Starting phenix.real_space_refine on Wed Jul 1 22:27:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i3u_35156/07_2026/8i3u_35156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3u_35156/07_2026/8i3u_35156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8i3u_35156/07_2026/8i3u_35156.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i3u_35156/07_2026/8i3u_35156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i3u_35156/07_2026/8i3u_35156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3u_35156/07_2026/8i3u_35156.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3u_35156/07_2026/8i3u_35156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3u_35156/07_2026/8i3u_35156.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 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 16 5.16 5 C 2161 2.51 5 N 579 2.21 5 O 652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3408 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 814 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.08, per 1000 atoms: 0.32 Number of scatterers: 3408 At special positions: 0 Unit cell: (63.65, 61.75, 106.4, 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 16 16.00 O 652 8.00 N 579 7.00 C 2161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.39 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 153.8 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 10.3% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.575A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.117A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.339A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.644A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.551A pdb=" N ILE H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.525A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.614A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.427A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 255 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: 0.49 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1100 1.34 - 1.46: 903 1.46 - 1.58: 1473 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 3496 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.42e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CA ILE A 410 " pdb=" CB ILE A 410 " ideal model delta sigma weight residual 1.527 1.538 -0.012 1.31e-02 5.83e+03 7.90e-01 ... (remaining 3491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 4629 1.35 - 2.71: 89 2.71 - 4.06: 22 4.06 - 5.41: 8 5.41 - 6.76: 1 Bond angle restraints: 4749 Sorted by residual: angle pdb=" C PRO L 95 " pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 119.84 113.08 6.76 1.25e+00 6.40e-01 2.93e+01 angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 110.70 114.12 -3.42 1.22e+00 6.72e-01 7.84e+00 angle pdb=" CA PRO L 95 " pdb=" C PRO L 95 " pdb=" N PRO L 95A" ideal model delta sigma weight residual 117.93 120.61 -2.68 1.20e+00 6.94e-01 4.98e+00 angle pdb=" C VAL H 48 " pdb=" N SER H 49 " pdb=" CA SER H 49 " ideal model delta sigma weight residual 122.21 118.76 3.45 1.62e+00 3.81e-01 4.53e+00 angle pdb=" C GLY A 476 " pdb=" N SER A 477 " pdb=" CA SER A 477 " ideal model delta sigma weight residual 121.54 125.09 -3.55 1.91e+00 2.74e-01 3.46e+00 ... (remaining 4744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.54: 1846 11.54 - 23.08: 136 23.08 - 34.61: 45 34.61 - 46.15: 9 46.15 - 57.69: 2 Dihedral angle restraints: 2038 sinusoidal: 791 harmonic: 1247 Sorted by residual: dihedral pdb=" CA PRO L 95 " pdb=" C PRO L 95 " pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR H 91 " pdb=" C TYR H 91 " pdb=" N CYS H 92 " pdb=" CA CYS H 92 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 118.67 -25.67 1 1.00e+01 1.00e-02 9.48e+00 ... (remaining 2035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 301 0.027 - 0.053: 126 0.053 - 0.080: 29 0.080 - 0.106: 37 0.106 - 0.132: 12 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA GLU H 26 " pdb=" N GLU H 26 " pdb=" C GLU H 26 " pdb=" CB GLU H 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA VAL A 382 " pdb=" N VAL A 382 " pdb=" C VAL A 382 " pdb=" CB VAL A 382 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 502 not shown) Planarity restraints: 621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO L 95A" 0.152 5.00e-02 4.00e+02 pdb=" CA PRO L 95A" -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 95A" -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 94 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO L 95 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.20e+00 pdb=" N PRO A 491 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " 0.015 5.00e-02 4.00e+02 ... (remaining 618 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 221 2.74 - 3.28: 3219 3.28 - 3.82: 5418 3.82 - 4.36: 6360 4.36 - 4.90: 11589 Nonbonded interactions: 26807 Sorted by model distance: nonbonded pdb=" O HIS L 49 " pdb=" OG1 THR L 53 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.268 3.040 nonbonded pdb=" NZ LYS A 417 " pdb=" OD2 ASP H 31 " model vdw 2.289 3.120 nonbonded pdb=" O ILE H 29 " pdb=" NH2 ARG H 71 " model vdw 2.308 3.120 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.319 3.120 ... (remaining 26802 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.990 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.490 Find NCS groups from input model: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.007 0.363 3502 Z= 0.331 Angle : 0.641 23.216 4762 Z= 0.343 Chirality : 0.041 0.132 505 Planarity : 0.005 0.088 620 Dihedral : 9.166 57.687 1237 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.09 % Allowed : 5.72 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.41), residues: 431 helix: -1.62 (0.94), residues: 27 sheet: 0.02 (0.46), residues: 132 loop : -0.34 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 18 TYR 0.011 0.001 TYR L 91 PHE 0.006 0.001 PHE A 456 TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 ( 3496) covalent geometry : angle 0.53518 / 0.30 ( 4749) SS BOND : bond 0.16245 / 8.12 ( 5) SS BOND : angle 7.71965 / 4.80 ( 10) hydrogen bonds : bond 0.17501 / 11.17 ( 102) hydrogen bonds : angle 9.43176 / 6.24 ( 255) link_NAG-ASN : bond 0.00215 / 0.11 ( 1) link_NAG-ASN : angle 0.96077 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.078 Fit side-chains REVERT: A 392 PHE cc_start: 0.7569 (m-80) cc_final: 0.7264 (m-80) REVERT: A 444 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8073 (mtmm) REVERT: H 34 MET cc_start: 0.8171 (mmm) cc_final: 0.7867 (mmm) REVERT: L 29 ILE cc_start: 0.7289 (mm) cc_final: 0.7057 (mm) outliers start: 4 outliers final: 0 residues processed: 115 average time/residue: 0.0519 time to fit residues: 7.1442 Evaluate side-chains 81 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN L 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131456 restraints weight = 4482.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135393 restraints weight = 2720.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137963 restraints weight = 1954.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139724 restraints weight = 1552.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140604 restraints weight = 1320.016| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3502 Z= 0.178 Angle : 0.597 8.443 4762 Z= 0.306 Chirality : 0.042 0.154 505 Planarity : 0.006 0.090 620 Dihedral : 4.708 25.976 484 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.54 % Allowed : 14.44 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.41), residues: 431 helix: -1.34 (1.00), residues: 28 sheet: 0.22 (0.47), residues: 130 loop : -0.44 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 100J TYR 0.018 0.001 TYR L 91 PHE 0.015 0.001 PHE A 342 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 3496) covalent geometry : angle 0.59517 / 0.31 ( 4749) SS BOND : bond 0.00472 / 0.23 ( 5) SS BOND : angle 1.03204 / 0.63 ( 10) hydrogen bonds : bond 0.03677 / 2.48 ( 102) hydrogen bonds : angle 6.98527 / 4.89 ( 255) link_NAG-ASN : bond 0.00174 / 0.09 ( 1) link_NAG-ASN : angle 0.79525 / 0.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.130 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.0849 time to fit residues: 9.4309 Evaluate side-chains 90 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.171821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145002 restraints weight = 4315.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.149314 restraints weight = 2652.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152107 restraints weight = 1927.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153765 restraints weight = 1548.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.155299 restraints weight = 1331.898| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3502 Z= 0.133 Angle : 0.565 7.976 4762 Z= 0.284 Chirality : 0.042 0.143 505 Planarity : 0.005 0.085 620 Dihedral : 4.532 22.618 484 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.27 % Allowed : 16.08 % Favored : 80.65 % 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 are not related in a simple way. whole: -0.49 (0.41), residues: 431 helix: -1.43 (0.98), residues: 28 sheet: 0.24 (0.47), residues: 131 loop : -0.45 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.015 0.001 TYR L 91 PHE 0.011 0.001 PHE H 27 TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 3496) covalent geometry : angle 0.56311 / 0.28 ( 4749) SS BOND : bond 0.00306 / 0.14 ( 5) SS BOND : angle 1.03840 / 0.64 ( 10) hydrogen bonds : bond 0.03047 / 2.07 ( 102) hydrogen bonds : angle 6.63463 / 4.69 ( 255) link_NAG-ASN : bond 0.00166 / 0.09 ( 1) link_NAG-ASN : angle 0.79544 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.129 Fit side-chains REVERT: A 365 TYR cc_start: 0.7627 (m-80) cc_final: 0.7415 (m-80) REVERT: A 468 ILE cc_start: 0.9132 (pt) cc_final: 0.8773 (mt) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.0802 time to fit residues: 8.5109 Evaluate side-chains 85 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.167734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.142559 restraints weight = 4157.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146581 restraints weight = 2618.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.149225 restraints weight = 1919.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150981 restraints weight = 1544.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151894 restraints weight = 1319.905| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3502 Z= 0.143 Angle : 0.584 9.014 4762 Z= 0.287 Chirality : 0.042 0.144 505 Planarity : 0.006 0.092 620 Dihedral : 4.610 24.082 484 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.09 % Allowed : 17.17 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.41), residues: 431 helix: -1.38 (0.99), residues: 28 sheet: 0.50 (0.47), residues: 127 loop : -0.56 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.011 0.001 TYR L 91 PHE 0.010 0.001 PHE H 27 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 3496) covalent geometry : angle 0.58302 / 0.29 ( 4749) SS BOND : bond 0.00279 / 0.13 ( 5) SS BOND : angle 0.96960 / 0.59 ( 10) hydrogen bonds : bond 0.02916 / 1.98 ( 102) hydrogen bonds : angle 6.40628 / 4.54 ( 255) link_NAG-ASN : bond 0.00117 / 0.06 ( 1) link_NAG-ASN : angle 0.83035 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.125 Fit side-chains REVERT: A 468 ILE cc_start: 0.9119 (pt) cc_final: 0.8783 (mt) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.0876 time to fit residues: 9.0743 Evaluate side-chains 87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 23 optimal weight: 0.0030 chunk 32 optimal weight: 0.2980 chunk 30 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 0.2568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.140354 restraints weight = 4470.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144216 restraints weight = 2704.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146678 restraints weight = 1946.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148479 restraints weight = 1551.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.149378 restraints weight = 1316.865| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3502 Z= 0.107 Angle : 0.551 8.821 4762 Z= 0.270 Chirality : 0.041 0.137 505 Planarity : 0.005 0.087 620 Dihedral : 4.430 23.433 484 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.45 % Allowed : 20.98 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.42), residues: 431 helix: -1.25 (1.02), residues: 28 sheet: 0.61 (0.48), residues: 129 loop : -0.55 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100J TYR 0.008 0.001 TYR A 365 PHE 0.009 0.001 PHE H 27 TRP 0.007 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 3496) covalent geometry : angle 0.54999 / 0.27 ( 4749) SS BOND : bond 0.00225 / 0.10 ( 5) SS BOND : angle 0.77828 / 0.47 ( 10) hydrogen bonds : bond 0.02717 / 1.81 ( 102) hydrogen bonds : angle 6.22026 / 4.41 ( 255) link_NAG-ASN : bond 0.00165 / 0.09 ( 1) link_NAG-ASN : angle 0.72945 / 0.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.126 Fit side-chains REVERT: A 468 ILE cc_start: 0.9137 (pt) cc_final: 0.8803 (mt) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.0819 time to fit residues: 8.0001 Evaluate side-chains 81 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.0060 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 64 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.160961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135648 restraints weight = 4345.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139515 restraints weight = 2658.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142109 restraints weight = 1936.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.143657 restraints weight = 1550.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.144957 restraints weight = 1335.388| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3502 Z= 0.132 Angle : 0.593 9.781 4762 Z= 0.286 Chirality : 0.042 0.141 505 Planarity : 0.005 0.091 620 Dihedral : 4.457 23.276 484 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.54 % Allowed : 19.62 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.42), residues: 431 helix: -1.24 (1.03), residues: 28 sheet: 0.58 (0.48), residues: 129 loop : -0.52 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 100J TYR 0.010 0.001 TYR A 365 PHE 0.009 0.001 PHE H 27 TRP 0.008 0.001 TRP H 47 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 3496) covalent geometry : angle 0.59254 / 0.29 ( 4749) SS BOND : bond 0.00249 / 0.12 ( 5) SS BOND : angle 0.77284 / 0.47 ( 10) hydrogen bonds : bond 0.02703 / 1.82 ( 102) hydrogen bonds : angle 6.16452 / 4.36 ( 255) link_NAG-ASN : bond 0.00132 / 0.07 ( 1) link_NAG-ASN : angle 0.81620 / 0.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.128 Fit side-chains REVERT: A 468 ILE cc_start: 0.9135 (pt) cc_final: 0.8790 (mt) outliers start: 13 outliers final: 12 residues processed: 83 average time/residue: 0.0804 time to fit residues: 7.9871 Evaluate side-chains 87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.157854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132424 restraints weight = 4470.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136373 restraints weight = 2717.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138918 restraints weight = 1961.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140619 restraints weight = 1573.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141629 restraints weight = 1347.238| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3502 Z= 0.175 Angle : 0.609 10.323 4762 Z= 0.298 Chirality : 0.042 0.145 505 Planarity : 0.006 0.093 620 Dihedral : 4.671 23.193 484 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.27 % Allowed : 20.44 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.42), residues: 431 helix: -1.26 (1.03), residues: 28 sheet: 0.38 (0.49), residues: 123 loop : -0.52 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100J TYR 0.010 0.001 TYR L 91 PHE 0.010 0.001 PHE H 27 TRP 0.009 0.001 TRP H 47 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 3496) covalent geometry : angle 0.60808 / 0.30 ( 4749) SS BOND : bond 0.00328 / 0.16 ( 5) SS BOND : angle 0.90213 / 0.54 ( 10) hydrogen bonds : bond 0.02869 / 1.93 ( 102) hydrogen bonds : angle 6.26900 / 4.45 ( 255) link_NAG-ASN : bond 0.00082 / 0.04 ( 1) link_NAG-ASN : angle 1.03788 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.077 Fit side-chains REVERT: A 468 ILE cc_start: 0.9140 (pt) cc_final: 0.8771 (mt) outliers start: 12 outliers final: 11 residues processed: 84 average time/residue: 0.0495 time to fit residues: 5.0029 Evaluate side-chains 82 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.153687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128072 restraints weight = 4609.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131891 restraints weight = 2723.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134456 restraints weight = 1945.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136216 restraints weight = 1548.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137261 restraints weight = 1314.695| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3502 Z= 0.147 Angle : 0.615 10.239 4762 Z= 0.295 Chirality : 0.042 0.144 505 Planarity : 0.006 0.091 620 Dihedral : 4.626 23.365 484 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.09 % Allowed : 18.80 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.42), residues: 431 helix: -1.14 (1.07), residues: 28 sheet: 0.52 (0.48), residues: 129 loop : -0.59 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100J TYR 0.009 0.001 TYR L 91 PHE 0.010 0.001 PHE H 27 TRP 0.009 0.001 TRP H 47 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 3496) covalent geometry : angle 0.61418 / 0.29 ( 4749) SS BOND : bond 0.00304 / 0.15 ( 5) SS BOND : angle 0.84736 / 0.51 ( 10) hydrogen bonds : bond 0.02725 / 1.83 ( 102) hydrogen bonds : angle 6.22034 / 4.42 ( 255) link_NAG-ASN : bond 0.00123 / 0.06 ( 1) link_NAG-ASN : angle 0.94344 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.142 Fit side-chains REVERT: A 468 ILE cc_start: 0.9122 (pt) cc_final: 0.8751 (mt) REVERT: L 61 ARG cc_start: 0.7330 (ptp-170) cc_final: 0.6944 (ptp-170) outliers start: 15 outliers final: 12 residues processed: 84 average time/residue: 0.0697 time to fit residues: 7.0707 Evaluate side-chains 84 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 19 optimal weight: 0.0770 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 64 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126196 restraints weight = 4500.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129855 restraints weight = 2737.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132336 restraints weight = 1991.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134018 restraints weight = 1597.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134878 restraints weight = 1370.381| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3502 Z= 0.169 Angle : 0.626 10.120 4762 Z= 0.304 Chirality : 0.043 0.145 505 Planarity : 0.006 0.093 620 Dihedral : 4.766 23.568 484 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.27 % Allowed : 20.16 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.42), residues: 431 helix: -1.13 (1.07), residues: 28 sheet: 0.46 (0.50), residues: 123 loop : -0.57 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 61 TYR 0.009 0.001 TYR A 453 PHE 0.010 0.001 PHE H 27 TRP 0.009 0.001 TRP H 47 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 3496) covalent geometry : angle 0.62489 / 0.30 ( 4749) SS BOND : bond 0.00332 / 0.17 ( 5) SS BOND : angle 0.83050 / 0.50 ( 10) hydrogen bonds : bond 0.02776 / 1.86 ( 102) hydrogen bonds : angle 6.24808 / 4.44 ( 255) link_NAG-ASN : bond 0.00106 / 0.06 ( 1) link_NAG-ASN : angle 1.00345 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.148 Fit side-chains REVERT: A 468 ILE cc_start: 0.9135 (pt) cc_final: 0.8760 (mt) REVERT: H 32 TYR cc_start: 0.8969 (m-80) cc_final: 0.8760 (m-10) REVERT: H 75 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8476 (mtpt) outliers start: 12 outliers final: 11 residues processed: 85 average time/residue: 0.0834 time to fit residues: 8.4947 Evaluate side-chains 86 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129294 restraints weight = 4582.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132767 restraints weight = 2783.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135290 restraints weight = 2032.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.136945 restraints weight = 1628.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138096 restraints weight = 1395.411| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3502 Z= 0.145 Angle : 0.627 9.745 4762 Z= 0.301 Chirality : 0.042 0.144 505 Planarity : 0.006 0.091 620 Dihedral : 4.691 23.487 484 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.00 % Allowed : 21.25 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.42), residues: 431 helix: -1.05 (1.09), residues: 28 sheet: 0.53 (0.48), residues: 129 loop : -0.59 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.009 0.001 TYR L 36 PHE 0.010 0.001 PHE H 27 TRP 0.010 0.001 TRP H 47 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 3496) covalent geometry : angle 0.62650 / 0.30 ( 4749) SS BOND : bond 0.00291 / 0.14 ( 5) SS BOND : angle 0.78646 / 0.47 ( 10) hydrogen bonds : bond 0.02691 / 1.80 ( 102) hydrogen bonds : angle 6.20714 / 4.41 ( 255) link_NAG-ASN : bond 0.00134 / 0.07 ( 1) link_NAG-ASN : angle 0.94616 / 0.54 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.127 Fit side-chains REVERT: A 468 ILE cc_start: 0.9141 (pt) cc_final: 0.8786 (mt) REVERT: H 75 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8542 (mtpt) outliers start: 11 outliers final: 11 residues processed: 83 average time/residue: 0.0695 time to fit residues: 6.9386 Evaluate side-chains 85 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126086 restraints weight = 4569.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129898 restraints weight = 2778.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132282 restraints weight = 2005.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133989 restraints weight = 1614.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135126 restraints weight = 1380.645| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3502 Z= 0.177 Angle : 0.622 10.084 4762 Z= 0.304 Chirality : 0.042 0.144 505 Planarity : 0.006 0.093 620 Dihedral : 4.766 23.795 484 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.27 % Allowed : 20.71 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.42), residues: 431 helix: -1.14 (1.07), residues: 28 sheet: 0.46 (0.48), residues: 129 loop : -0.60 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100J TYR 0.013 0.001 TYR H 32 PHE 0.010 0.001 PHE H 27 TRP 0.009 0.001 TRP H 47 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 3496) covalent geometry : angle 0.62091 / 0.30 ( 4749) SS BOND : bond 0.00359 / 0.18 ( 5) SS BOND : angle 0.85399 / 0.51 ( 10) hydrogen bonds : bond 0.02764 / 1.85 ( 102) hydrogen bonds : angle 6.28960 / 4.48 ( 255) link_NAG-ASN : bond 0.00096 / 0.05 ( 1) link_NAG-ASN : angle 1.03065 / 0.58 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 906.43 seconds wall clock time: 16 minutes 17.39 seconds (977.39 seconds total)