Starting phenix.real_space_refine on Sat Apr 4 22:07:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wml_66096/04_2026/9wml_66096_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wml_66096/04_2026/9wml_66096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wml_66096/04_2026/9wml_66096_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wml_66096/04_2026/9wml_66096_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wml_66096/04_2026/9wml_66096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wml_66096/04_2026/9wml_66096.map" } resolution = 2.79 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= 0.132 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: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3010 2.51 5 N 663 2.21 5 O 729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4438 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4273 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 165 Unusual residues: {' CL': 1, ' NA': 2, 'CLR': 3, 'Y01': 2} Inner-chain residues flagged as termini: ['pdbres="8LJ A 704 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'8LJ%COO:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 0.92, per 1000 atoms: 0.21 Number of scatterers: 4438 At special positions: 0 Unit cell: (86.4, 72.36, 72.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 2 11.00 O 729 8.00 N 663 7.00 C 3010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " 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: 0.35 Conformation dependent library (CDL) restraints added in 281.5 milliseconds 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.631A pdb=" N VAL A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.544A pdb=" N TYR A 65 " --> pdb=" O TRP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 86 removed outlier: 3.616A pdb=" N LEU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 106 through 114 Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 115 through 147 removed outlier: 3.968A pdb=" N GLY A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 263 removed outlier: 3.602A pdb=" N TYR A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 3.863A pdb=" N GLY A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 removed outlier: 3.641A pdb=" N SER A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.144A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 353 removed outlier: 3.652A pdb=" N VAL A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.649A pdb=" N VAL A 359 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 377 Proline residue: A 372 - end of helix removed outlier: 3.506A pdb=" N MET A 377 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 415 removed outlier: 3.566A pdb=" N TRP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.607A pdb=" N THR A 443 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 444' Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.773A pdb=" N TRP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.727A pdb=" N SER A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.732A pdb=" N TYR A 591 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 592 " --> pdb=" O GLY A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 588 through 592' Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526 282 hydrogen bonds defined for protein. 822 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: 0.67 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 651 1.32 - 1.45: 1323 1.45 - 1.57: 2554 1.57 - 1.69: 2 1.69 - 1.82: 53 Bond restraints: 4583 Sorted by residual: bond pdb=" CG 8LJ A 704 " pdb=" CD 8LJ A 704 " ideal model delta sigma weight residual 1.334 1.587 -0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" N 8LJ A 704 " pdb=" CD 8LJ A 704 " ideal model delta sigma weight residual 1.473 1.579 -0.106 1.40e-02 5.10e+03 5.71e+01 bond pdb=" N PHE A 63 " pdb=" CA PHE A 63 " ideal model delta sigma weight residual 1.462 1.488 -0.026 7.70e-03 1.69e+04 1.12e+01 bond pdb=" N ASN A 59 " pdb=" CA ASN A 59 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.33e-02 5.65e+03 6.92e+00 bond pdb=" N ASN A 162 " pdb=" CA ASN A 162 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.70e+00 ... (remaining 4578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 6074 1.65 - 3.30: 149 3.30 - 4.95: 39 4.95 - 6.60: 8 6.60 - 8.26: 3 Bond angle restraints: 6273 Sorted by residual: angle pdb=" CA TYR A 297 " pdb=" C TYR A 297 " pdb=" O TYR A 297 " ideal model delta sigma weight residual 121.00 116.12 4.88 1.05e+00 9.07e-01 2.16e+01 angle pdb=" CA GLU A 567 " pdb=" C GLU A 567 " pdb=" O GLU A 567 " ideal model delta sigma weight residual 120.42 115.55 4.87 1.06e+00 8.90e-01 2.11e+01 angle pdb=" N 8LJ A 704 " pdb=" CA 8LJ A 704 " pdb=" CB 8LJ A 704 " ideal model delta sigma weight residual 103.00 107.61 -4.61 1.10e+00 8.26e-01 1.76e+01 angle pdb=" N 8LJ A 704 " pdb=" CA 8LJ A 704 " pdb=" C 8LJ A 704 " ideal model delta sigma weight residual 112.10 103.84 8.26 2.50e+00 1.60e-01 1.09e+01 angle pdb=" N GLY A 42 " pdb=" CA GLY A 42 " pdb=" C GLY A 42 " ideal model delta sigma weight residual 110.38 115.08 -4.70 1.48e+00 4.57e-01 1.01e+01 ... (remaining 6268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.07: 2637 24.07 - 48.13: 173 48.13 - 72.20: 26 72.20 - 96.26: 2 96.26 - 120.33: 6 Dihedral angle restraints: 2844 sinusoidal: 1291 harmonic: 1553 Sorted by residual: dihedral pdb=" C10 CLR A 706 " pdb=" C1 CLR A 706 " pdb=" C2 CLR A 706 " pdb=" C3 CLR A 706 " ideal model delta sinusoidal sigma weight residual -56.83 63.50 -120.33 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CB CYS A 157 " pdb=" SG CYS A 157 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -118.94 32.94 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" C1 CLR A 709 " pdb=" C2 CLR A 709 " pdb=" C3 CLR A 709 " pdb=" O1 CLR A 709 " ideal model delta sinusoidal sigma weight residual 180.04 67.53 112.51 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 2841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 490 0.035 - 0.070: 158 0.070 - 0.105: 49 0.105 - 0.139: 13 0.139 - 0.174: 4 Chirality restraints: 714 Sorted by residual: chirality pdb=" CA ILE A 51 " pdb=" N ILE A 51 " pdb=" C ILE A 51 " pdb=" CB ILE A 51 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ASN A 59 " pdb=" N ASN A 59 " pdb=" C ASN A 59 " pdb=" CB ASN A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 711 not shown) Planarity restraints: 735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 8LJ A 704 " 0.034 2.00e-02 2.50e+03 4.53e-02 2.06e+01 pdb=" CB 8LJ A 704 " -0.036 2.00e-02 2.50e+03 pdb=" CG 8LJ A 704 " 0.054 2.00e-02 2.50e+03 pdb=" CD 8LJ A 704 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 37 " -0.213 9.50e-02 1.11e+02 9.60e-02 7.30e+00 pdb=" NE ARG A 37 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 37 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 37 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 37 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 297 " 0.029 2.00e-02 2.50e+03 1.71e-02 5.85e+00 pdb=" CG TYR A 297 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR A 297 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 297 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 297 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 297 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 297 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 297 " 0.015 2.00e-02 2.50e+03 ... (remaining 732 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 31 2.57 - 3.15: 3722 3.15 - 3.73: 7318 3.73 - 4.32: 10383 4.32 - 4.90: 17362 Nonbonded interactions: 38816 Sorted by model distance: nonbonded pdb=" OD1 ASN A 59 " pdb="NA NA A 701 " model vdw 1.986 2.470 nonbonded pdb=" OG SER A 298 " pdb="NA NA A 701 " model vdw 1.989 2.470 nonbonded pdb=" ND2 ASN A 59 " pdb=" OG SER A 298 " model vdw 2.232 3.120 nonbonded pdb=" O GLU A 405 " pdb=" OG1 THR A 409 " model vdw 2.254 3.040 nonbonded pdb=" O GLN A 373 " pdb=" OG1 THR A 376 " model vdw 2.274 3.040 ... (remaining 38811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.540 Find NCS groups from input model: 0.020 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:8.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.005 0.253 4584 Z= 0.291 Angle : 0.679 8.255 6275 Z= 0.362 Chirality : 0.041 0.174 714 Planarity : 0.006 0.096 735 Dihedral : 16.127 120.329 1857 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 16.11 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.36), residues: 537 helix: 0.54 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.79 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 37 TYR 0.030 0.002 TYR A 297 PHE 0.021 0.001 PHE A 401 TRP 0.021 0.002 TRP A 109 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 4583) covalent geometry : angle 0.67798 ( 6273) SS BOND : bond 0.00347 ( 1) SS BOND : angle 1.71753 ( 2) hydrogen bonds : bond 0.14381 ( 282) hydrogen bonds : angle 7.24171 ( 822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.146 Fit side-chains REVERT: A 272 GLN cc_start: 0.7822 (tt0) cc_final: 0.7605 (tt0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.5074 time to fit residues: 43.7524 Evaluate side-chains 73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129452 restraints weight = 5246.020| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.53 r_work: 0.3460 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4584 Z= 0.152 Angle : 0.592 7.162 6275 Z= 0.286 Chirality : 0.041 0.204 714 Planarity : 0.004 0.044 735 Dihedral : 9.412 59.851 926 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.65 % Allowed : 15.45 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.98 (0.36), residues: 537 helix: 1.17 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.47 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.018 0.002 TYR A 418 PHE 0.015 0.001 PHE A 229 TRP 0.013 0.001 TRP A 109 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4583) covalent geometry : angle 0.59086 ( 6273) SS BOND : bond 0.00011 ( 1) SS BOND : angle 1.80038 ( 2) hydrogen bonds : bond 0.04867 ( 282) hydrogen bonds : angle 5.18866 ( 822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.104 Fit side-chains REVERT: A 541 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7238 (mp) REVERT: A 562 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7090 (tp30) REVERT: A 567 GLU cc_start: 0.7218 (tp30) cc_final: 0.6884 (mp0) outliers start: 12 outliers final: 4 residues processed: 87 average time/residue: 0.4820 time to fit residues: 43.6937 Evaluate side-chains 82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115598 restraints weight = 5111.636| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.68 r_work: 0.3264 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4584 Z= 0.175 Angle : 0.583 6.506 6275 Z= 0.284 Chirality : 0.041 0.199 714 Planarity : 0.004 0.040 735 Dihedral : 9.294 58.735 926 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.75 % Allowed : 15.23 % Favored : 81.02 % 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: 1.02 (0.36), residues: 537 helix: 1.23 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.51 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.021 0.002 TYR A 418 PHE 0.015 0.001 PHE A 229 TRP 0.013 0.001 TRP A 109 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 4583) covalent geometry : angle 0.58236 ( 6273) SS BOND : bond 0.00038 ( 1) SS BOND : angle 1.98706 ( 2) hydrogen bonds : bond 0.04836 ( 282) hydrogen bonds : angle 5.04429 ( 822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.147 Fit side-chains REVERT: A 272 GLN cc_start: 0.7693 (tt0) cc_final: 0.7077 (tp40) REVERT: A 541 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6896 (mp) REVERT: A 567 GLU cc_start: 0.6871 (tp30) cc_final: 0.6633 (mp0) outliers start: 17 outliers final: 10 residues processed: 94 average time/residue: 0.4484 time to fit residues: 43.9397 Evaluate side-chains 87 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127082 restraints weight = 5160.116| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.54 r_work: 0.3430 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4584 Z= 0.145 Angle : 0.544 6.086 6275 Z= 0.265 Chirality : 0.039 0.196 714 Planarity : 0.004 0.038 735 Dihedral : 9.280 59.505 926 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.53 % Allowed : 15.45 % Favored : 81.02 % 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: 1.21 (0.36), residues: 537 helix: 1.34 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -0.36 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.020 0.002 TYR A 418 PHE 0.016 0.001 PHE A 401 TRP 0.012 0.001 TRP A 109 HIS 0.002 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4583) covalent geometry : angle 0.54294 ( 6273) SS BOND : bond 0.00046 ( 1) SS BOND : angle 1.70929 ( 2) hydrogen bonds : bond 0.04546 ( 282) hydrogen bonds : angle 4.86401 ( 822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.129 Fit side-chains REVERT: A 44 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7252 (mp) REVERT: A 110 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8319 (ttmm) REVERT: A 124 LEU cc_start: 0.8747 (tp) cc_final: 0.8442 (mt) REVERT: A 272 GLN cc_start: 0.7945 (tt0) cc_final: 0.7384 (tp40) REVERT: A 541 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7152 (mp) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 0.4581 time to fit residues: 41.5903 Evaluate side-chains 85 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124949 restraints weight = 5186.164| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.50 r_work: 0.3393 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4584 Z= 0.159 Angle : 0.555 6.003 6275 Z= 0.272 Chirality : 0.040 0.195 714 Planarity : 0.004 0.037 735 Dihedral : 9.199 59.470 926 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.75 % Allowed : 14.57 % Favored : 81.68 % 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: 1.25 (0.37), residues: 537 helix: 1.35 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -0.29 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 62 TYR 0.022 0.002 TYR A 418 PHE 0.017 0.001 PHE A 401 TRP 0.012 0.001 TRP A 109 HIS 0.002 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 4583) covalent geometry : angle 0.55385 ( 6273) SS BOND : bond 0.00011 ( 1) SS BOND : angle 1.81098 ( 2) hydrogen bonds : bond 0.04633 ( 282) hydrogen bonds : angle 4.87573 ( 822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.095 Fit side-chains REVERT: A 110 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8313 (ttmm) REVERT: A 124 LEU cc_start: 0.8760 (tp) cc_final: 0.8429 (mt) REVERT: A 272 GLN cc_start: 0.7960 (tt0) cc_final: 0.7382 (tp40) REVERT: A 541 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7201 (mp) outliers start: 17 outliers final: 12 residues processed: 87 average time/residue: 0.4842 time to fit residues: 43.7692 Evaluate side-chains 90 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.0060 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.2772 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.147550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129295 restraints weight = 5190.870| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.49 r_work: 0.3479 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4584 Z= 0.107 Angle : 0.497 5.789 6275 Z= 0.244 Chirality : 0.037 0.189 714 Planarity : 0.004 0.037 735 Dihedral : 8.896 59.787 926 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.09 % Allowed : 15.23 % Favored : 81.68 % 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: 1.66 (0.37), residues: 537 helix: 1.66 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.15 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 62 TYR 0.022 0.001 TYR A 418 PHE 0.016 0.001 PHE A 401 TRP 0.012 0.001 TRP A 109 HIS 0.002 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 4583) covalent geometry : angle 0.49610 ( 6273) SS BOND : bond 0.00073 ( 1) SS BOND : angle 1.41259 ( 2) hydrogen bonds : bond 0.04002 ( 282) hydrogen bonds : angle 4.58288 ( 822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.138 Fit side-chains REVERT: A 272 GLN cc_start: 0.7813 (tt0) cc_final: 0.7246 (tp40) outliers start: 14 outliers final: 9 residues processed: 87 average time/residue: 0.4543 time to fit residues: 41.1294 Evaluate side-chains 85 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.0270 chunk 22 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.144768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126432 restraints weight = 5219.364| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.51 r_work: 0.3439 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4584 Z= 0.137 Angle : 0.531 5.873 6275 Z= 0.261 Chirality : 0.039 0.197 714 Planarity : 0.004 0.038 735 Dihedral : 8.654 57.157 926 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.86 % Favored : 97.95 % Rotamer: Outliers : 3.09 % Allowed : 15.67 % Favored : 81.24 % 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: 1.60 (0.37), residues: 537 helix: 1.62 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.18 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.014 0.001 TYR A 132 PHE 0.016 0.001 PHE A 401 TRP 0.010 0.001 TRP A 109 HIS 0.001 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4583) covalent geometry : angle 0.52992 ( 6273) SS BOND : bond 0.00017 ( 1) SS BOND : angle 1.58752 ( 2) hydrogen bonds : bond 0.04379 ( 282) hydrogen bonds : angle 4.69768 ( 822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.152 Fit side-chains REVERT: A 110 LYS cc_start: 0.8432 (ttmm) cc_final: 0.7938 (ttmm) REVERT: A 124 LEU cc_start: 0.8693 (tp) cc_final: 0.8406 (mt) outliers start: 14 outliers final: 12 residues processed: 86 average time/residue: 0.4876 time to fit residues: 43.6414 Evaluate side-chains 88 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.143952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125666 restraints weight = 5183.187| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.49 r_work: 0.3415 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4584 Z= 0.148 Angle : 0.538 5.896 6275 Z= 0.264 Chirality : 0.039 0.196 714 Planarity : 0.004 0.037 735 Dihedral : 8.412 54.959 926 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.68 % Favored : 98.14 % Rotamer: Outliers : 3.53 % Allowed : 15.23 % Favored : 81.24 % 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: 1.55 (0.37), residues: 537 helix: 1.57 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.17 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 530 TYR 0.021 0.002 TYR A 418 PHE 0.021 0.001 PHE A 401 TRP 0.010 0.001 TRP A 109 HIS 0.002 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4583) covalent geometry : angle 0.53692 ( 6273) SS BOND : bond 0.00022 ( 1) SS BOND : angle 1.67041 ( 2) hydrogen bonds : bond 0.04484 ( 282) hydrogen bonds : angle 4.74122 ( 822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.093 Fit side-chains REVERT: A 110 LYS cc_start: 0.8461 (ttmm) cc_final: 0.7977 (ttmm) REVERT: A 124 LEU cc_start: 0.8754 (tp) cc_final: 0.8455 (mt) REVERT: A 541 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7253 (mp) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.4641 time to fit residues: 41.5579 Evaluate side-chains 90 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0670 chunk 15 optimal weight: 0.0060 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.3934 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.145829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127701 restraints weight = 5194.201| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.48 r_work: 0.3460 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4584 Z= 0.120 Angle : 0.516 5.803 6275 Z= 0.254 Chirality : 0.038 0.193 714 Planarity : 0.004 0.036 735 Dihedral : 8.244 54.904 926 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.49 % Favored : 98.32 % Rotamer: Outliers : 2.43 % Allowed : 16.56 % Favored : 81.02 % 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: 1.70 (0.37), residues: 537 helix: 1.67 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.11 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 530 TYR 0.022 0.001 TYR A 418 PHE 0.023 0.001 PHE A 401 TRP 0.012 0.001 TRP A 109 HIS 0.001 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4583) covalent geometry : angle 0.51496 ( 6273) SS BOND : bond 0.00004 ( 1) SS BOND : angle 1.50713 ( 2) hydrogen bonds : bond 0.04251 ( 282) hydrogen bonds : angle 4.63762 ( 822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.212 Fit side-chains REVERT: A 124 LEU cc_start: 0.8690 (tp) cc_final: 0.8393 (mt) REVERT: A 272 GLN cc_start: 0.7834 (tt0) cc_final: 0.7279 (tp40) REVERT: A 541 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7221 (mp) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.4599 time to fit residues: 41.2338 Evaluate side-chains 85 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.143232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125070 restraints weight = 5204.401| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.49 r_work: 0.3412 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4584 Z= 0.160 Angle : 0.553 5.931 6275 Z= 0.273 Chirality : 0.040 0.192 714 Planarity : 0.004 0.037 735 Dihedral : 8.170 54.080 926 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.86 % Favored : 97.95 % Rotamer: Outliers : 2.65 % Allowed : 16.11 % Favored : 81.24 % 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: 1.54 (0.37), residues: 537 helix: 1.55 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.14 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 530 TYR 0.014 0.002 TYR A 132 PHE 0.028 0.001 PHE A 401 TRP 0.009 0.001 TRP A 109 HIS 0.002 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4583) covalent geometry : angle 0.55221 ( 6273) SS BOND : bond 0.00025 ( 1) SS BOND : angle 1.79266 ( 2) hydrogen bonds : bond 0.04602 ( 282) hydrogen bonds : angle 4.78359 ( 822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.151 Fit side-chains REVERT: A 124 LEU cc_start: 0.8687 (tp) cc_final: 0.8367 (mt) REVERT: A 541 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7287 (mp) outliers start: 12 outliers final: 12 residues processed: 83 average time/residue: 0.4722 time to fit residues: 40.8481 Evaluate side-chains 88 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125664 restraints weight = 5152.837| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.46 r_work: 0.3419 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4584 Z= 0.150 Angle : 0.546 5.908 6275 Z= 0.269 Chirality : 0.040 0.194 714 Planarity : 0.004 0.037 735 Dihedral : 8.116 53.691 926 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.68 % Favored : 98.14 % Rotamer: Outliers : 2.43 % Allowed : 16.56 % Favored : 81.02 % 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: 1.56 (0.37), residues: 537 helix: 1.57 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.15 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 530 TYR 0.014 0.001 TYR A 132 PHE 0.030 0.001 PHE A 401 TRP 0.010 0.001 TRP A 109 HIS 0.002 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4583) covalent geometry : angle 0.54501 ( 6273) SS BOND : bond 0.00019 ( 1) SS BOND : angle 1.72850 ( 2) hydrogen bonds : bond 0.04563 ( 282) hydrogen bonds : angle 4.77376 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1539.79 seconds wall clock time: 27 minutes 2.18 seconds (1622.18 seconds total)