Starting phenix.real_space_refine on Tue Mar 3 11:34:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws2_32741/03_2026/7ws2_32741.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws2_32741/03_2026/7ws2_32741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws2_32741/03_2026/7ws2_32741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws2_32741/03_2026/7ws2_32741.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws2_32741/03_2026/7ws2_32741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws2_32741/03_2026/7ws2_32741.cif" } resolution = 3.3 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= -0.003 sd= 0.025 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 15 5.16 5 C 2120 2.51 5 N 558 2.21 5 O 650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3343 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1578 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 0.74, per 1000 atoms: 0.22 Number of scatterers: 3343 At special positions: 0 Unit cell: (91.84, 55.76, 95.94, 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 15 16.00 O 650 8.00 N 558 7.00 C 2120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " 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 E 22 " - pdb=" SG CYS E 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 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 137.7 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 12.3% alpha, 30.4% 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 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.596A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.534A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.825A 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 502 through 506 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.987A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.741A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AA3, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.922A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.111A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.893A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.744A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR E 112 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 94 " --> pdb=" O THR E 117 " (cutoff:3.500A) 105 hydrogen bonds defined for protein. 258 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: 0.32 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1071 1.34 - 1.46: 843 1.46 - 1.58: 1496 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3428 Sorted by residual: bond pdb=" N ASP E 31 " pdb=" CA ASP E 31 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.25e-02 6.40e+03 7.53e+00 bond pdb=" N GLN D 6 " pdb=" CA GLN D 6 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.19e-02 7.06e+03 7.17e+00 bond pdb=" N ASN A 450 " pdb=" CA ASN A 450 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 7.02e+00 bond pdb=" N THR A 500 " pdb=" CA THR A 500 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.32e-02 5.74e+03 6.85e+00 bond pdb=" N THR A 345 " pdb=" CA THR A 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.26e-02 6.30e+03 6.34e+00 ... (remaining 3423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 4347 1.13 - 2.27: 240 2.27 - 3.40: 56 3.40 - 4.54: 11 4.54 - 5.67: 6 Bond angle restraints: 4660 Sorted by residual: angle pdb=" CA LEU E 105 " pdb=" C LEU E 105 " pdb=" O LEU E 105 " ideal model delta sigma weight residual 122.13 118.28 3.85 1.13e+00 7.83e-01 1.16e+01 angle pdb=" CA ASN A 501 " pdb=" C ASN A 501 " pdb=" O ASN A 501 " ideal model delta sigma weight residual 121.87 118.39 3.48 1.16e+00 7.43e-01 9.02e+00 angle pdb=" N LYS D 39 " pdb=" CA LYS D 39 " pdb=" C LYS D 39 " ideal model delta sigma weight residual 109.50 105.76 3.74 1.47e+00 4.63e-01 6.47e+00 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 113.61 109.90 3.71 1.50e+00 4.44e-01 6.12e+00 angle pdb=" CA GLU E 103 " pdb=" C GLU E 103 " pdb=" O GLU E 103 " ideal model delta sigma weight residual 121.78 118.63 3.15 1.28e+00 6.10e-01 6.04e+00 ... (remaining 4655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 1795 15.53 - 31.07: 170 31.07 - 46.60: 45 46.60 - 62.13: 7 62.13 - 77.67: 4 Dihedral angle restraints: 2021 sinusoidal: 775 harmonic: 1246 Sorted by residual: dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -121.73 35.73 1 1.00e+01 1.00e-02 1.81e+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 93.00 122.28 -29.28 1 1.00e+01 1.00e-02 1.23e+01 ... (remaining 2018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 297 0.031 - 0.062: 135 0.062 - 0.092: 33 0.092 - 0.123: 25 0.123 - 0.154: 9 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA LYS D 39 " pdb=" N LYS D 39 " pdb=" C LYS D 39 " pdb=" CB LYS D 39 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA THR D 94 " pdb=" N THR D 94 " pdb=" C THR D 94 " pdb=" CB THR D 94 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA LYS A 444 " pdb=" N LYS A 444 " pdb=" C LYS A 444 " pdb=" CB LYS A 444 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 496 not shown) Planarity restraints: 606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 479 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 527 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A 384 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.028 5.00e-02 4.00e+02 ... (remaining 603 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 747 2.79 - 3.32: 2829 3.32 - 3.84: 5241 3.84 - 4.37: 6298 4.37 - 4.90: 11020 Nonbonded interactions: 26135 Sorted by model distance: nonbonded pdb=" NH1 ARG D 61 " pdb=" OD2 ASP D 82 " model vdw 2.258 3.120 nonbonded pdb=" OH TYR D 97 " pdb=" O ILE E 104 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.269 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.292 3.040 nonbonded pdb=" O SER A 530 " pdb=" OG SER A 530 " model vdw 2.302 3.040 ... (remaining 26130 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: 11.110 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.840 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.003 0.035 3434 Z= 0.223 Angle : 0.636 5.672 4672 Z= 0.375 Chirality : 0.045 0.154 499 Planarity : 0.005 0.052 606 Dihedral : 13.310 77.666 1213 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.86 (0.40), residues: 425 helix: -4.57 (0.37), residues: 33 sheet: -0.50 (0.44), residues: 158 loop : -1.21 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 24 TYR 0.007 0.001 TYR A 495 PHE 0.009 0.001 PHE D 83 TRP 0.003 0.001 TRP E 53 HIS 0.001 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3428) covalent geometry : angle 0.63558 ( 4660) SS BOND : bond 0.00395 ( 6) SS BOND : angle 0.74764 ( 12) hydrogen bonds : bond 0.30626 ( 94) hydrogen bonds : angle 10.91442 ( 258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.119 Fit side-chains REVERT: D 54 LEU cc_start: 0.8957 (tt) cc_final: 0.8657 (tp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0824 time to fit residues: 8.7699 Evaluate side-chains 82 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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: 0.4980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 ASN D 89 GLN A 394 ASN A 501 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123364 restraints weight = 5295.754| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.98 r_work: 0.3450 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3434 Z= 0.195 Angle : 0.641 5.626 4672 Z= 0.342 Chirality : 0.047 0.156 499 Planarity : 0.005 0.051 606 Dihedral : 4.961 27.374 475 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.37 % Allowed : 9.89 % Favored : 88.74 % 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: -1.76 (0.39), residues: 425 helix: -3.51 (0.66), residues: 27 sheet: -0.50 (0.43), residues: 152 loop : -1.32 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 24 TYR 0.017 0.002 TYR A 489 PHE 0.014 0.002 PHE A 490 TRP 0.009 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 3428) covalent geometry : angle 0.63903 ( 4660) SS BOND : bond 0.00777 ( 6) SS BOND : angle 1.09526 ( 12) hydrogen bonds : bond 0.04551 ( 94) hydrogen bonds : angle 7.04114 ( 258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.091 Fit side-chains REVERT: A 418 ILE cc_start: 0.9393 (mt) cc_final: 0.9192 (mt) outliers start: 5 outliers final: 3 residues processed: 93 average time/residue: 0.0681 time to fit residues: 7.7004 Evaluate side-chains 91 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.133922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121857 restraints weight = 5380.400| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.11 r_work: 0.3424 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3434 Z= 0.165 Angle : 0.606 5.842 4672 Z= 0.318 Chirality : 0.046 0.152 499 Planarity : 0.005 0.051 606 Dihedral : 4.927 26.505 475 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.75 % Allowed : 11.26 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.39), residues: 425 helix: -3.23 (0.76), residues: 27 sheet: -0.59 (0.42), residues: 153 loop : -1.36 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.015 0.002 TYR D 92 PHE 0.011 0.001 PHE A 490 TRP 0.006 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3428) covalent geometry : angle 0.60440 ( 4660) SS BOND : bond 0.00713 ( 6) SS BOND : angle 1.08762 ( 12) hydrogen bonds : bond 0.03719 ( 94) hydrogen bonds : angle 6.48491 ( 258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.123 Fit side-chains REVERT: A 418 ILE cc_start: 0.9413 (mt) cc_final: 0.9202 (mt) outliers start: 10 outliers final: 4 residues processed: 90 average time/residue: 0.0665 time to fit residues: 7.3133 Evaluate side-chains 86 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 ASN D 89 GLN A 394 ASN A 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122174 restraints weight = 5220.071| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.96 r_work: 0.3427 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3434 Z= 0.182 Angle : 0.621 7.313 4672 Z= 0.324 Chirality : 0.046 0.149 499 Planarity : 0.005 0.053 606 Dihedral : 5.061 25.568 475 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.30 % Allowed : 15.11 % Favored : 81.59 % 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: -1.75 (0.39), residues: 425 helix: -3.14 (0.79), residues: 27 sheet: -0.54 (0.42), residues: 153 loop : -1.33 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 19 TYR 0.023 0.002 TYR E 80 PHE 0.014 0.002 PHE A 490 TRP 0.007 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 3428) covalent geometry : angle 0.61961 ( 4660) SS BOND : bond 0.00703 ( 6) SS BOND : angle 1.07761 ( 12) hydrogen bonds : bond 0.03555 ( 94) hydrogen bonds : angle 6.26411 ( 258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.110 Fit side-chains REVERT: A 418 ILE cc_start: 0.9411 (mt) cc_final: 0.9195 (mt) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.0752 time to fit residues: 8.3036 Evaluate side-chains 93 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121188 restraints weight = 5260.650| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.98 r_work: 0.3418 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3434 Z= 0.207 Angle : 0.653 6.594 4672 Z= 0.341 Chirality : 0.047 0.169 499 Planarity : 0.005 0.055 606 Dihedral : 5.357 30.122 475 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.30 % Allowed : 16.76 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.81 (0.39), residues: 425 helix: -3.05 (0.81), residues: 27 sheet: -0.48 (0.42), residues: 149 loop : -1.45 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 19 TYR 0.021 0.002 TYR E 80 PHE 0.016 0.002 PHE A 490 TRP 0.006 0.001 TRP E 47 HIS 0.003 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 3428) covalent geometry : angle 0.64782 ( 4660) SS BOND : bond 0.00538 ( 6) SS BOND : angle 1.79510 ( 12) hydrogen bonds : bond 0.03602 ( 94) hydrogen bonds : angle 6.18949 ( 258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.121 Fit side-chains REVERT: D 106 GLU cc_start: 0.7725 (tp30) cc_final: 0.7525 (tp30) REVERT: A 418 ILE cc_start: 0.9399 (mt) cc_final: 0.9179 (mt) outliers start: 12 outliers final: 10 residues processed: 90 average time/residue: 0.0733 time to fit residues: 7.9212 Evaluate side-chains 91 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123373 restraints weight = 5172.897| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.86 r_work: 0.3454 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3434 Z= 0.181 Angle : 0.636 6.247 4672 Z= 0.326 Chirality : 0.046 0.177 499 Planarity : 0.005 0.057 606 Dihedral : 5.251 28.414 475 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.85 % Allowed : 17.86 % Favored : 78.30 % 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: -1.77 (0.39), residues: 425 helix: -3.01 (0.82), residues: 27 sheet: -0.51 (0.41), residues: 160 loop : -1.41 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.020 0.002 TYR E 80 PHE 0.014 0.001 PHE A 490 TRP 0.007 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 3428) covalent geometry : angle 0.63142 ( 4660) SS BOND : bond 0.00545 ( 6) SS BOND : angle 1.63935 ( 12) hydrogen bonds : bond 0.03366 ( 94) hydrogen bonds : angle 5.98667 ( 258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.133 Fit side-chains REVERT: D 106 GLU cc_start: 0.7764 (tp30) cc_final: 0.7530 (tp30) REVERT: A 418 ILE cc_start: 0.9379 (mt) cc_final: 0.9160 (mt) outliers start: 14 outliers final: 12 residues processed: 86 average time/residue: 0.0684 time to fit residues: 7.2016 Evaluate side-chains 86 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.0050 chunk 3 optimal weight: 0.5980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123443 restraints weight = 5375.830| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.06 r_work: 0.3454 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3434 Z= 0.126 Angle : 0.593 7.010 4672 Z= 0.303 Chirality : 0.045 0.171 499 Planarity : 0.005 0.055 606 Dihedral : 5.041 25.910 475 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.85 % Allowed : 17.86 % Favored : 78.30 % 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: -1.75 (0.39), residues: 425 helix: -2.95 (0.84), residues: 27 sheet: -0.49 (0.42), residues: 152 loop : -1.39 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 19 TYR 0.017 0.001 TYR D 92 PHE 0.009 0.001 PHE D 83 TRP 0.006 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3428) covalent geometry : angle 0.58973 ( 4660) SS BOND : bond 0.00449 ( 6) SS BOND : angle 1.34574 ( 12) hydrogen bonds : bond 0.02967 ( 94) hydrogen bonds : angle 5.74782 ( 258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.160 Fit side-chains REVERT: D 106 GLU cc_start: 0.7729 (tp30) cc_final: 0.7480 (tp30) REVERT: A 418 ILE cc_start: 0.9385 (mt) cc_final: 0.9158 (mt) outliers start: 14 outliers final: 10 residues processed: 88 average time/residue: 0.0731 time to fit residues: 7.8264 Evaluate side-chains 89 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124918 restraints weight = 5300.606| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.96 r_work: 0.3464 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3434 Z= 0.142 Angle : 0.609 7.692 4672 Z= 0.309 Chirality : 0.045 0.172 499 Planarity : 0.005 0.057 606 Dihedral : 4.998 25.556 475 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.02 % Allowed : 19.51 % Favored : 77.47 % 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: -1.64 (0.40), residues: 425 helix: -2.92 (0.86), residues: 27 sheet: -0.44 (0.40), residues: 161 loop : -1.32 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 24 TYR 0.018 0.001 TYR D 92 PHE 0.012 0.001 PHE A 490 TRP 0.007 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3428) covalent geometry : angle 0.60631 ( 4660) SS BOND : bond 0.00434 ( 6) SS BOND : angle 1.35891 ( 12) hydrogen bonds : bond 0.03045 ( 94) hydrogen bonds : angle 5.66638 ( 258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.121 Fit side-chains REVERT: D 106 GLU cc_start: 0.7750 (tp30) cc_final: 0.7546 (tp30) REVERT: A 418 ILE cc_start: 0.9372 (mt) cc_final: 0.9147 (mt) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.0673 time to fit residues: 7.2414 Evaluate side-chains 86 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.0040 chunk 18 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124766 restraints weight = 5269.823| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.90 r_work: 0.3469 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3434 Z= 0.147 Angle : 0.613 7.314 4672 Z= 0.311 Chirality : 0.045 0.169 499 Planarity : 0.005 0.057 606 Dihedral : 5.047 26.134 475 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.02 % Allowed : 19.51 % Favored : 77.47 % 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: -1.61 (0.39), residues: 425 helix: -3.17 (0.78), residues: 27 sheet: -0.28 (0.42), residues: 152 loop : -1.34 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 24 TYR 0.018 0.001 TYR D 92 PHE 0.012 0.001 PHE A 490 TRP 0.007 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3428) covalent geometry : angle 0.60951 ( 4660) SS BOND : bond 0.00435 ( 6) SS BOND : angle 1.43265 ( 12) hydrogen bonds : bond 0.03078 ( 94) hydrogen bonds : angle 5.67020 ( 258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.144 Fit side-chains REVERT: A 418 ILE cc_start: 0.9382 (mt) cc_final: 0.9162 (mt) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.0744 time to fit residues: 7.6639 Evaluate side-chains 86 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122604 restraints weight = 5235.657| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.92 r_work: 0.3444 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3434 Z= 0.209 Angle : 0.668 7.155 4672 Z= 0.344 Chirality : 0.047 0.170 499 Planarity : 0.005 0.060 606 Dihedral : 5.317 26.447 475 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.75 % Allowed : 19.78 % Favored : 77.47 % 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: -1.67 (0.39), residues: 425 helix: -3.25 (0.77), residues: 27 sheet: -0.23 (0.42), residues: 151 loop : -1.45 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.020 0.002 TYR D 92 PHE 0.017 0.002 PHE A 490 TRP 0.007 0.001 TRP E 47 HIS 0.003 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 3428) covalent geometry : angle 0.66360 ( 4660) SS BOND : bond 0.00565 ( 6) SS BOND : angle 1.62283 ( 12) hydrogen bonds : bond 0.03495 ( 94) hydrogen bonds : angle 5.81034 ( 258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.125 Fit side-chains REVERT: D 106 GLU cc_start: 0.7709 (tp30) cc_final: 0.7445 (tp30) REVERT: A 418 ILE cc_start: 0.9390 (mt) cc_final: 0.9183 (mt) REVERT: E 39 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7708 (tp-100) outliers start: 10 outliers final: 9 residues processed: 85 average time/residue: 0.0768 time to fit residues: 7.8340 Evaluate side-chains 88 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124153 restraints weight = 5332.364| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.89 r_work: 0.3467 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3434 Z= 0.164 Angle : 0.627 7.217 4672 Z= 0.320 Chirality : 0.046 0.173 499 Planarity : 0.005 0.059 606 Dihedral : 5.119 24.737 475 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.75 % Allowed : 20.33 % Favored : 76.92 % 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: -1.58 (0.39), residues: 425 helix: -3.28 (0.76), residues: 27 sheet: -0.06 (0.42), residues: 147 loop : -1.43 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 19 TYR 0.019 0.002 TYR D 92 PHE 0.013 0.001 PHE A 490 TRP 0.007 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3428) covalent geometry : angle 0.62401 ( 4660) SS BOND : bond 0.00459 ( 6) SS BOND : angle 1.42376 ( 12) hydrogen bonds : bond 0.03246 ( 94) hydrogen bonds : angle 5.69466 ( 258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1254.58 seconds wall clock time: 22 minutes 13.39 seconds (1333.39 seconds total)