 651 Planarity : 0.004 0.035 686 Dihedral : 3.568 14.017 570 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.96 % Allowed : 8.17 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.37), residues: 513 helix: 1.71 (0.27), residues: 357 sheet: -2.28 (1.39), residues: 10 loop : 0.98 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 PHE 0.014 0.001 PHE A 358 TYR 0.018 0.002 TYR A 272 ARG 0.003 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 1) link_NAG-ASN : angle 0.94929 ( 3) hydrogen bonds : bond 0.04618 ( 267) hydrogen bonds : angle 3.96705 ( 762) SS BOND : bond 0.00176 ( 2) SS BOND : angle 1.44486 ( 4) covalent geometry : bond 0.00304 ( 4044) covalent geometry : angle 0.52235 ( 5515) *********************** 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 54 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.412 Fit side-chains REVERT: A 10 VAL cc_start: 0.7775 (t) cc_final: 0.7572 (p) REVERT: A 272 TYR cc_start: 0.6801 (p90) cc_final: 0.5380 (m-10) outliers start: 4 outliers final: 4 residues processed: 51 average time/residue: 0.1041 time to fit residues: 7.7258 Evaluate side-chains 52 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.163545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117474 restraints weight = 4455.875| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.58 r_work: 0.3237 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2787 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= 0.125 Angle : 0.533 10.659 5522 Z= 0.257 Chirality : 0.038 0.137 651 Planarity : 0.004 0.033 686 Dihedral : 3.503 13.610 570 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.72 % Allowed : 9.38 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.37), residues: 513 helix: 1.81 (0.27), residues: 357 sheet: -2.30 (1.42), residues: 10 loop : 0.99 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.014 0.001 PHE A 358 TYR 0.018 0.002 TYR A 272 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 1) link_NAG-ASN : angle 0.96197 ( 3) hydrogen bonds : bond 0.04503 ( 267) hydrogen bonds : angle 3.92347 ( 762) SS BOND : bond 0.00182 ( 2) SS BOND : angle 1.34766 ( 4) covalent geometry : bond 0.00283 ( 4044) covalent geometry : angle 0.53169 ( 5515) *********************** 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 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.430 Fit side-chains REVERT: A 10 VAL cc_start: 0.7738 (t) cc_final: 0.7538 (p) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.1047 time to fit residues: 7.3741 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 : 0.424 ------------------------------------------------------------------------------- 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 494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 7 optimal weight: 0.0070 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.164574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118644 restraints weight = 4432.964| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.58 r_work: 0.3253 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2959 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= 0.116 Angle : 0.525 10.106 5522 Z= 0.253 Chirality : 0.037 0.138 651 Planarity : 0.004 0.032 686 Dihedral : 3.420 12.697 570 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.20 % Allowed : 9.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.37), residues: 513 helix: 1.95 (0.27), residues: 357 sheet: -2.48 (1.38), residues: 10 loop : 0.99 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.000 HIS A 242 PHE 0.013 0.001 PHE A 358 TYR 0.011 0.001 TYR A 272 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 1) link_NAG-ASN : angle 0.91124 ( 3) hydrogen bonds : bond 0.04250 ( 267) hydrogen bonds : angle 3.85686 ( 762) SS BOND : bond 0.00154 ( 2) SS BOND : angle 1.27588 ( 4) covalent geometry : bond 0.00254 ( 4044) covalent geometry : angle 0.52382 ( 5515) *********************** 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: 5 poor density : 51 time to evaluate : 0.468 Fit side-chains REVERT: A 425 GLU cc_start: 0.7276 (tt0) cc_final: 0.7014 (tm-30) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 0.1069 time to fit residues: 8.1995 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 : 0.446 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 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 = 0.3875 r_free = 0.3875 target = 0.162588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116484 restraints weight = 4401.344| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.57 r_work: 0.3226 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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= 0.136 Angle : 0.541 10.435 5522 Z= 0.261 Chirality : 0.038 0.139 651 Planarity : 0.004 0.033 686 Dihedral : 3.438 14.036 570 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.37), residues: 513 helix: 1.96 (0.27), residues: 356 sheet: -2.73 (1.37), residues: 10 loop : 1.02 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 PHE 0.015 0.001 PHE A 358 TYR 0.013 0.001 TYR A 272 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 1) link_NAG-ASN : angle 0.95237 ( 3) hydrogen bonds : bond 0.04593 ( 267) hydrogen bonds : angle 3.89982 ( 762) SS BOND : bond 0.00192 ( 2) SS BOND : angle 1.34464 ( 4) covalent geometry : bond 0.00315 ( 4044) covalent geometry : angle 0.53918 ( 5515) *********************** 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 : 0.399 Fit side-chains REVERT: A 272 TYR cc_start: 0.7450 (p90) cc_final: 0.5561 (m-10) REVERT: A 425 GLU cc_start: 0.7549 (tt0) cc_final: 0.7123 (tm-30) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.0932 time to fit residues: 7.0780 Evaluate side-chains 50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 449 THR 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 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.162019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115743 restraints weight = 4464.733| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.50 r_work: 0.3243 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3016 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= 0.139 Angle : 0.539 10.613 5522 Z= 0.261 Chirality : 0.038 0.138 651 Planarity : 0.004 0.032 686 Dihedral : 3.444 14.131 570 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.20 % Allowed : 9.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.37), residues: 513 helix: 1.97 (0.27), residues: 356 sheet: -2.66 (1.44), residues: 10 loop : 1.03 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 PHE 0.015 0.001 PHE A 358 TYR 0.013 0.001 TYR A 272 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 1) link_NAG-ASN : angle 0.93393 ( 3) hydrogen bonds : bond 0.04604 ( 267) hydrogen bonds : angle 3.89950 ( 762) SS BOND : bond 0.00200 ( 2) SS BOND : angle 1.34194 ( 4) covalent geometry : bond 0.00324 ( 4044) covalent geometry : angle 0.53722 ( 5515) *********************** 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 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.401 Fit side-chains REVERT: A 272 TYR cc_start: 0.7516 (p90) cc_final: 0.5647 (m-10) REVERT: A 425 GLU cc_start: 0.7520 (tt0) cc_final: 0.7114 (tm-30) outliers start: 5 outliers final: 5 residues processed: 46 average time/residue: 0.1075 time to fit residues: 7.2135 Evaluate side-chains 52 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 449 THR 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 22 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.0970 chunk 49 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.164644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118790 restraints weight = 4451.693| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.50 r_work: 0.3284 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4047 Z= 0.111 Angle : 0.517 10.724 5522 Z= 0.248 Chirality : 0.037 0.141 651 Planarity : 0.004 0.030 686 Dihedral : 3.339 12.076 570 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.96 % Allowed : 10.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.37), residues: 513 helix: 2.13 (0.27), residues: 357 sheet: -2.48 (1.55), residues: 10 loop : 1.00 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.000 HIS A 242 PHE 0.012 0.001 PHE A 358 TYR 0.012 0.001 TYR A 272 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 1) link_NAG-ASN : angle 0.87999 ( 3) hydrogen bonds : bond 0.04053 ( 267) hydrogen bonds : angle 3.78714 ( 762) SS BOND : bond 0.00129 ( 2) SS BOND : angle 1.17477 ( 4) covalent geometry : bond 0.00240 ( 4044) covalent geometry : angle 0.51613 ( 5515) ********************** 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 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.421 Fit side-chains REVERT: A 272 TYR cc_start: 0.7446 (p90) cc_final: 0.5637 (m-10) REVERT: A 425 GLU cc_start: 0.7488 (tt0) cc_final: 0.7104 (tm-30) outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.0985 time to fit residues: 7.0595 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 : 0.420 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.0570 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.168115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121208 restraints weight = 4356.511| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.55 r_work: 0.3277 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4047 Z= 0.110 Angle : 0.512 10.456 5522 Z= 0.245 Chirality : 0.037 0.140 651 Planarity : 0.004 0.031 686 Dihedral : 3.270 11.510 570 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.20 % Allowed : 10.34 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.37), residues: 513 helix: 2.21 (0.27), residues: 357 sheet: -2.35 (1.68), residues: 10 loop : 1.03 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.000 HIS A 242 PHE 0.012 0.001 PHE A 358 TYR 0.013 0.001 TYR A 272 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 1) link_NAG-ASN : angle 0.86925 ( 3) hydrogen bonds : bond 0.04035 ( 267) hydrogen bonds : angle 3.74793 ( 762) SS BOND : bond 0.00118 ( 2) SS BOND : angle 1.16062 ( 4) covalent geometry : bond 0.00237 ( 4044) covalent geometry : angle 0.51083 ( 5515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2500.96 seconds wall clock time: 44 minutes 3.23 seconds (2643.23 seconds total)