Starting phenix.real_space_refine on Wed Jul 1 21:02:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zsd_14930/07_2026/7zsd_14930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zsd_14930/07_2026/7zsd_14930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zsd_14930/07_2026/7zsd_14930.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zsd_14930/07_2026/7zsd_14930.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zsd_14930/07_2026/7zsd_14930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zsd_14930/07_2026/7zsd_14930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zsd_14930/07_2026/7zsd_14930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zsd_14930/07_2026/7zsd_14930.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 9 5.16 5 C 1363 2.51 5 N 362 2.21 5 O 386 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2120 Number of models: 1 Model: "" Number of chains: 3 Chain: "M" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1573 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain: "P" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.50, per 1000 atoms: 0.24 Number of scatterers: 2120 At special positions: 0 Unit cell: (77.7546, 60.4758, 70.3494, 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 9 16.00 O 386 8.00 N 362 7.00 C 1363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.03 Simple disulfide: pdb=" SG CYS M 391 " - pdb=" SG CYS M 525 " distance=2.03 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN M 343 " Time building additional restraints: 0.12 Conformation dependent library (CDL) restraints added in 48.7 milliseconds 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 33.0% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'M' and resid 337 through 343 Processing helix chain 'M' and resid 349 through 353 Processing helix chain 'M' and resid 365 through 371 removed outlier: 3.735A pdb=" N TYR M 369 " --> pdb=" O TYR M 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 390 Processing helix chain 'M' and resid 405 through 410 removed outlier: 4.645A pdb=" N ARG M 408 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'P' and resid 3 through 24 Processing helix chain 'P' and resid 26 through 49 removed outlier: 3.633A pdb=" N ALA P 30 " --> pdb=" O ASN P 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 354 through 358 removed outlier: 3.835A pdb=" N VAL M 395 " --> pdb=" O ILE M 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 452 through 454 76 hydrogen bonds defined for protein. 210 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: 0.16 Time building geometry restraints manager: 0.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 676 1.34 - 1.46: 533 1.46 - 1.58: 960 1.58 - 1.70: 0 1.70 - 1.81: 10 Bond restraints: 2179 Sorted by residual: bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" CB LYS M 444 " pdb=" CG LYS M 444 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" C3 NAG A 1 " pdb=" O3 NAG A 1 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.01e+00 ... (remaining 2174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2863 1.44 - 2.88: 75 2.88 - 4.32: 16 4.32 - 5.76: 2 5.76 - 7.20: 3 Bond angle restraints: 2959 Sorted by residual: angle pdb=" CB LYS M 444 " pdb=" CG LYS M 444 " pdb=" CD LYS M 444 " ideal model delta sigma weight residual 111.30 117.10 -5.80 2.30e+00 1.89e-01 6.35e+00 angle pdb=" CA LEU M 390 " pdb=" CB LEU M 390 " pdb=" CG LEU M 390 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.23e+00 angle pdb=" CA LYS M 444 " pdb=" CB LYS M 444 " pdb=" CG LYS M 444 " ideal model delta sigma weight residual 114.10 118.21 -4.11 2.00e+00 2.50e-01 4.22e+00 angle pdb=" C THR P 1 " pdb=" N ASN P 2 " pdb=" CA ASN P 2 " ideal model delta sigma weight residual 121.54 125.02 -3.48 1.91e+00 2.74e-01 3.32e+00 angle pdb=" CB GLU M 465 " pdb=" CG GLU M 465 " pdb=" CD GLU M 465 " ideal model delta sigma weight residual 112.60 115.67 -3.07 1.70e+00 3.46e-01 3.26e+00 ... (remaining 2954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1158 17.94 - 35.89: 94 35.89 - 53.83: 20 53.83 - 71.78: 7 71.78 - 89.72: 2 Dihedral angle restraints: 1281 sinusoidal: 517 harmonic: 764 Sorted by residual: dihedral pdb=" CB CYS M 391 " pdb=" SG CYS M 391 " pdb=" SG CYS M 525 " pdb=" CB CYS M 525 " ideal model delta sinusoidal sigma weight residual -86.00 -143.35 57.35 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" CB CYS M 480 " pdb=" SG CYS M 480 " pdb=" SG CYS M 488 " pdb=" CB CYS M 488 " ideal model delta sinusoidal sigma weight residual -86.00 -125.54 39.54 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CA ASP M 389 " pdb=" C ASP M 389 " pdb=" N LEU M 390 " pdb=" CA LEU M 390 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 1278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 252 0.056 - 0.111: 58 0.111 - 0.167: 3 0.167 - 0.222: 0 0.222 - 0.278: 1 Chirality restraints: 314 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN M 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE M 402 " pdb=" N ILE M 402 " pdb=" C ILE M 402 " pdb=" CB ILE M 402 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA ILE M 434 " pdb=" N ILE M 434 " pdb=" C ILE M 434 " pdb=" CB ILE M 434 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 311 not shown) Planarity restraints: 387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P 53 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO P 54 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO P 54 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO P 54 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 40 " 0.007 2.00e-02 2.50e+03 7.37e-03 1.09e+00 pdb=" CG TYR P 40 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR P 40 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR P 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR P 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR P 40 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR P 40 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR P 40 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 334 " -0.004 2.00e-02 2.50e+03 7.69e-03 5.91e-01 pdb=" C ASN M 334 " 0.013 2.00e-02 2.50e+03 pdb=" O ASN M 334 " -0.005 2.00e-02 2.50e+03 pdb=" N LEU M 335 " -0.004 2.00e-02 2.50e+03 ... (remaining 384 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 338 2.76 - 3.30: 2127 3.30 - 3.83: 3418 3.83 - 4.37: 3929 4.37 - 4.90: 6641 Nonbonded interactions: 16453 Sorted by model distance: nonbonded pdb=" O ARG P 35 " pdb=" NE2 GLN P 39 " model vdw 2.226 3.120 nonbonded pdb=" OD2 ASP M 398 " pdb=" OH TYR M 423 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASN M 487 " pdb=" OH TYR M 489 " model vdw 2.299 3.040 nonbonded pdb=" O LEU M 518 " pdb=" ND1 HIS M 519 " model vdw 2.308 3.120 nonbonded pdb=" ND2 ASN M 439 " pdb=" OE1 GLN M 506 " model vdw 2.360 3.120 ... (remaining 16448 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: 1.210 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.570 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 2185 Z= 0.137 Angle : 0.608 7.202 2973 Z= 0.298 Chirality : 0.046 0.278 314 Planarity : 0.003 0.031 386 Dihedral : 14.292 89.722 783 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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: -0.09 (0.53), residues: 257 helix: 0.40 (0.56), residues: 89 sheet: 0.67 (0.79), residues: 42 loop : -0.57 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 32 TYR 0.017 0.002 TYR P 40 PHE 0.011 0.001 PHE M 377 TRP 0.003 0.001 TRP M 353 HIS 0.003 0.001 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 2179) covalent geometry : angle 0.59816 / 0.29 ( 2959) SS BOND : bond 0.00272 / 0.12 ( 4) SS BOND : angle 1.30150 / 0.68 ( 8) hydrogen bonds : bond 0.17487 / 11.19 ( 76) hydrogen bonds : angle 7.09382 / 4.76 ( 210) link_BETA1-4 : bond 0.01047 / 0.55 ( 1) link_BETA1-4 : angle 1.93473 / 0.95 ( 3) link_NAG-ASN : bond 0.00504 / 0.27 ( 1) link_NAG-ASN : angle 2.32489 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0453 time to fit residues: 2.3080 Evaluate side-chains 33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.0980 chunk 13 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.130694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.113083 restraints weight = 5097.893| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.05 r_work: 0.3669 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2185 Z= 0.124 Angle : 0.597 8.548 2973 Z= 0.295 Chirality : 0.045 0.218 314 Planarity : 0.004 0.024 386 Dihedral : 4.386 17.235 294 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.45 % Allowed : 11.21 % Favored : 88.34 % 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: -0.08 (0.53), residues: 257 helix: 0.46 (0.57), residues: 88 sheet: 1.16 (0.91), residues: 34 loop : -0.69 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 32 TYR 0.011 0.001 TYR M 495 PHE 0.011 0.001 PHE M 377 TRP 0.002 0.000 TRP M 436 HIS 0.005 0.002 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 2179) covalent geometry : angle 0.59004 / 0.29 ( 2959) SS BOND : bond 0.00178 / 0.07 ( 4) SS BOND : angle 0.85703 / 0.48 ( 8) hydrogen bonds : bond 0.03933 / 2.61 ( 76) hydrogen bonds : angle 5.78216 / 3.80 ( 210) link_BETA1-4 : bond 0.00853 / 0.45 ( 1) link_BETA1-4 : angle 1.54311 / 0.75 ( 3) link_NAG-ASN : bond 0.00426 / 0.22 ( 1) link_NAG-ASN : angle 2.36803 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.048 Fit side-chains REVERT: M 495 TYR cc_start: 0.7553 (m-80) cc_final: 0.7347 (m-80) REVERT: P 5 GLU cc_start: 0.6712 (mp0) cc_final: 0.6442 (mp0) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.0432 time to fit residues: 2.0288 Evaluate side-chains 33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.124925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106483 restraints weight = 5179.792| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.11 r_work: 0.3548 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2185 Z= 0.137 Angle : 0.563 5.460 2973 Z= 0.285 Chirality : 0.045 0.239 314 Planarity : 0.004 0.021 386 Dihedral : 4.467 21.128 294 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.79 % Allowed : 12.11 % Favored : 86.10 % 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: -0.38 (0.53), residues: 257 helix: 0.33 (0.57), residues: 88 sheet: 1.04 (0.92), residues: 32 loop : -0.96 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 32 TYR 0.016 0.002 TYR P 47 PHE 0.006 0.001 PHE M 375 TRP 0.006 0.001 TRP M 353 HIS 0.004 0.002 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 2179) covalent geometry : angle 0.55216 / 0.28 ( 2959) SS BOND : bond 0.00286 / 0.12 ( 4) SS BOND : angle 1.15739 / 0.66 ( 8) hydrogen bonds : bond 0.03765 / 2.53 ( 76) hydrogen bonds : angle 5.19582 / 3.39 ( 210) link_BETA1-4 : bond 0.00873 / 0.46 ( 1) link_BETA1-4 : angle 1.79743 / 0.89 ( 3) link_NAG-ASN : bond 0.00348 / 0.18 ( 1) link_NAG-ASN : angle 2.53135 / 1.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.047 Fit side-chains revert: symmetry clash REVERT: M 392 PHE cc_start: 0.7624 (m-80) cc_final: 0.7289 (m-80) REVERT: M 430 THR cc_start: 0.8837 (p) cc_final: 0.8562 (p) REVERT: M 495 TYR cc_start: 0.7612 (m-80) cc_final: 0.7351 (m-80) REVERT: P 5 GLU cc_start: 0.7069 (mp0) cc_final: 0.6728 (mp0) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.0400 time to fit residues: 1.7550 Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.125040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106788 restraints weight = 5013.679| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.01 r_work: 0.3553 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2185 Z= 0.134 Angle : 0.568 5.852 2973 Z= 0.287 Chirality : 0.045 0.241 314 Planarity : 0.004 0.023 386 Dihedral : 4.408 19.095 294 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.59 % Allowed : 11.66 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.52), residues: 257 helix: 0.38 (0.57), residues: 88 sheet: 0.83 (0.90), residues: 32 loop : -1.02 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 32 TYR 0.010 0.001 TYR P 55 PHE 0.008 0.001 PHE M 374 TRP 0.007 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 2179) covalent geometry : angle 0.55789 / 0.29 ( 2959) SS BOND : bond 0.00249 / 0.10 ( 4) SS BOND : angle 0.99314 / 0.56 ( 8) hydrogen bonds : bond 0.03495 / 2.37 ( 76) hydrogen bonds : angle 5.10293 / 3.33 ( 210) link_BETA1-4 : bond 0.00962 / 0.51 ( 1) link_BETA1-4 : angle 1.83575 / 0.90 ( 3) link_NAG-ASN : bond 0.00350 / 0.18 ( 1) link_NAG-ASN : angle 2.50500 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.045 Fit side-chains revert: symmetry clash REVERT: M 392 PHE cc_start: 0.7545 (m-80) cc_final: 0.7270 (m-80) REVERT: M 430 THR cc_start: 0.8826 (p) cc_final: 0.8548 (p) REVERT: M 495 TYR cc_start: 0.7602 (m-80) cc_final: 0.7314 (m-80) REVERT: P 5 GLU cc_start: 0.7132 (mp0) cc_final: 0.6751 (mp0) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.0393 time to fit residues: 1.9524 Evaluate side-chains 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.123047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104753 restraints weight = 5065.655| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.01 r_work: 0.3522 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2185 Z= 0.160 Angle : 0.598 7.222 2973 Z= 0.301 Chirality : 0.045 0.259 314 Planarity : 0.004 0.026 386 Dihedral : 4.558 20.588 294 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.59 % Allowed : 12.56 % Favored : 83.86 % 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: -0.69 (0.52), residues: 257 helix: 0.29 (0.56), residues: 88 sheet: -0.43 (0.77), residues: 42 loop : -0.94 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 32 TYR 0.011 0.002 TYR P 40 PHE 0.009 0.001 PHE M 375 TRP 0.007 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 2179) covalent geometry : angle 0.58599 / 0.30 ( 2959) SS BOND : bond 0.00283 / 0.12 ( 4) SS BOND : angle 1.30722 / 0.74 ( 8) hydrogen bonds : bond 0.03698 / 2.48 ( 76) hydrogen bonds : angle 5.11287 / 3.36 ( 210) link_BETA1-4 : bond 0.00909 / 0.48 ( 1) link_BETA1-4 : angle 2.08393 / 1.03 ( 3) link_NAG-ASN : bond 0.00300 / 0.16 ( 1) link_NAG-ASN : angle 2.70014 / 1.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.047 Fit side-chains revert: symmetry clash REVERT: M 430 THR cc_start: 0.8865 (p) cc_final: 0.8599 (p) REVERT: M 495 TYR cc_start: 0.7594 (m-80) cc_final: 0.7318 (m-80) REVERT: P 5 GLU cc_start: 0.7016 (mp0) cc_final: 0.6606 (mp0) outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 0.0297 time to fit residues: 1.4780 Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 375 PHE Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.124085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105967 restraints weight = 4951.982| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.99 r_work: 0.3540 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2185 Z= 0.129 Angle : 0.583 6.354 2973 Z= 0.293 Chirality : 0.044 0.247 314 Planarity : 0.004 0.023 386 Dihedral : 4.467 19.058 294 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.24 % Allowed : 14.80 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.52), residues: 257 helix: 0.39 (0.57), residues: 88 sheet: 0.57 (0.88), residues: 32 loop : -0.95 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 32 TYR 0.010 0.001 TYR P 40 PHE 0.006 0.001 PHE M 515 TRP 0.006 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 2179) covalent geometry : angle 0.57183 / 0.29 ( 2959) SS BOND : bond 0.00238 / 0.10 ( 4) SS BOND : angle 1.18926 / 0.66 ( 8) hydrogen bonds : bond 0.03230 / 2.17 ( 76) hydrogen bonds : angle 5.00622 / 3.28 ( 210) link_BETA1-4 : bond 0.00867 / 0.46 ( 1) link_BETA1-4 : angle 1.91751 / 0.94 ( 3) link_NAG-ASN : bond 0.00306 / 0.16 ( 1) link_NAG-ASN : angle 2.56519 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 430 THR cc_start: 0.8815 (p) cc_final: 0.8547 (p) REVERT: M 495 TYR cc_start: 0.7518 (m-80) cc_final: 0.7292 (m-80) outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 0.0270 time to fit residues: 1.3778 Evaluate side-chains 35 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.0010 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.0030 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.125065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106946 restraints weight = 5020.353| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.05 r_work: 0.3556 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2185 Z= 0.116 Angle : 0.590 7.311 2973 Z= 0.293 Chirality : 0.044 0.235 314 Planarity : 0.004 0.023 386 Dihedral : 4.346 17.653 294 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.69 % Allowed : 15.25 % Favored : 82.06 % 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: -0.39 (0.52), residues: 257 helix: 0.50 (0.57), residues: 88 sheet: 0.47 (0.87), residues: 32 loop : -0.93 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 32 TYR 0.024 0.002 TYR P 47 PHE 0.005 0.001 PHE M 497 TRP 0.005 0.001 TRP M 353 HIS 0.007 0.003 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 2179) covalent geometry : angle 0.58113 / 0.29 ( 2959) SS BOND : bond 0.00174 / 0.07 ( 4) SS BOND : angle 1.04074 / 0.59 ( 8) hydrogen bonds : bond 0.02980 / 2.00 ( 76) hydrogen bonds : angle 5.00653 / 3.31 ( 210) link_BETA1-4 : bond 0.00717 / 0.38 ( 1) link_BETA1-4 : angle 1.74806 / 0.86 ( 3) link_NAG-ASN : bond 0.00355 / 0.19 ( 1) link_NAG-ASN : angle 2.36804 / 1.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 430 THR cc_start: 0.8815 (p) cc_final: 0.8539 (p) REVERT: M 465 GLU cc_start: 0.4564 (tp30) cc_final: 0.4266 (tp30) REVERT: M 495 TYR cc_start: 0.7589 (m-80) cc_final: 0.7274 (m-80) REVERT: P 5 GLU cc_start: 0.6753 (mp0) cc_final: 0.6364 (mp0) REVERT: P 32 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7921 (ttp-110) outliers start: 6 outliers final: 6 residues processed: 41 average time/residue: 0.0502 time to fit residues: 2.4088 Evaluate side-chains 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 5 optimal weight: 0.0470 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.125090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106913 restraints weight = 5051.644| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.11 r_work: 0.3554 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2185 Z= 0.116 Angle : 0.581 6.534 2973 Z= 0.293 Chirality : 0.044 0.234 314 Planarity : 0.003 0.022 386 Dihedral : 4.258 17.086 294 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.14 % Allowed : 16.14 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.52), residues: 257 helix: 0.55 (0.57), residues: 88 sheet: 0.39 (0.87), residues: 32 loop : -0.90 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 32 TYR 0.016 0.001 TYR P 47 PHE 0.008 0.001 PHE M 392 TRP 0.006 0.001 TRP M 353 HIS 0.007 0.002 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 2179) covalent geometry : angle 0.57266 / 0.29 ( 2959) SS BOND : bond 0.00178 / 0.08 ( 4) SS BOND : angle 1.03440 / 0.59 ( 8) hydrogen bonds : bond 0.02942 / 2.02 ( 76) hydrogen bonds : angle 4.91975 / 3.25 ( 210) link_BETA1-4 : bond 0.00862 / 0.45 ( 1) link_BETA1-4 : angle 1.80319 / 0.89 ( 3) link_NAG-ASN : bond 0.00340 / 0.18 ( 1) link_NAG-ASN : angle 2.33677 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 392 PHE cc_start: 0.7815 (m-80) cc_final: 0.7587 (m-80) REVERT: M 465 GLU cc_start: 0.4482 (tp30) cc_final: 0.4212 (tp30) REVERT: M 495 TYR cc_start: 0.7582 (m-80) cc_final: 0.7261 (m-80) REVERT: P 5 GLU cc_start: 0.6677 (mp0) cc_final: 0.6252 (mp0) REVERT: P 32 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7957 (ttp-110) outliers start: 7 outliers final: 7 residues processed: 37 average time/residue: 0.0591 time to fit residues: 2.6162 Evaluate side-chains 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 515 PHE Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.125290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107187 restraints weight = 5095.046| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.09 r_work: 0.3552 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2185 Z= 0.119 Angle : 0.602 6.661 2973 Z= 0.298 Chirality : 0.044 0.234 314 Planarity : 0.003 0.022 386 Dihedral : 4.236 17.224 294 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.59 % Allowed : 15.25 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.52), residues: 257 helix: 0.56 (0.57), residues: 88 sheet: 0.31 (0.86), residues: 32 loop : -0.89 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 32 TYR 0.015 0.001 TYR P 47 PHE 0.008 0.001 PHE M 392 TRP 0.005 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2179) covalent geometry : angle 0.59306 / 0.30 ( 2959) SS BOND : bond 0.00201 / 0.09 ( 4) SS BOND : angle 1.11110 / 0.63 ( 8) hydrogen bonds : bond 0.02914 / 1.99 ( 76) hydrogen bonds : angle 4.85113 / 3.21 ( 210) link_BETA1-4 : bond 0.00833 / 0.44 ( 1) link_BETA1-4 : angle 1.80348 / 0.89 ( 3) link_NAG-ASN : bond 0.00336 / 0.18 ( 1) link_NAG-ASN : angle 2.29679 / 1.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 465 GLU cc_start: 0.4318 (tp30) cc_final: 0.4077 (tp30) REVERT: M 495 TYR cc_start: 0.7602 (m-80) cc_final: 0.7218 (m-80) REVERT: P 5 GLU cc_start: 0.7002 (mp0) cc_final: 0.6637 (mp0) REVERT: P 32 ARG cc_start: 0.8230 (ttp-110) cc_final: 0.8005 (ttp-110) outliers start: 8 outliers final: 7 residues processed: 37 average time/residue: 0.0605 time to fit residues: 2.6573 Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 515 PHE Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.125293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107180 restraints weight = 5143.527| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.15 r_work: 0.3561 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2185 Z= 0.119 Angle : 0.598 7.019 2973 Z= 0.300 Chirality : 0.044 0.230 314 Planarity : 0.003 0.022 386 Dihedral : 4.183 16.897 294 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.14 % Allowed : 16.59 % Favored : 80.27 % 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: -0.38 (0.52), residues: 257 helix: 0.52 (0.57), residues: 88 sheet: 0.29 (0.85), residues: 32 loop : -0.89 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 32 TYR 0.014 0.001 TYR P 47 PHE 0.009 0.001 PHE M 392 TRP 0.006 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 2179) covalent geometry : angle 0.59072 / 0.30 ( 2959) SS BOND : bond 0.00135 / 0.06 ( 4) SS BOND : angle 0.94944 / 0.54 ( 8) hydrogen bonds : bond 0.02887 / 1.99 ( 76) hydrogen bonds : angle 4.81753 / 3.18 ( 210) link_BETA1-4 : bond 0.00818 / 0.43 ( 1) link_BETA1-4 : angle 1.76952 / 0.87 ( 3) link_NAG-ASN : bond 0.00357 / 0.19 ( 1) link_NAG-ASN : angle 2.26007 / 1.10 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 465 GLU cc_start: 0.4272 (tp30) cc_final: 0.4035 (tp30) REVERT: M 495 TYR cc_start: 0.7634 (m-80) cc_final: 0.7271 (m-80) REVERT: P 5 GLU cc_start: 0.7002 (mp0) cc_final: 0.6633 (mp0) REVERT: P 32 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.8009 (ttp-110) outliers start: 7 outliers final: 7 residues processed: 39 average time/residue: 0.0447 time to fit residues: 2.0989 Evaluate side-chains 41 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 515 PHE Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.125725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.107784 restraints weight = 5176.342| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.11 r_work: 0.3568 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2185 Z= 0.118 Angle : 0.609 6.997 2973 Z= 0.302 Chirality : 0.044 0.229 314 Planarity : 0.003 0.022 386 Dihedral : 4.187 16.827 294 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.14 % Allowed : 16.59 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.52), residues: 257 helix: 0.47 (0.57), residues: 88 sheet: 0.33 (0.84), residues: 32 loop : -0.82 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 32 TYR 0.014 0.001 TYR P 47 PHE 0.007 0.001 PHE M 392 TRP 0.005 0.001 TRP M 353 HIS 0.005 0.002 HIS M 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 2179) covalent geometry : angle 0.60131 / 0.30 ( 2959) SS BOND : bond 0.00199 / 0.08 ( 4) SS BOND : angle 1.00348 / 0.56 ( 8) hydrogen bonds : bond 0.02857 / 1.95 ( 76) hydrogen bonds : angle 4.82059 / 3.21 ( 210) link_BETA1-4 : bond 0.00869 / 0.46 ( 1) link_BETA1-4 : angle 1.79794 / 0.88 ( 3) link_NAG-ASN : bond 0.00347 / 0.18 ( 1) link_NAG-ASN : angle 2.23544 / 1.09 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 631.15 seconds wall clock time: 11 minutes 29.59 seconds (689.59 seconds total)