Starting phenix.real_space_refine on Wed Sep 17 02:57:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zsd_14930/09_2025/7zsd_14930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zsd_14930/09_2025/7zsd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zsd_14930/09_2025/7zsd_14930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zsd_14930/09_2025/7zsd_14930.map" model { file = "/net/cci-nas-00/data/ceres_data/7zsd_14930/09_2025/7zsd_14930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zsd_14930/09_2025/7zsd_14930.cif" } 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-2.0-5805/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.46, per 1000 atoms: 0.22 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: 0.19 Conformation dependent library (CDL) restraints added in 42.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.14 Time building geometry restraints manager: 0.14 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 - 21.64: 1206 21.64 - 43.29: 88 43.29 - 64.93: 13 64.93 - 86.58: 11 86.58 - 108.22: 5 Dihedral angle restraints: 1323 sinusoidal: 559 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=" C2 NAG A 1 " pdb=" C3 NAG A 1 " pdb=" C4 NAG A 1 " pdb=" C5 NAG A 1 " ideal model delta sinusoidal sigma weight residual 53.78 -54.44 108.22 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 1320 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: 1.040 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.480 Find NCS groups from input model: 0.000 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:0.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 17.984 108.222 825 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 aren 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 covalent geometry : bond 0.00302 ( 2179) covalent geometry : angle 0.59816 ( 2959) SS BOND : bond 0.00272 ( 4) SS BOND : angle 1.30150 ( 8) hydrogen bonds : bond 0.17487 ( 76) hydrogen bonds : angle 7.09382 ( 210) link_BETA1-4 : bond 0.01047 ( 1) link_BETA1-4 : angle 1.93473 ( 3) link_NAG-ASN : bond 0.00504 ( 1) link_NAG-ASN : angle 2.32489 ( 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 : 0.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0436 time to fit residues: 2.2090 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 : 0.043 ------------------------------------------------------------------------------- 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: 6.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.130788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.113048 restraints weight = 5102.859| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.07 r_work: 0.3681 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2185 Z= 0.120 Angle : 0.637 8.550 2973 Z= 0.302 Chirality : 0.047 0.236 314 Planarity : 0.004 0.023 386 Dihedral : 14.674 86.230 336 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.45 % Allowed : 10.31 % Favored : 89.24 % 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 aren not related in a simple way. whole: -0.07 (0.53), residues: 257 helix: 0.49 (0.57), residues: 88 sheet: 1.10 (0.90), residues: 34 loop : -0.67 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 32 TYR 0.012 0.001 TYR M 495 PHE 0.013 0.001 PHE M 377 TRP 0.003 0.001 TRP M 436 HIS 0.006 0.002 HIS M 519 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 2179) covalent geometry : angle 0.62190 ( 2959) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.92964 ( 8) hydrogen bonds : bond 0.03853 ( 76) hydrogen bonds : angle 5.66887 ( 210) link_BETA1-4 : bond 0.00986 ( 1) link_BETA1-4 : angle 3.50934 ( 3) link_NAG-ASN : bond 0.00320 ( 1) link_NAG-ASN : angle 2.41988 ( 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 40 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.043 Fit side-chains REVERT: M 495 TYR cc_start: 0.7471 (m-80) cc_final: 0.7262 (m-80) REVERT: P 5 GLU cc_start: 0.6721 (mp0) cc_final: 0.6430 (mp0) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.0367 time to fit residues: 1.7326 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 : 0.043 ------------------------------------------------------------------------------- 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: 3.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.123237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104976 restraints weight = 5156.249| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.02 r_work: 0.3532 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2185 Z= 0.159 Angle : 0.632 6.801 2973 Z= 0.305 Chirality : 0.048 0.249 314 Planarity : 0.004 0.022 386 Dihedral : 13.219 75.588 336 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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 aren not related in a simple way. whole: -0.44 (0.53), residues: 257 helix: 0.30 (0.57), residues: 88 sheet: 0.94 (0.91), residues: 32 loop : -0.98 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 32 TYR 0.015 0.002 TYR P 47 PHE 0.007 0.001 PHE M 375 TRP 0.007 0.001 TRP M 353 HIS 0.004 0.002 HIS M 519 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 2179) covalent geometry : angle 0.61040 ( 2959) SS BOND : bond 0.00319 ( 4) SS BOND : angle 1.24038 ( 8) hydrogen bonds : bond 0.03938 ( 76) hydrogen bonds : angle 5.24527 ( 210) link_BETA1-4 : bond 0.01148 ( 1) link_BETA1-4 : angle 3.76994 ( 3) link_NAG-ASN : bond 0.00394 ( 1) link_NAG-ASN : angle 3.15275 ( 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 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.045 Fit side-chains revert: symmetry clash REVERT: M 430 THR cc_start: 0.8824 (p) cc_final: 0.8552 (p) REVERT: M 495 TYR cc_start: 0.7506 (m-80) cc_final: 0.7295 (m-80) REVERT: P 5 GLU cc_start: 0.7010 (mp0) cc_final: 0.6656 (mp0) outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.0385 time to fit residues: 1.6331 Evaluate side-chains 32 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.044 ------------------------------------------------------------------------------- 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: 0.0270 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.125860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107866 restraints weight = 5012.178| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.03 r_work: 0.3571 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2185 Z= 0.116 Angle : 0.618 7.005 2973 Z= 0.294 Chirality : 0.047 0.255 314 Planarity : 0.003 0.023 386 Dihedral : 11.752 65.026 336 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.59 % Allowed : 12.11 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.52), residues: 257 helix: 0.34 (0.57), residues: 88 sheet: 0.89 (0.89), residues: 32 loop : -1.00 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 32 TYR 0.011 0.001 TYR P 47 PHE 0.011 0.001 PHE M 374 TRP 0.006 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 2179) covalent geometry : angle 0.59641 ( 2959) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.92584 ( 8) hydrogen bonds : bond 0.03185 ( 76) hydrogen bonds : angle 5.02168 ( 210) link_BETA1-4 : bond 0.01240 ( 1) link_BETA1-4 : angle 3.82936 ( 3) link_NAG-ASN : bond 0.00352 ( 1) link_NAG-ASN : angle 3.32535 ( 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 49 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.046 Fit side-chains revert: symmetry clash REVERT: M 365 TYR cc_start: 0.8080 (m-80) cc_final: 0.7750 (m-80) REVERT: M 392 PHE cc_start: 0.7553 (m-80) cc_final: 0.7270 (m-80) REVERT: M 465 GLU cc_start: 0.4578 (tp30) cc_final: 0.4291 (tp30) REVERT: M 495 TYR cc_start: 0.7550 (m-80) cc_final: 0.7263 (m-80) REVERT: P 5 GLU cc_start: 0.7154 (mp0) cc_final: 0.6749 (mp0) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.0327 time to fit residues: 1.8114 Evaluate side-chains 41 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 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: 4.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.126471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108545 restraints weight = 5062.962| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.04 r_work: 0.3584 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2079 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= 0.118 Angle : 0.646 7.204 2973 Z= 0.303 Chirality : 0.047 0.287 314 Planarity : 0.004 0.022 386 Dihedral : 10.646 58.713 336 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % 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 aren not related in a simple way. whole: -0.40 (0.52), residues: 257 helix: 0.41 (0.57), residues: 88 sheet: 0.87 (0.88), residues: 32 loop : -0.98 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 32 TYR 0.018 0.001 TYR P 47 PHE 0.005 0.001 PHE M 374 TRP 0.005 0.001 TRP M 353 HIS 0.007 0.002 HIS M 519 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2179) covalent geometry : angle 0.62127 ( 2959) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.99377 ( 8) hydrogen bonds : bond 0.03072 ( 76) hydrogen bonds : angle 4.93833 ( 210) link_BETA1-4 : bond 0.01299 ( 1) link_BETA1-4 : angle 3.95249 ( 3) link_NAG-ASN : bond 0.00391 ( 1) link_NAG-ASN : angle 3.76240 ( 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 44 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: M 365 TYR cc_start: 0.8035 (m-80) cc_final: 0.7660 (m-80) REVERT: M 392 PHE cc_start: 0.7618 (m-80) cc_final: 0.7261 (m-80) REVERT: M 465 GLU cc_start: 0.4267 (tp30) cc_final: 0.4025 (tp30) REVERT: M 495 TYR cc_start: 0.7464 (m-80) cc_final: 0.7171 (m-80) outliers start: 8 outliers final: 8 residues processed: 40 average time/residue: 0.0537 time to fit residues: 2.6491 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 : 0.092 ------------------------------------------------------------------------------- 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 390 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.0870 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.126537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.108718 restraints weight = 4981.065| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.03 r_work: 0.3591 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2217 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 : 0.631 7.158 2973 Z= 0.299 Chirality : 0.047 0.291 314 Planarity : 0.003 0.022 386 Dihedral : 10.094 54.920 336 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.62 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 aren not related in a simple way. whole: -0.34 (0.52), residues: 257 helix: 0.49 (0.58), residues: 88 sheet: 0.73 (0.88), 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 0.012 0.001 TYR P 47 PHE 0.005 0.001 PHE M 497 TRP 0.006 0.001 TRP M 353 HIS 0.007 0.002 HIS M 519 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2179) covalent geometry : angle 0.60475 ( 2959) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.98421 ( 8) hydrogen bonds : bond 0.02977 ( 76) hydrogen bonds : angle 4.84958 ( 210) link_BETA1-4 : bond 0.01260 ( 1) link_BETA1-4 : angle 3.99762 ( 3) link_NAG-ASN : bond 0.00405 ( 1) link_NAG-ASN : angle 3.94683 ( 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 46 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: M 365 TYR cc_start: 0.8111 (m-80) cc_final: 0.7712 (m-80) REVERT: M 392 PHE cc_start: 0.7732 (m-80) cc_final: 0.7401 (m-80) REVERT: M 465 GLU cc_start: 0.3819 (tp30) cc_final: 0.3540 (tp30) REVERT: M 495 TYR cc_start: 0.7478 (m-80) cc_final: 0.7093 (m-80) REVERT: P 5 GLU cc_start: 0.7036 (mp0) cc_final: 0.6696 (mp0) REVERT: P 32 ARG cc_start: 0.8212 (ttp-110) cc_final: 0.7988 (ttp-110) outliers start: 8 outliers final: 8 residues processed: 42 average time/residue: 0.0773 time to fit residues: 3.7370 Evaluate side-chains 41 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 390 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=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: 2.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.125597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107965 restraints weight = 5059.422| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.98 r_work: 0.3560 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2185 Z= 0.127 Angle : 0.657 7.256 2973 Z= 0.309 Chirality : 0.047 0.309 314 Planarity : 0.004 0.022 386 Dihedral : 9.750 52.049 336 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.59 % Allowed : 16.59 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.53), residues: 257 helix: 0.47 (0.58), residues: 88 sheet: 0.58 (0.88), residues: 32 loop : -0.87 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 32 TYR 0.011 0.001 TYR P 47 PHE 0.005 0.001 PHE M 375 TRP 0.005 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2179) covalent geometry : angle 0.62792 ( 2959) SS BOND : bond 0.00239 ( 4) SS BOND : angle 1.06599 ( 8) hydrogen bonds : bond 0.03023 ( 76) hydrogen bonds : angle 4.99216 ( 210) link_BETA1-4 : bond 0.01411 ( 1) link_BETA1-4 : angle 4.20529 ( 3) link_NAG-ASN : bond 0.00463 ( 1) link_NAG-ASN : angle 4.21872 ( 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 44 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: M 365 TYR cc_start: 0.8080 (m-80) cc_final: 0.7777 (m-80) REVERT: M 392 PHE cc_start: 0.7736 (m-80) cc_final: 0.7534 (m-80) REVERT: M 465 GLU cc_start: 0.3913 (tp30) cc_final: 0.3636 (tp30) REVERT: M 495 TYR cc_start: 0.7428 (m-80) cc_final: 0.7079 (m-80) REVERT: P 32 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7871 (ttp-110) outliers start: 8 outliers final: 8 residues processed: 41 average time/residue: 0.0734 time to fit residues: 3.5080 Evaluate side-chains 41 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 390 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 0.3980 chunk 5 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.126848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.109310 restraints weight = 5049.657| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.01 r_work: 0.3587 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2185 Z= 0.115 Angle : 0.654 7.080 2973 Z= 0.309 Chirality : 0.047 0.302 314 Planarity : 0.003 0.022 386 Dihedral : 9.453 49.480 336 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.59 % Allowed : 16.14 % 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 aren not related in a simple way. whole: -0.33 (0.53), residues: 257 helix: 0.49 (0.58), residues: 88 sheet: 0.45 (0.87), residues: 32 loop : -0.83 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 32 TYR 0.011 0.001 TYR P 47 PHE 0.004 0.001 PHE M 497 TRP 0.006 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2179) covalent geometry : angle 0.62656 ( 2959) SS BOND : bond 0.00164 ( 4) SS BOND : angle 0.94659 ( 8) hydrogen bonds : bond 0.02826 ( 76) hydrogen bonds : angle 4.88062 ( 210) link_BETA1-4 : bond 0.01364 ( 1) link_BETA1-4 : angle 4.10478 ( 3) link_NAG-ASN : bond 0.00486 ( 1) link_NAG-ASN : angle 4.22636 ( 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 43 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: M 362 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8902 (m) REVERT: M 365 TYR cc_start: 0.8019 (m-80) cc_final: 0.7712 (m-80) REVERT: M 465 GLU cc_start: 0.3814 (tp30) cc_final: 0.3581 (tp30) REVERT: M 495 TYR cc_start: 0.7365 (m-80) cc_final: 0.6995 (m-80) REVERT: P 5 GLU cc_start: 0.7043 (mp0) cc_final: 0.6694 (mp0) REVERT: P 32 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7925 (ttp-110) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.0671 time to fit residues: 3.0823 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 : 0.081 ------------------------------------------------------------------------------- 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: 10.0000 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 0 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.2514 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.131082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.113960 restraints weight = 5187.389| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.10 r_work: 0.3687 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2612 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= 0.115 Angle : 0.663 7.007 2973 Z= 0.311 Chirality : 0.046 0.294 314 Planarity : 0.003 0.022 386 Dihedral : 9.004 46.023 336 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.59 % Allowed : 16.14 % 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 aren not related in a simple way. whole: -0.31 (0.53), residues: 257 helix: 0.49 (0.58), residues: 88 sheet: 0.28 (0.87), residues: 32 loop : -0.75 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 32 TYR 0.011 0.001 TYR P 47 PHE 0.005 0.001 PHE M 400 TRP 0.003 0.000 TRP M 353 HIS 0.006 0.002 HIS M 519 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 2179) covalent geometry : angle 0.63744 ( 2959) SS BOND : bond 0.00138 ( 4) SS BOND : angle 0.84083 ( 8) hydrogen bonds : bond 0.02627 ( 76) hydrogen bonds : angle 4.75143 ( 210) link_BETA1-4 : bond 0.01372 ( 1) link_BETA1-4 : angle 4.05849 ( 3) link_NAG-ASN : bond 0.00480 ( 1) link_NAG-ASN : angle 4.13850 ( 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 44 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: M 362 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8882 (m) REVERT: M 465 GLU cc_start: 0.3681 (tp30) cc_final: 0.3471 (tp30) REVERT: M 495 TYR cc_start: 0.7352 (m-80) cc_final: 0.6973 (m-80) REVERT: P 5 GLU cc_start: 0.7088 (mp0) cc_final: 0.6704 (mp0) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.0669 time to fit residues: 3.0350 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 : 0.086 ------------------------------------------------------------------------------- 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: 0.9980 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.0470 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.130262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.113019 restraints weight = 5232.998| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.08 r_work: 0.3674 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2185 Z= 0.119 Angle : 0.671 7.210 2973 Z= 0.317 Chirality : 0.047 0.306 314 Planarity : 0.003 0.022 386 Dihedral : 8.868 44.596 336 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.14 % Allowed : 17.04 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.53), residues: 257 helix: 0.52 (0.58), residues: 88 sheet: 0.36 (0.86), residues: 32 loop : -0.74 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 32 TYR 0.011 0.001 TYR P 47 PHE 0.005 0.001 PHE M 400 TRP 0.006 0.001 TRP M 353 HIS 0.005 0.002 HIS M 519 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 2179) covalent geometry : angle 0.64322 ( 2959) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.97669 ( 8) hydrogen bonds : bond 0.02812 ( 76) hydrogen bonds : angle 4.73443 ( 210) link_BETA1-4 : bond 0.01389 ( 1) link_BETA1-4 : angle 4.17942 ( 3) link_NAG-ASN : bond 0.00513 ( 1) link_NAG-ASN : angle 4.29845 ( 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 41 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 362 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8920 (m) REVERT: M 465 GLU cc_start: 0.3991 (tp30) cc_final: 0.3756 (tp30) REVERT: M 495 TYR cc_start: 0.7328 (m-80) cc_final: 0.6849 (m-80) REVERT: P 5 GLU cc_start: 0.6996 (mp0) cc_final: 0.6626 (mp0) outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 0.0538 time to fit residues: 2.4335 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 : 0.087 ------------------------------------------------------------------------------- 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: 8.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.0370 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 0.8678 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.128906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.111444 restraints weight = 5285.443| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.11 r_work: 0.3645 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2699 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= 0.129 Angle : 0.702 7.314 2973 Z= 0.330 Chirality : 0.048 0.314 314 Planarity : 0.004 0.033 386 Dihedral : 8.893 44.404 336 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.14 % Allowed : 17.04 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.53), residues: 257 helix: 0.46 (0.58), residues: 88 sheet: 0.39 (0.87), residues: 32 loop : -0.74 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 32 TYR 0.011 0.001 TYR P 47 PHE 0.005 0.001 PHE M 400 TRP 0.005 0.001 TRP M 353 HIS 0.005 0.002 HIS M 519 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2179) covalent geometry : angle 0.67355 ( 2959) SS BOND : bond 0.00205 ( 4) SS BOND : angle 1.05151 ( 8) hydrogen bonds : bond 0.02935 ( 76) hydrogen bonds : angle 4.81085 ( 210) link_BETA1-4 : bond 0.01397 ( 1) link_BETA1-4 : angle 4.24066 ( 3) link_NAG-ASN : bond 0.00539 ( 1) link_NAG-ASN : angle 4.44804 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 701.48 seconds wall clock time: 12 minutes 45.26 seconds (765.26 seconds total)