Starting phenix.real_space_refine on Wed Jul 23 07:51:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zsd_14930/07_2025/7zsd_14930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zsd_14930/07_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_14930/07_2025/7zsd_14930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zsd_14930/07_2025/7zsd_14930.map" model { file = "/net/cci-nas-00/data/ceres_data/7zsd_14930/07_2025/7zsd_14930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zsd_14930/07_2025/7zsd_14930.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 2.69, per 1000 atoms: 1.27 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: 0.80 Conformation dependent library (CDL) restraints added in 230.7 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: 0.22 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: 0.49 Time building geometry restraints manager: 0.90 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: 0.920 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.790 Find NCS groups from input model: 0.030 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.001 TRP M 353 HIS 0.003 0.001 HIS M 519 PHE 0.011 0.001 PHE M 377 TYR 0.017 0.002 TYR P 40 ARG 0.003 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 1) link_NAG-ASN : angle 2.32489 ( 3) link_BETA1-4 : bond 0.01047 ( 1) link_BETA1-4 : angle 1.93473 ( 3) hydrogen bonds : bond 0.17487 ( 76) hydrogen bonds : angle 7.09382 ( 210) SS BOND : bond 0.00272 ( 4) SS BOND : angle 1.30150 ( 8) covalent geometry : bond 0.00302 ( 2179) covalent geometry : angle 0.59816 ( 2959) *********************** 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 : 0.243 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1744 time to fit residues: 8.8513 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 : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.125012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.107438 restraints weight = 5043.373| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.98 r_work: 0.3587 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2185 Z= 0.189 Angle : 0.689 8.566 2973 Z= 0.330 Chirality : 0.050 0.281 314 Planarity : 0.004 0.024 386 Dihedral : 14.515 84.321 336 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 1.35 % Allowed : 10.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.52), residues: 257 helix: 0.41 (0.57), residues: 88 sheet: 0.49 (0.84), residues: 34 loop : -0.89 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 436 HIS 0.006 0.002 HIS M 519 PHE 0.012 0.002 PHE M 377 TYR 0.015 0.002 TYR P 55 ARG 0.004 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 3.04096 ( 3) link_BETA1-4 : bond 0.01358 ( 1) link_BETA1-4 : angle 4.29784 ( 3) hydrogen bonds : bond 0.04315 ( 76) hydrogen bonds : angle 5.66328 ( 210) SS BOND : bond 0.00328 ( 4) SS BOND : angle 1.45732 ( 8) covalent geometry : bond 0.00444 ( 2179) covalent geometry : angle 0.66600 ( 2959) *********************** 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 38 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.235 Fit side-chains REVERT: M 430 THR cc_start: 0.8934 (p) cc_final: 0.8729 (p) REVERT: M 465 GLU cc_start: 0.4236 (tp30) cc_final: 0.4014 (tp30) REVERT: M 495 TYR cc_start: 0.7613 (m-80) cc_final: 0.7408 (m-80) REVERT: P 5 GLU cc_start: 0.6801 (mp0) cc_final: 0.6492 (mp0) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.1540 time to fit residues: 6.7279 Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 418 ILE Chi-restraints excluded: chain M residue 481 ASN 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 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.124307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.106191 restraints weight = 5026.259| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.04 r_work: 0.3555 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1688 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= 0.125 Angle : 0.606 6.640 2973 Z= 0.293 Chirality : 0.047 0.239 314 Planarity : 0.004 0.024 386 Dihedral : 13.431 76.932 336 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.24 % Allowed : 11.21 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.52), residues: 257 helix: 0.32 (0.57), residues: 88 sheet: 0.92 (0.90), residues: 32 loop : -1.03 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 353 HIS 0.005 0.002 HIS M 519 PHE 0.006 0.001 PHE M 497 TYR 0.011 0.001 TYR P 55 ARG 0.006 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 1) link_NAG-ASN : angle 3.10814 ( 3) link_BETA1-4 : bond 0.01083 ( 1) link_BETA1-4 : angle 3.57113 ( 3) hydrogen bonds : bond 0.03620 ( 76) hydrogen bonds : angle 5.22940 ( 210) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.95095 ( 8) covalent geometry : bond 0.00286 ( 2179) covalent geometry : angle 0.58685 ( 2959) *********************** 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 46 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: M 392 PHE cc_start: 0.7538 (m-80) cc_final: 0.7220 (m-80) REVERT: M 430 THR cc_start: 0.8827 (p) cc_final: 0.8562 (p) REVERT: M 518 LEU cc_start: 0.6482 (tp) cc_final: 0.6269 (tt) REVERT: P 5 GLU cc_start: 0.6722 (mp0) cc_final: 0.6298 (mp0) outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.1373 time to fit residues: 7.3495 Evaluate side-chains 36 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.0010 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.126252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108401 restraints weight = 5010.983| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.02 r_work: 0.3581 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2185 Z= 0.112 Angle : 0.617 6.996 2973 Z= 0.295 Chirality : 0.047 0.254 314 Planarity : 0.003 0.023 386 Dihedral : 11.802 65.395 336 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.52), residues: 257 helix: 0.27 (0.57), residues: 88 sheet: 0.93 (0.88), residues: 32 loop : -0.95 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.011 0.001 PHE M 374 TYR 0.018 0.001 TYR P 47 ARG 0.006 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 1) link_NAG-ASN : angle 3.28015 ( 3) link_BETA1-4 : bond 0.01228 ( 1) link_BETA1-4 : angle 3.81207 ( 3) hydrogen bonds : bond 0.03214 ( 76) hydrogen bonds : angle 5.03315 ( 210) SS BOND : bond 0.00168 ( 4) SS BOND : angle 0.91486 ( 8) covalent geometry : bond 0.00250 ( 2179) covalent geometry : angle 0.59546 ( 2959) *********************** 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 : 0.240 Fit side-chains revert: symmetry clash REVERT: M 392 PHE cc_start: 0.7642 (m-80) cc_final: 0.7419 (m-80) REVERT: M 465 GLU cc_start: 0.4310 (tp30) cc_final: 0.4033 (tp30) REVERT: M 495 TYR cc_start: 0.7563 (m-80) cc_final: 0.7351 (m-80) REVERT: P 3 MET cc_start: 0.5751 (mmt) cc_final: 0.5543 (tpp) REVERT: P 5 GLU cc_start: 0.7131 (mp0) cc_final: 0.6724 (mp0) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 0.1222 time to fit residues: 6.6515 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 : 0.243 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.123316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.105225 restraints weight = 5091.958| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.09 r_work: 0.3519 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2185 Z= 0.152 Angle : 0.675 7.336 2973 Z= 0.317 Chirality : 0.049 0.308 314 Planarity : 0.004 0.024 386 Dihedral : 10.825 59.540 336 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.14 % Allowed : 13.45 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.52), residues: 257 helix: 0.33 (0.57), residues: 88 sheet: 0.76 (0.89), residues: 32 loop : -1.01 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.009 0.001 PHE M 375 TYR 0.012 0.001 TYR P 47 ARG 0.004 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 1) link_NAG-ASN : angle 3.97164 ( 3) link_BETA1-4 : bond 0.01439 ( 1) link_BETA1-4 : angle 4.25433 ( 3) hydrogen bonds : bond 0.03476 ( 76) hydrogen bonds : angle 5.04830 ( 210) SS BOND : bond 0.00295 ( 4) SS BOND : angle 1.29699 ( 8) covalent geometry : bond 0.00356 ( 2179) covalent geometry : angle 0.64706 ( 2959) *********************** 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: 7 poor density : 37 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: M 430 THR cc_start: 0.8874 (p) cc_final: 0.8593 (p) REVERT: M 495 TYR cc_start: 0.7598 (m-80) cc_final: 0.7385 (m-80) outliers start: 7 outliers final: 7 residues processed: 41 average time/residue: 0.1508 time to fit residues: 7.3346 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 : 0.240 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.123676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.105780 restraints weight = 4990.515| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.01 r_work: 0.3539 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2284 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= 0.135 Angle : 0.654 7.247 2973 Z= 0.311 Chirality : 0.048 0.306 314 Planarity : 0.004 0.024 386 Dihedral : 10.457 57.267 336 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.59 % Allowed : 13.90 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.52), residues: 257 helix: 0.33 (0.57), residues: 88 sheet: 0.56 (0.87), residues: 32 loop : -1.01 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.007 0.001 PHE M 375 TYR 0.011 0.001 TYR P 47 ARG 0.007 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 1) link_NAG-ASN : angle 4.18252 ( 3) link_BETA1-4 : bond 0.01353 ( 1) link_BETA1-4 : angle 4.20924 ( 3) hydrogen bonds : bond 0.03249 ( 76) hydrogen bonds : angle 5.00670 ( 210) SS BOND : bond 0.00244 ( 4) SS BOND : angle 1.18904 ( 8) covalent geometry : bond 0.00316 ( 2179) covalent geometry : angle 0.62450 ( 2959) *********************** 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 45 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: M 430 THR cc_start: 0.8852 (p) cc_final: 0.8587 (p) REVERT: M 465 GLU cc_start: 0.4685 (tp30) cc_final: 0.4395 (tp30) REVERT: M 495 TYR cc_start: 0.7552 (m-80) cc_final: 0.7318 (m-80) REVERT: P 3 MET cc_start: 0.6069 (mmt) cc_final: 0.5848 (tpp) REVERT: P 5 GLU cc_start: 0.6961 (mp0) cc_final: 0.6561 (mp0) outliers start: 8 outliers final: 8 residues processed: 42 average time/residue: 0.1131 time to fit residues: 5.8358 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 : 0.234 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 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 = 0.3927 r_free = 0.3927 target = 0.125112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.107359 restraints weight = 5099.389| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.05 r_work: 0.3566 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2397 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= 0.119 Angle : 0.659 7.150 2973 Z= 0.309 Chirality : 0.047 0.298 314 Planarity : 0.004 0.024 386 Dihedral : 10.069 53.936 336 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.59 % Allowed : 14.80 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.52), residues: 257 helix: 0.34 (0.57), residues: 88 sheet: 0.51 (0.86), residues: 32 loop : -0.94 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.008 0.001 PHE M 392 TYR 0.009 0.001 TYR P 40 ARG 0.005 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 1) link_NAG-ASN : angle 4.14825 ( 3) link_BETA1-4 : bond 0.01381 ( 1) link_BETA1-4 : angle 4.06207 ( 3) hydrogen bonds : bond 0.02916 ( 76) hydrogen bonds : angle 5.02455 ( 210) SS BOND : bond 0.00172 ( 4) SS BOND : angle 1.04797 ( 8) covalent geometry : bond 0.00270 ( 2179) covalent geometry : angle 0.63219 ( 2959) *********************** 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 46 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: M 465 GLU cc_start: 0.4501 (tp30) cc_final: 0.4244 (tp30) REVERT: M 495 TYR cc_start: 0.7490 (m-80) cc_final: 0.7270 (m-80) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.1751 time to fit residues: 8.7790 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 : 0.300 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 17 optimal weight: 8.9990 chunk 7 optimal weight: 0.0370 chunk 21 optimal weight: 2.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.126382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108605 restraints weight = 5162.828| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.15 r_work: 0.3580 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2185 Z= 0.115 Angle : 0.656 7.099 2973 Z= 0.313 Chirality : 0.047 0.296 314 Planarity : 0.003 0.024 386 Dihedral : 9.571 50.226 336 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.52), residues: 257 helix: 0.33 (0.57), residues: 88 sheet: 0.39 (0.84), residues: 32 loop : -0.91 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.009 0.001 PHE M 392 TYR 0.011 0.001 TYR M 369 ARG 0.009 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 1) link_NAG-ASN : angle 4.13028 ( 3) link_BETA1-4 : bond 0.01343 ( 1) link_BETA1-4 : angle 4.00969 ( 3) hydrogen bonds : bond 0.02884 ( 76) hydrogen bonds : angle 4.91075 ( 210) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.90357 ( 8) covalent geometry : bond 0.00262 ( 2179) covalent geometry : angle 0.63023 ( 2959) *********************** 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 46 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 390 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8614 (pp) REVERT: M 465 GLU cc_start: 0.4252 (tp30) cc_final: 0.4021 (tp30) REVERT: M 495 TYR cc_start: 0.7595 (m-80) cc_final: 0.7259 (m-80) REVERT: P 5 GLU cc_start: 0.6720 (mp0) cc_final: 0.6338 (mp0) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.1761 time to fit residues: 8.5998 Evaluate side-chains 42 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 1 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- 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 = 0.125964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108365 restraints weight = 5108.214| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.08 r_work: 0.3579 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2561 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= 0.123 Angle : 0.679 7.162 2973 Z= 0.320 Chirality : 0.047 0.307 314 Planarity : 0.004 0.029 386 Dihedral : 9.297 48.045 336 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.04 % Allowed : 16.59 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.52), residues: 257 helix: 0.31 (0.56), residues: 88 sheet: 0.35 (0.85), residues: 32 loop : -0.89 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.009 0.001 PHE M 456 TYR 0.011 0.001 TYR M 369 ARG 0.009 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 1) link_NAG-ASN : angle 4.26576 ( 3) link_BETA1-4 : bond 0.01428 ( 1) link_BETA1-4 : angle 4.14603 ( 3) hydrogen bonds : bond 0.02841 ( 76) hydrogen bonds : angle 4.85055 ( 210) SS BOND : bond 0.00171 ( 4) SS BOND : angle 1.00533 ( 8) covalent geometry : bond 0.00283 ( 2179) covalent geometry : angle 0.65139 ( 2959) *********************** 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 45 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 418 ILE cc_start: 0.9126 (mm) cc_final: 0.8917 (tp) REVERT: M 465 GLU cc_start: 0.3770 (tp30) cc_final: 0.3501 (tp30) REVERT: M 495 TYR cc_start: 0.7530 (m-80) cc_final: 0.7273 (m-80) REVERT: P 5 GLU cc_start: 0.6720 (mp0) cc_final: 0.6312 (mp0) outliers start: 9 outliers final: 8 residues processed: 41 average time/residue: 0.1216 time to fit residues: 6.1062 Evaluate side-chains 42 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain P residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.126629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.108970 restraints weight = 5065.617| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.16 r_work: 0.3580 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2185 Z= 0.119 Angle : 0.670 7.137 2973 Z= 0.317 Chirality : 0.047 0.307 314 Planarity : 0.004 0.029 386 Dihedral : 9.102 46.294 336 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.59 % Allowed : 15.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.52), residues: 257 helix: 0.28 (0.56), residues: 88 sheet: 0.37 (0.84), residues: 32 loop : -0.85 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 353 HIS 0.005 0.002 HIS M 519 PHE 0.007 0.001 PHE M 456 TYR 0.011 0.001 TYR M 369 ARG 0.008 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 1) link_NAG-ASN : angle 4.35078 ( 3) link_BETA1-4 : bond 0.01384 ( 1) link_BETA1-4 : angle 4.13475 ( 3) hydrogen bonds : bond 0.02830 ( 76) hydrogen bonds : angle 4.80024 ( 210) SS BOND : bond 0.00177 ( 4) SS BOND : angle 1.02590 ( 8) covalent geometry : bond 0.00275 ( 2179) covalent geometry : angle 0.64190 ( 2959) ********************** 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 44 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 465 GLU cc_start: 0.3792 (tp30) cc_final: 0.3513 (tp30) REVERT: M 495 TYR cc_start: 0.7561 (m-80) cc_final: 0.7236 (m-80) REVERT: P 5 GLU cc_start: 0.6711 (mp0) cc_final: 0.6288 (mp0) outliers start: 8 outliers final: 8 residues processed: 41 average time/residue: 0.1074 time to fit residues: 5.5119 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 : 0.239 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain P residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.126316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.108638 restraints weight = 5010.788| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.16 r_work: 0.3579 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2185 Z= 0.123 Angle : 0.685 7.248 2973 Z= 0.321 Chirality : 0.047 0.313 314 Planarity : 0.004 0.028 386 Dihedral : 8.976 45.198 336 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.52), residues: 257 helix: 0.31 (0.56), residues: 88 sheet: 0.34 (0.84), residues: 32 loop : -0.80 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 353 HIS 0.005 0.002 HIS M 519 PHE 0.008 0.001 PHE M 374 TYR 0.010 0.001 TYR M 369 ARG 0.009 0.000 ARG P 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 1) link_NAG-ASN : angle 4.43945 ( 3) link_BETA1-4 : bond 0.01417 ( 1) link_BETA1-4 : angle 4.19972 ( 3) hydrogen bonds : bond 0.02864 ( 76) hydrogen bonds : angle 4.78214 ( 210) SS BOND : bond 0.00184 ( 4) SS BOND : angle 1.03486 ( 8) covalent geometry : bond 0.00286 ( 2179) covalent geometry : angle 0.65621 ( 2959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1641.65 seconds wall clock time: 28 minutes 51.47 seconds (1731.47 seconds total)