Starting phenix.real_space_refine on Fri May 9 21:57:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1j_44081/05_2025/9b1j_44081.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1j_44081/05_2025/9b1j_44081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b1j_44081/05_2025/9b1j_44081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1j_44081/05_2025/9b1j_44081.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1j_44081/05_2025/9b1j_44081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1j_44081/05_2025/9b1j_44081.cif" } resolution = 3.0 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= 0.001 sd= 0.032 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 30 5.16 5 C 2570 2.51 5 N 666 2.21 5 O 686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3953 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'NAG': 1, 'PO4': 1, 'URC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.97, per 1000 atoms: 1.00 Number of scatterers: 3953 At special positions: 0 Unit cell: (57.761, 90.211, 99.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 1 15.00 O 686 8.00 N 666 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: 1.10 Conformation dependent library (CDL) restraints added in 499.5 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: 32 helices and 2 sheets defined 81.9% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 14 through 37 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: 3.732A 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: 3.745A 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: 3.536A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) 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 221 removed outlier: 3.560A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 removed outlier: 6.174A pdb=" N ARG A 225 " --> pdb=" O THR A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.277A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.805A 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 274 removed outlier: 4.102A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.603A pdb=" N GLN A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.975A pdb=" N ALA A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.882A pdb=" N VAL A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 4.173A pdb=" N PHE A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 364 removed outlier: 4.642A pdb=" N PHE A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 356 " --> pdb=" O CYS A 352 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 357 " --> pdb=" O TRP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 400 through 422 removed outlier: 4.053A pdb=" N THR A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 452 removed outlier: 3.695A pdb=" N THR A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 483 through 489 removed outlier: 4.042A pdb=" N VAL A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 4.145A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Proline residue: A 501 - end of helix removed outlier: 3.699A 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 86 through 88 268 hydrogen bonds defined for protein. 768 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: 1.17 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1241 1.34 - 1.46: 920 1.46 - 1.58: 1844 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4052 Sorted by residual: bond pdb=" C2 URC A 602 " pdb=" O11 URC A 602 " ideal model delta sigma weight residual 1.213 1.364 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" C8 URC A 602 " pdb=" O24 URC A 602 " ideal model delta sigma weight residual 1.215 1.353 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C4 URC A 602 " pdb=" C5 URC A 602 " ideal model delta sigma weight residual 1.358 1.495 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" C6 URC A 602 " pdb=" O13 URC A 602 " ideal model delta sigma weight residual 1.218 1.348 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C8 URC A 602 " pdb=" N7 URC A 602 " ideal model delta sigma weight residual 1.360 1.435 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 4047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 5453 2.71 - 5.42: 61 5.42 - 8.13: 8 8.13 - 10.84: 4 10.84 - 13.55: 3 Bond angle restraints: 5529 Sorted by residual: angle pdb=" N1 URC A 602 " pdb=" C2 URC A 602 " pdb=" N3 URC A 602 " ideal model delta sigma weight residual 114.62 128.17 -13.55 3.00e+00 1.11e-01 2.04e+01 angle pdb=" N7 URC A 602 " pdb=" C8 URC A 602 " pdb=" N9 URC A 602 " ideal model delta sigma weight residual 104.73 116.67 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C2 URC A 602 " pdb=" N1 URC A 602 " pdb=" C6 URC A 602 " ideal model delta sigma weight residual 129.31 117.54 11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA ARG A 473 " pdb=" CB ARG A 473 " pdb=" CG ARG A 473 " ideal model delta sigma weight residual 114.10 107.00 7.10 2.00e+00 2.50e-01 1.26e+01 angle pdb=" C5 URC A 602 " pdb=" C6 URC A 602 " pdb=" N1 URC A 602 " ideal model delta sigma weight residual 111.19 121.50 -10.31 3.00e+00 1.11e-01 1.18e+01 ... (remaining 5524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 2229 16.05 - 32.11: 131 32.11 - 48.16: 21 48.16 - 64.22: 7 64.22 - 80.27: 3 Dihedral angle restraints: 2391 sinusoidal: 919 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 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PHE A 361 " pdb=" C PHE A 361 " pdb=" N GLY A 362 " pdb=" CA GLY A 362 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+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 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 356 0.026 - 0.051: 176 0.051 - 0.077: 74 0.077 - 0.103: 31 0.103 - 0.128: 14 Chirality restraints: 651 Sorted by residual: chirality pdb=" CA PRO A 52 " pdb=" N PRO A 52 " pdb=" C PRO A 52 " pdb=" CB PRO A 52 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-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 2.59 0.12 2.00e-01 2.50e+01 3.84e-01 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 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 648 not shown) Planarity restraints: 686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 358 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C PHE A 358 " -0.027 2.00e-02 2.50e+03 pdb=" O PHE A 358 " 0.010 2.00e-02 2.50e+03 pdb=" N THR A 359 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 297 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C ARG A 297 " 0.026 2.00e-02 2.50e+03 pdb=" O ARG A 297 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 298 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 483 " -0.116 9.50e-02 1.11e+02 5.18e-02 1.65e+00 pdb=" NE ARG A 483 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 483 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 483 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 483 " -0.004 2.00e-02 2.50e+03 ... (remaining 683 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1557 2.89 - 3.39: 3985 3.39 - 3.90: 6535 3.90 - 4.40: 7587 4.40 - 4.90: 12585 Nonbonded interactions: 32249 Sorted by model distance: nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.389 3.040 nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.409 3.040 nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.450 3.040 nonbonded pdb=" NE ARG A 473 " pdb=" O3 PO4 A 603 " model vdw 2.467 3.120 nonbonded pdb=" OD1 ASN A 56 " pdb=" OG1 THR A 58 " model vdw 2.494 3.040 ... (remaining 32244 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.650 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.006 0.151 4055 Z= 0.322 Angle : 0.836 13.548 5536 Z= 0.410 Chirality : 0.040 0.128 651 Planarity : 0.005 0.052 685 Dihedral : 11.220 80.271 1435 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 0.31 (0.36), residues: 513 helix: 0.01 (0.26), residues: 358 sheet: -1.68 (1.59), residues: 10 loop : 1.41 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.004 0.001 HIS A 398 PHE 0.015 0.002 PHE A 356 TYR 0.020 0.002 TYR A 272 ARG 0.004 0.001 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00805 ( 1) link_NAG-ASN : angle 0.30345 ( 3) hydrogen bonds : bond 0.13468 ( 268) hydrogen bonds : angle 5.75888 ( 768) SS BOND : bond 0.00286 ( 2) SS BOND : angle 2.51881 ( 4) covalent geometry : bond 0.00646 ( 4052) covalent geometry : angle 0.83327 ( 5529) *********************** 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 61 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.426 Fit side-chains REVERT: A 115 ASP cc_start: 0.8474 (m-30) cc_final: 0.8099 (m-30) REVERT: A 126 SER cc_start: 0.8831 (t) cc_final: 0.8425 (m) REVERT: A 144 MET cc_start: 0.7503 (ttm) cc_final: 0.7286 (ttt) REVERT: A 225 ARG cc_start: 0.6953 (ptt180) cc_final: 0.6463 (ptp-170) REVERT: A 285 ILE cc_start: 0.7800 (mt) cc_final: 0.7474 (mp) REVERT: A 295 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6880 (mm-30) REVERT: A 390 MET cc_start: 0.7370 (mmm) cc_final: 0.7162 (mmp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.9396 time to fit residues: 59.9983 Evaluate side-chains 53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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: 0.5980 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 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 = 0.4109 r_free = 0.4109 target = 0.193663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143217 restraints weight = 4044.434| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.93 r_work: 0.3495 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4055 Z= 0.146 Angle : 0.579 6.416 5536 Z= 0.295 Chirality : 0.041 0.124 651 Planarity : 0.005 0.041 685 Dihedral : 4.291 16.272 569 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.44 % Allowed : 7.93 % Favored : 90.62 % 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: 1.51 (0.37), residues: 513 helix: 0.93 (0.27), residues: 354 sheet: None (None), residues: 0 loop : 1.57 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 50 HIS 0.004 0.001 HIS A 139 PHE 0.014 0.002 PHE A 354 TYR 0.019 0.002 TYR A 272 ARG 0.003 0.000 ARG A 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 1) link_NAG-ASN : angle 0.55541 ( 3) hydrogen bonds : bond 0.05207 ( 268) hydrogen bonds : angle 4.55395 ( 768) SS BOND : bond 0.00055 ( 2) SS BOND : angle 1.83138 ( 4) covalent geometry : bond 0.00323 ( 4052) covalent geometry : angle 0.57727 ( 5529) *********************** 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 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.340 Fit side-chains REVERT: A 115 ASP cc_start: 0.8329 (m-30) cc_final: 0.8104 (m-30) REVERT: A 126 SER cc_start: 0.8887 (t) cc_final: 0.8406 (m) REVERT: A 225 ARG cc_start: 0.7062 (ptt180) cc_final: 0.6507 (ptp-170) REVERT: A 285 ILE cc_start: 0.7882 (mt) cc_final: 0.7549 (mt) REVERT: A 295 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7043 (mm-30) outliers start: 6 outliers final: 2 residues processed: 55 average time/residue: 0.9028 time to fit residues: 52.2660 Evaluate side-chains 48 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 272 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 33 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 0.0070 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.190883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140675 restraints weight = 4056.148| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.95 r_work: 0.3527 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4055 Z= 0.121 Angle : 0.536 7.811 5536 Z= 0.267 Chirality : 0.039 0.119 651 Planarity : 0.004 0.039 685 Dihedral : 3.848 15.081 569 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.92 % Allowed : 8.89 % 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: 1.83 (0.37), residues: 513 helix: 1.33 (0.27), residues: 354 sheet: -1.83 (1.70), residues: 10 loop : 1.53 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.003 0.001 HIS A 242 PHE 0.015 0.001 PHE A 354 TYR 0.020 0.002 TYR A 272 ARG 0.001 0.000 ARG A 15 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 1) link_NAG-ASN : angle 0.86070 ( 3) hydrogen bonds : bond 0.04536 ( 268) hydrogen bonds : angle 4.32044 ( 768) SS BOND : bond 0.00119 ( 2) SS BOND : angle 1.43510 ( 4) covalent geometry : bond 0.00261 ( 4052) covalent geometry : angle 0.53462 ( 5529) *********************** 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 46 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.417 Fit side-chains REVERT: A 126 SER cc_start: 0.8871 (t) cc_final: 0.8367 (m) REVERT: A 225 ARG cc_start: 0.7126 (ptt180) cc_final: 0.6517 (ptp-170) REVERT: A 285 ILE cc_start: 0.7817 (mt) cc_final: 0.7482 (mt) REVERT: A 401 ARG cc_start: 0.3940 (OUTLIER) cc_final: 0.3187 (mpt180) outliers start: 8 outliers final: 2 residues processed: 43 average time/residue: 1.0303 time to fit residues: 46.4069 Evaluate side-chains 42 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.192270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143973 restraints weight = 4071.140| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.84 r_work: 0.3436 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4055 Z= 0.134 Angle : 0.537 7.412 5536 Z= 0.267 Chirality : 0.040 0.118 651 Planarity : 0.004 0.038 685 Dihedral : 3.760 14.422 569 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.16 % Allowed : 9.62 % 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 (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: 1.67 (0.37), residues: 513 helix: 1.25 (0.27), residues: 363 sheet: -2.35 (1.53), residues: 10 loop : 1.38 (0.57), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.003 0.001 HIS A 242 PHE 0.015 0.002 PHE A 354 TYR 0.019 0.002 TYR A 272 ARG 0.003 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 0.78218 ( 3) hydrogen bonds : bond 0.04652 ( 268) hydrogen bonds : angle 4.29141 ( 768) SS BOND : bond 0.00131 ( 2) SS BOND : angle 1.39780 ( 4) covalent geometry : bond 0.00307 ( 4052) covalent geometry : angle 0.53617 ( 5529) *********************** 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: 9 poor density : 43 time to evaluate : 0.430 Fit side-chains REVERT: A 6 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6467 (mm) REVERT: A 126 SER cc_start: 0.8866 (t) cc_final: 0.8363 (m) REVERT: A 165 ASP cc_start: 0.7651 (m-30) cc_final: 0.7386 (m-30) REVERT: A 219 MET cc_start: 0.7197 (mtp) cc_final: 0.6990 (mtp) REVERT: A 225 ARG cc_start: 0.7173 (ptt180) cc_final: 0.6654 (ptp-170) REVERT: A 312 THR cc_start: 0.7045 (OUTLIER) cc_final: 0.6800 (t) REVERT: A 401 ARG cc_start: 0.3968 (OUTLIER) cc_final: 0.3251 (mmt180) REVERT: A 446 THR cc_start: 0.6736 (m) cc_final: 0.6385 (p) outliers start: 9 outliers final: 4 residues processed: 50 average time/residue: 0.9559 time to fit residues: 50.1206 Evaluate side-chains 45 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.195066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147760 restraints weight = 4183.089| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.84 r_work: 0.3471 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4055 Z= 0.113 Angle : 0.510 7.407 5536 Z= 0.251 Chirality : 0.038 0.119 651 Planarity : 0.004 0.036 685 Dihedral : 3.597 13.709 569 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.44 % Allowed : 11.06 % Favored : 87.50 % 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: 2.21 (0.37), residues: 513 helix: 1.78 (0.27), residues: 344 sheet: -2.45 (1.56), residues: 10 loop : 1.27 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.003 0.001 HIS A 242 PHE 0.013 0.001 PHE A 354 TYR 0.016 0.002 TYR A 272 ARG 0.002 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 1) link_NAG-ASN : angle 0.78852 ( 3) hydrogen bonds : bond 0.04153 ( 268) hydrogen bonds : angle 4.14317 ( 768) SS BOND : bond 0.00140 ( 2) SS BOND : angle 1.17841 ( 4) covalent geometry : bond 0.00242 ( 4052) covalent geometry : angle 0.50875 ( 5529) *********************** 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 47 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.382 Fit side-chains REVERT: A 126 SER cc_start: 0.8852 (t) cc_final: 0.8347 (m) REVERT: A 219 MET cc_start: 0.7137 (mtp) cc_final: 0.6905 (mtp) REVERT: A 225 ARG cc_start: 0.7147 (ptt180) cc_final: 0.6615 (ptp-170) REVERT: A 312 THR cc_start: 0.7011 (OUTLIER) cc_final: 0.6780 (t) REVERT: A 446 THR cc_start: 0.6731 (m) cc_final: 0.6352 (p) REVERT: A 485 LEU cc_start: 0.7087 (mt) cc_final: 0.6871 (mt) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.8308 time to fit residues: 39.4258 Evaluate side-chains 39 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 49 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 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 = 0.4085 r_free = 0.4085 target = 0.191067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143757 restraints weight = 4115.801| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.80 r_work: 0.3451 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4055 Z= 0.135 Angle : 0.536 8.002 5536 Z= 0.264 Chirality : 0.039 0.118 651 Planarity : 0.004 0.036 685 Dihedral : 3.596 13.186 569 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.64 % Allowed : 10.58 % Favored : 86.78 % 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 (0.38), residues: 513 helix: 1.61 (0.27), residues: 350 sheet: -2.38 (1.69), residues: 10 loop : 1.41 (0.56), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.003 0.001 HIS A 242 PHE 0.015 0.002 PHE A 354 TYR 0.019 0.002 TYR A 272 ARG 0.003 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 1) link_NAG-ASN : angle 0.81320 ( 3) hydrogen bonds : bond 0.04544 ( 268) hydrogen bonds : angle 4.20850 ( 768) SS BOND : bond 0.00136 ( 2) SS BOND : angle 1.25399 ( 4) covalent geometry : bond 0.00312 ( 4052) covalent geometry : angle 0.53476 ( 5529) *********************** 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 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.386 Fit side-chains REVERT: A 126 SER cc_start: 0.8879 (t) cc_final: 0.8366 (m) REVERT: A 219 MET cc_start: 0.7175 (mtp) cc_final: 0.6855 (mtp) REVERT: A 225 ARG cc_start: 0.7192 (ptt180) cc_final: 0.6641 (ptp-170) REVERT: A 401 ARG cc_start: 0.4027 (OUTLIER) cc_final: 0.3287 (mmt180) REVERT: A 485 LEU cc_start: 0.7142 (mt) cc_final: 0.6880 (mt) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 0.9624 time to fit residues: 47.3874 Evaluate side-chains 42 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 49 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.194202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.148813 restraints weight = 4086.848| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.73 r_work: 0.3489 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4055 Z= 0.112 Angle : 0.508 7.623 5536 Z= 0.249 Chirality : 0.038 0.119 651 Planarity : 0.004 0.034 685 Dihedral : 3.504 13.270 569 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.16 % Allowed : 11.06 % Favored : 86.78 % 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: 2.37 (0.38), residues: 513 helix: 1.89 (0.27), residues: 344 sheet: -2.32 (1.75), residues: 10 loop : 1.36 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.003 0.001 HIS A 242 PHE 0.012 0.001 PHE A 354 TYR 0.014 0.002 TYR A 272 ARG 0.002 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 0.76364 ( 3) hydrogen bonds : bond 0.04073 ( 268) hydrogen bonds : angle 4.09641 ( 768) SS BOND : bond 0.00128 ( 2) SS BOND : angle 1.22431 ( 4) covalent geometry : bond 0.00244 ( 4052) covalent geometry : angle 0.50659 ( 5529) *********************** 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 47 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.391 Fit side-chains REVERT: A 126 SER cc_start: 0.8863 (t) cc_final: 0.8352 (m) REVERT: A 219 MET cc_start: 0.7160 (mtp) cc_final: 0.6924 (mtp) REVERT: A 225 ARG cc_start: 0.7179 (ptt180) cc_final: 0.6600 (ptp-170) REVERT: A 312 THR cc_start: 0.7098 (OUTLIER) cc_final: 0.6845 (t) REVERT: A 401 ARG cc_start: 0.4115 (OUTLIER) cc_final: 0.3359 (mmt180) REVERT: A 446 THR cc_start: 0.6677 (m) cc_final: 0.6329 (p) REVERT: A 485 LEU cc_start: 0.7154 (mt) cc_final: 0.6940 (mt) outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.9964 time to fit residues: 46.9308 Evaluate side-chains 42 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 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 = 0.4105 r_free = 0.4105 target = 0.193479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147094 restraints weight = 4077.389| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.76 r_work: 0.3438 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4055 Z= 0.142 Angle : 0.550 8.051 5536 Z= 0.270 Chirality : 0.040 0.122 651 Planarity : 0.004 0.036 685 Dihedral : 3.566 12.950 569 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.92 % Allowed : 11.54 % Favored : 86.54 % 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: 2.13 (0.38), residues: 513 helix: 1.64 (0.27), residues: 350 sheet: -2.51 (1.72), residues: 10 loop : 1.47 (0.56), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.002 0.001 HIS A 139 PHE 0.015 0.002 PHE A 354 TYR 0.020 0.002 TYR A 272 ARG 0.002 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 1) link_NAG-ASN : angle 0.84261 ( 3) hydrogen bonds : bond 0.04631 ( 268) hydrogen bonds : angle 4.20232 ( 768) SS BOND : bond 0.00161 ( 2) SS BOND : angle 1.27953 ( 4) covalent geometry : bond 0.00333 ( 4052) covalent geometry : angle 0.54887 ( 5529) *********************** 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 47 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.445 Fit side-chains REVERT: A 126 SER cc_start: 0.8869 (t) cc_final: 0.8336 (m) REVERT: A 219 MET cc_start: 0.7122 (mtp) cc_final: 0.6882 (mtp) REVERT: A 225 ARG cc_start: 0.7165 (ptt180) cc_final: 0.6594 (ptp-170) REVERT: A 401 ARG cc_start: 0.3949 (OUTLIER) cc_final: 0.3195 (mmt180) REVERT: A 414 LEU cc_start: 0.7329 (mt) cc_final: 0.7099 (mt) REVERT: A 446 THR cc_start: 0.6740 (m) cc_final: 0.6348 (p) REVERT: A 485 LEU cc_start: 0.7171 (mt) cc_final: 0.6894 (mt) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 1.0298 time to fit residues: 49.6584 Evaluate side-chains 42 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 19 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 33 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.195252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.149589 restraints weight = 4110.187| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.75 r_work: 0.3487 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4055 Z= 0.107 Angle : 0.510 8.387 5536 Z= 0.248 Chirality : 0.038 0.119 651 Planarity : 0.004 0.034 685 Dihedral : 3.453 13.019 569 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.44 % Allowed : 12.02 % Favored : 86.54 % 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: 2.50 (0.38), residues: 513 helix: 1.98 (0.27), residues: 344 sheet: -2.26 (1.74), residues: 10 loop : 1.45 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.003 0.001 HIS A 242 PHE 0.011 0.001 PHE A 354 TYR 0.023 0.002 TYR A 272 ARG 0.002 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 0.73881 ( 3) hydrogen bonds : bond 0.03895 ( 268) hydrogen bonds : angle 4.05354 ( 768) SS BOND : bond 0.00106 ( 2) SS BOND : angle 1.19606 ( 4) covalent geometry : bond 0.00226 ( 4052) covalent geometry : angle 0.50875 ( 5529) *********************** 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 40 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.411 Fit side-chains REVERT: A 126 SER cc_start: 0.8864 (t) cc_final: 0.8333 (m) REVERT: A 219 MET cc_start: 0.7106 (mtp) cc_final: 0.6866 (mtp) REVERT: A 401 ARG cc_start: 0.3997 (OUTLIER) cc_final: 0.3220 (mmt180) REVERT: A 414 LEU cc_start: 0.7314 (mt) cc_final: 0.7058 (mt) REVERT: A 446 THR cc_start: 0.6643 (m) cc_final: 0.6260 (p) REVERT: A 485 LEU cc_start: 0.7101 (mt) cc_final: 0.6877 (mt) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.9052 time to fit residues: 37.1997 Evaluate side-chains 39 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 19 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.193910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148050 restraints weight = 4096.317| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.75 r_work: 0.3468 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4055 Z= 0.122 Angle : 0.536 8.731 5536 Z= 0.261 Chirality : 0.039 0.136 651 Planarity : 0.004 0.035 685 Dihedral : 3.457 12.555 569 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.68 % Allowed : 11.78 % Favored : 86.54 % 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: 2.41 (0.38), residues: 513 helix: 1.91 (0.27), residues: 344 sheet: -2.46 (1.69), residues: 10 loop : 1.43 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.003 0.001 HIS A 242 PHE 0.013 0.001 PHE A 354 TYR 0.015 0.002 TYR A 272 ARG 0.002 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 1) link_NAG-ASN : angle 0.77364 ( 3) hydrogen bonds : bond 0.04229 ( 268) hydrogen bonds : angle 4.09623 ( 768) SS BOND : bond 0.00119 ( 2) SS BOND : angle 1.23704 ( 4) covalent geometry : bond 0.00277 ( 4052) covalent geometry : angle 0.53478 ( 5529) ********************** 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 45 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.421 Fit side-chains REVERT: A 126 SER cc_start: 0.8881 (t) cc_final: 0.8346 (m) REVERT: A 219 MET cc_start: 0.7114 (mtp) cc_final: 0.6877 (mtp) REVERT: A 225 ARG cc_start: 0.7187 (ptt180) cc_final: 0.6583 (ptp-170) REVERT: A 401 ARG cc_start: 0.4076 (OUTLIER) cc_final: 0.3302 (mmt180) REVERT: A 414 LEU cc_start: 0.7375 (mt) cc_final: 0.7133 (mt) REVERT: A 446 THR cc_start: 0.6717 (m) cc_final: 0.6334 (p) REVERT: A 485 LEU cc_start: 0.7198 (mt) cc_final: 0.6967 (mt) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.9618 time to fit residues: 44.5059 Evaluate side-chains 41 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.191303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144886 restraints weight = 4145.583| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.77 r_work: 0.3434 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4055 Z= 0.154 Angle : 0.572 8.482 5536 Z= 0.281 Chirality : 0.040 0.130 651 Planarity : 0.004 0.036 685 Dihedral : 3.605 13.379 569 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.92 % Allowed : 11.54 % Favored : 86.54 % 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: 2.19 (0.38), residues: 513 helix: 1.66 (0.27), residues: 349 sheet: -2.65 (1.69), residues: 10 loop : 1.56 (0.56), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.002 0.001 HIS A 242 PHE 0.015 0.002 PHE A 354 TYR 0.020 0.002 TYR A 272 ARG 0.003 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 0.87308 ( 3) hydrogen bonds : bond 0.04823 ( 268) hydrogen bonds : angle 4.23050 ( 768) SS BOND : bond 0.00151 ( 2) SS BOND : angle 1.32608 ( 4) covalent geometry : bond 0.00367 ( 4052) covalent geometry : angle 0.57072 ( 5529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3230.12 seconds wall clock time: 56 minutes 33.73 seconds (3393.73 seconds total)