Starting phenix.real_space_refine on Wed Sep 17 04:20:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5u_19750/09_2025/8s5u_19750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5u_19750/09_2025/8s5u_19750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8s5u_19750/09_2025/8s5u_19750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5u_19750/09_2025/8s5u_19750.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s5u_19750/09_2025/8s5u_19750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5u_19750/09_2025/8s5u_19750.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 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 20 5.16 5 C 2652 2.51 5 N 620 2.21 5 O 706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3998 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 982 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "A" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2984 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'NAG': 1, 'VIB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.20, per 1000 atoms: 0.30 Number of scatterers: 3998 At special positions: 0 Unit cell: (107.1, 72.25, 64.6, 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 20 16.00 O 706 8.00 N 620 7.00 C 2652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 45 " Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 158.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 3 sheets defined 66.9% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.728A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 removed outlier: 3.503A pdb=" N THR B 113 " --> pdb=" O ASN B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'A' and resid 12 through 28 removed outlier: 3.721A pdb=" N THR A 16 " --> pdb=" O TRP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.884A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 78 through 99 removed outlier: 4.364A pdb=" N VAL A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 119 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.504A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 166 removed outlier: 3.540A pdb=" N ARG A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.805A pdb=" N LEU A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 removed outlier: 4.120A pdb=" N SER A 274 " --> pdb=" O GLU A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.505A pdb=" N GLN A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 311 through 335 removed outlier: 3.571A pdb=" N TYR A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.757A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 397 removed outlier: 3.529A pdb=" N CYS A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 426 Processing helix chain 'A' and resid 434 through 455 removed outlier: 4.267A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.896A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.371A pdb=" N VAL B 12 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.371A pdb=" N VAL B 12 " --> pdb=" O SER B 127 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 630 1.32 - 1.44: 1220 1.44 - 1.56: 2225 1.56 - 1.68: 1 1.68 - 1.81: 32 Bond restraints: 4108 Sorted by residual: bond pdb=" C5 VIB A 602 " pdb=" S1 VIB A 602 " ideal model delta sigma weight residual 1.721 1.508 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C4 VIB A 602 " pdb=" N3 VIB A 602 " ideal model delta sigma weight residual 1.385 1.572 -0.187 2.00e-02 2.50e+03 8.79e+01 bond pdb=" C2A VIB A 602 " pdb=" N3A VIB A 602 " ideal model delta sigma weight residual 1.323 1.478 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C2A VIB A 602 " pdb=" N1A VIB A 602 " ideal model delta sigma weight residual 1.331 1.481 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C2 VIB A 602 " pdb=" S1 VIB A 602 " ideal model delta sigma weight residual 1.670 1.539 0.131 2.00e-02 2.50e+03 4.30e+01 ... (remaining 4103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 5562 3.33 - 6.67: 40 6.67 - 10.00: 1 10.00 - 13.34: 0 13.34 - 16.67: 1 Bond angle restraints: 5604 Sorted by residual: angle pdb=" N TYR A 79 " pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 112.34 120.30 -7.96 1.30e+00 5.92e-01 3.75e+01 angle pdb=" C2 VIB A 602 " pdb=" S1 VIB A 602 " pdb=" C5 VIB A 602 " ideal model delta sigma weight residual 91.25 107.92 -16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" N LEU A 95 " pdb=" CA LEU A 95 " pdb=" C LEU A 95 " ideal model delta sigma weight residual 113.23 107.31 5.92 1.24e+00 6.50e-01 2.28e+01 angle pdb=" N SER A 353 " pdb=" CA SER A 353 " pdb=" C SER A 353 " ideal model delta sigma weight residual 112.90 107.37 5.53 1.31e+00 5.83e-01 1.78e+01 angle pdb=" N LEU A 97 " pdb=" CA LEU A 97 " pdb=" C LEU A 97 " ideal model delta sigma weight residual 112.23 106.92 5.31 1.26e+00 6.30e-01 1.77e+01 ... (remaining 5599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 2015 15.89 - 31.78: 247 31.78 - 47.68: 73 47.68 - 63.57: 14 63.57 - 79.46: 6 Dihedral angle restraints: 2355 sinusoidal: 880 harmonic: 1475 Sorted by residual: dihedral pdb=" CA TYR A 126 " pdb=" C TYR A 126 " pdb=" N ILE A 127 " pdb=" CA ILE A 127 " ideal model delta harmonic sigma weight residual -180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CG ARG A 402 " pdb=" CD ARG A 402 " pdb=" NE ARG A 402 " pdb=" CZ ARG A 402 " ideal model delta sinusoidal sigma weight residual 90.00 133.07 -43.07 2 1.50e+01 4.44e-03 9.95e+00 dihedral pdb=" CA LYS A 306 " pdb=" CB LYS A 306 " pdb=" CG LYS A 306 " pdb=" CD LYS A 306 " ideal model delta sinusoidal sigma weight residual -180.00 -121.08 -58.92 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 478 0.044 - 0.088: 133 0.088 - 0.133: 23 0.133 - 0.177: 5 0.177 - 0.221: 3 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA TYR A 273 " pdb=" N TYR A 273 " pdb=" C TYR A 273 " pdb=" CB TYR A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA TYR A 79 " pdb=" N TYR A 79 " pdb=" C TYR A 79 " pdb=" CB TYR A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 45 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 639 not shown) Planarity restraints: 682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " -0.359 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG A 601 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " 0.541 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 80 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO A 81 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 352 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C PHE A 352 " -0.027 2.00e-02 2.50e+03 pdb=" O PHE A 352 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 353 " 0.009 2.00e-02 2.50e+03 ... (remaining 679 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1493 2.85 - 3.36: 3830 3.36 - 3.88: 6459 3.88 - 4.39: 7731 4.39 - 4.90: 13382 Nonbonded interactions: 32895 Sorted by model distance: nonbonded pdb=" OG1 THR B 106 " pdb=" OD2 ASP A 304 " model vdw 2.338 3.040 nonbonded pdb=" O LEU A 377 " pdb=" OG SER A 381 " model vdw 2.394 3.040 nonbonded pdb=" OG SER A 309 " pdb=" OD1 ASP A 311 " model vdw 2.402 3.040 nonbonded pdb=" O ARG B 31 " pdb=" O PRO B 102 " model vdw 2.404 3.040 nonbonded pdb=" O SER B 117 " pdb=" OG SER B 117 " model vdw 2.408 3.040 ... (remaining 32890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.840 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.009 0.213 4110 Z= 0.493 Angle : 0.713 16.670 5609 Z= 0.415 Chirality : 0.043 0.221 642 Planarity : 0.012 0.306 681 Dihedral : 15.772 79.460 1412 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.47 % Allowed : 17.73 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.38), residues: 496 helix: 0.13 (0.30), residues: 290 sheet: -1.03 (0.78), residues: 46 loop : -1.07 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.008 0.001 TYR A 171 PHE 0.026 0.001 PHE A 71 TRP 0.014 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00902 ( 4108) covalent geometry : angle 0.70825 ( 5604) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.31327 ( 2) hydrogen bonds : bond 0.24479 ( 255) hydrogen bonds : angle 8.56255 ( 753) link_NAG-ASN : bond 0.02207 ( 1) link_NAG-ASN : angle 3.53661 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.160 Fit side-chains REVERT: A 75 ASP cc_start: 0.8172 (m-30) cc_final: 0.7907 (m-30) REVERT: A 421 MET cc_start: 0.7598 (ttp) cc_final: 0.7123 (ttp) outliers start: 2 outliers final: 0 residues processed: 69 average time/residue: 0.0754 time to fit residues: 6.6158 Evaluate side-chains 60 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN A 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.127154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114779 restraints weight = 5250.805| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.24 r_work: 0.3086 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4110 Z= 0.164 Angle : 0.563 5.719 5609 Z= 0.304 Chirality : 0.042 0.142 642 Planarity : 0.005 0.063 681 Dihedral : 6.126 58.718 575 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.89 % Allowed : 19.39 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.38), residues: 496 helix: 1.11 (0.30), residues: 300 sheet: -0.74 (0.74), residues: 46 loop : -0.74 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 19 TYR 0.014 0.001 TYR A 445 PHE 0.019 0.002 PHE A 90 TRP 0.020 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4108) covalent geometry : angle 0.56040 ( 5604) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.39737 ( 2) hydrogen bonds : bond 0.06018 ( 255) hydrogen bonds : angle 4.88698 ( 753) link_NAG-ASN : bond 0.00573 ( 1) link_NAG-ASN : angle 2.49343 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.162 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 69 average time/residue: 0.0540 time to fit residues: 5.1249 Evaluate side-chains 55 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.0030 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.127573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.114988 restraints weight = 5127.045| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.26 r_work: 0.3088 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4110 Z= 0.160 Angle : 0.515 5.828 5609 Z= 0.280 Chirality : 0.042 0.140 642 Planarity : 0.005 0.063 681 Dihedral : 5.476 58.350 575 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.36 % Allowed : 20.57 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.38), residues: 496 helix: 1.56 (0.30), residues: 300 sheet: -0.50 (0.73), residues: 46 loop : -0.49 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 429 TYR 0.013 0.001 TYR A 445 PHE 0.021 0.002 PHE A 71 TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4108) covalent geometry : angle 0.51460 ( 5604) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.29033 ( 2) hydrogen bonds : bond 0.05273 ( 255) hydrogen bonds : angle 4.53882 ( 753) link_NAG-ASN : bond 0.00004 ( 1) link_NAG-ASN : angle 1.43667 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.181 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.0556 time to fit residues: 4.8988 Evaluate side-chains 59 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 chunk 21 optimal weight: 0.2980 chunk 19 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.129499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.116903 restraints weight = 5082.476| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.27 r_work: 0.3116 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4110 Z= 0.132 Angle : 0.492 5.778 5609 Z= 0.267 Chirality : 0.041 0.134 642 Planarity : 0.004 0.060 681 Dihedral : 5.339 57.330 575 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.13 % Allowed : 21.75 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.38), residues: 496 helix: 1.77 (0.30), residues: 300 sheet: -0.26 (0.75), residues: 46 loop : -0.27 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 38 TYR 0.014 0.001 TYR A 14 PHE 0.018 0.001 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4108) covalent geometry : angle 0.49083 ( 5604) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.15044 ( 2) hydrogen bonds : bond 0.04752 ( 255) hydrogen bonds : angle 4.33520 ( 753) link_NAG-ASN : bond 0.00000 ( 1) link_NAG-ASN : angle 1.28525 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.145 Fit side-chains REVERT: A 455 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6196 (ttp) outliers start: 9 outliers final: 5 residues processed: 62 average time/residue: 0.0549 time to fit residues: 4.7308 Evaluate side-chains 60 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 22 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3335 r_free = 0.3335 target = 0.127415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.114812 restraints weight = 5170.689| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.27 r_work: 0.3084 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4110 Z= 0.171 Angle : 0.522 5.963 5609 Z= 0.283 Chirality : 0.042 0.141 642 Planarity : 0.004 0.057 681 Dihedral : 5.316 54.828 575 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.84 % Allowed : 21.28 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.39), residues: 496 helix: 1.80 (0.30), residues: 300 sheet: -0.21 (0.73), residues: 46 loop : -0.27 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.023 0.001 TYR A 14 PHE 0.022 0.002 PHE A 71 TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 4108) covalent geometry : angle 0.52119 ( 5604) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.34343 ( 2) hydrogen bonds : bond 0.05149 ( 255) hydrogen bonds : angle 4.37406 ( 753) link_NAG-ASN : bond 0.00048 ( 1) link_NAG-ASN : angle 1.34172 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.117 Fit side-chains REVERT: A 455 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6169 (ttp) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.0592 time to fit residues: 5.1272 Evaluate side-chains 63 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.127833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115235 restraints weight = 5209.491| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.27 r_work: 0.3089 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4110 Z= 0.157 Angle : 0.519 5.910 5609 Z= 0.279 Chirality : 0.042 0.139 642 Planarity : 0.004 0.055 681 Dihedral : 5.203 51.364 575 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.84 % Allowed : 21.51 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.39), residues: 496 helix: 1.86 (0.30), residues: 300 sheet: -0.17 (0.72), residues: 46 loop : -0.30 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.012 0.001 TYR A 445 PHE 0.020 0.002 PHE A 71 TRP 0.018 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 4108) covalent geometry : angle 0.51862 ( 5604) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.20067 ( 2) hydrogen bonds : bond 0.04927 ( 255) hydrogen bonds : angle 4.30033 ( 753) link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 1.30835 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.148 Fit side-chains REVERT: A 455 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6176 (ttp) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.0529 time to fit residues: 4.5281 Evaluate side-chains 64 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 24 optimal weight: 0.0050 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.3172 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.129851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.116985 restraints weight = 5180.452| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.43 r_work: 0.3109 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4110 Z= 0.130 Angle : 0.504 6.376 5609 Z= 0.271 Chirality : 0.040 0.133 642 Planarity : 0.004 0.054 681 Dihedral : 5.053 48.137 575 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.60 % Allowed : 21.75 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.39), residues: 496 helix: 2.01 (0.30), residues: 300 sheet: -0.05 (0.74), residues: 46 loop : -0.24 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.012 0.001 TYR A 445 PHE 0.016 0.001 PHE A 71 TRP 0.018 0.001 TRP A 94 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4108) covalent geometry : angle 0.50316 ( 5604) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.23473 ( 2) hydrogen bonds : bond 0.04495 ( 255) hydrogen bonds : angle 4.19715 ( 753) link_NAG-ASN : bond 0.00083 ( 1) link_NAG-ASN : angle 1.19344 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.164 Fit side-chains REVERT: A 74 THR cc_start: 0.8453 (m) cc_final: 0.8103 (m) REVERT: A 294 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7136 (mm110) REVERT: A 455 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6107 (ttp) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.0625 time to fit residues: 5.1306 Evaluate side-chains 63 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.125768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.113404 restraints weight = 5140.331| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.25 r_work: 0.3068 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4110 Z= 0.212 Angle : 0.560 6.152 5609 Z= 0.300 Chirality : 0.044 0.146 642 Planarity : 0.004 0.056 681 Dihedral : 5.236 47.306 575 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.84 % Allowed : 21.51 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.39), residues: 496 helix: 1.78 (0.30), residues: 300 sheet: -0.19 (0.73), residues: 46 loop : -0.35 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 456 TYR 0.019 0.002 TYR A 280 PHE 0.024 0.002 PHE A 71 TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 4108) covalent geometry : angle 0.55919 ( 5604) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.29741 ( 2) hydrogen bonds : bond 0.05467 ( 255) hydrogen bonds : angle 4.38871 ( 753) link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 1.41316 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.152 Fit side-chains REVERT: A 455 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6233 (ttp) outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.0498 time to fit residues: 4.3039 Evaluate side-chains 65 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.128434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.115563 restraints weight = 5175.304| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.44 r_work: 0.3090 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4110 Z= 0.150 Angle : 0.525 6.919 5609 Z= 0.283 Chirality : 0.042 0.141 642 Planarity : 0.004 0.054 681 Dihedral : 5.123 47.053 575 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.84 % Allowed : 21.75 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.39), residues: 496 helix: 1.90 (0.30), residues: 300 sheet: -0.13 (0.74), residues: 46 loop : -0.31 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.014 0.001 TYR A 280 PHE 0.019 0.001 PHE A 71 TRP 0.019 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4108) covalent geometry : angle 0.52411 ( 5604) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.09290 ( 2) hydrogen bonds : bond 0.04813 ( 255) hydrogen bonds : angle 4.25052 ( 753) link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 1.28116 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.151 Fit side-chains REVERT: A 74 THR cc_start: 0.8495 (m) cc_final: 0.8155 (m) REVERT: A 455 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6068 (ttp) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 0.0499 time to fit residues: 4.2343 Evaluate side-chains 62 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.0070 chunk 12 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.0670 overall best weight: 0.2336 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.131938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.119045 restraints weight = 5015.407| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.41 r_work: 0.3136 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4110 Z= 0.117 Angle : 0.487 7.377 5609 Z= 0.262 Chirality : 0.040 0.132 642 Planarity : 0.004 0.052 681 Dihedral : 4.920 47.200 575 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.36 % Allowed : 21.75 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.39), residues: 496 helix: 2.04 (0.30), residues: 302 sheet: 0.02 (0.74), residues: 46 loop : -0.21 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.013 0.001 TYR A 280 PHE 0.015 0.001 PHE A 71 TRP 0.019 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4108) covalent geometry : angle 0.48618 ( 5604) SS BOND : bond 0.00148 ( 1) SS BOND : angle 0.17713 ( 2) hydrogen bonds : bond 0.04198 ( 255) hydrogen bonds : angle 4.10936 ( 753) link_NAG-ASN : bond 0.00132 ( 1) link_NAG-ASN : angle 1.06308 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.114 Fit side-chains REVERT: A 74 THR cc_start: 0.8359 (m) cc_final: 0.8018 (m) REVERT: A 455 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.5789 (ttp) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.0532 time to fit residues: 4.4952 Evaluate side-chains 63 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.128991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119506 restraints weight = 5125.995| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.02 r_work: 0.3131 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4110 Z= 0.155 Angle : 0.530 7.379 5609 Z= 0.285 Chirality : 0.042 0.140 642 Planarity : 0.004 0.053 681 Dihedral : 5.025 47.005 575 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.89 % Allowed : 22.93 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.39), residues: 496 helix: 1.96 (0.30), residues: 301 sheet: -0.06 (0.73), residues: 46 loop : -0.28 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.013 0.001 TYR A 445 PHE 0.019 0.002 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4108) covalent geometry : angle 0.52946 ( 5604) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.09577 ( 2) hydrogen bonds : bond 0.04766 ( 255) hydrogen bonds : angle 4.20399 ( 753) link_NAG-ASN : bond 0.00114 ( 1) link_NAG-ASN : angle 1.23910 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1166.82 seconds wall clock time: 20 minutes 46.82 seconds (1246.82 seconds total)