Starting phenix.real_space_refine on Wed Jul 1 22:19:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eqf_28537/07_2026/8eqf_28537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqf_28537/07_2026/8eqf_28537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eqf_28537/07_2026/8eqf_28537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqf_28537/07_2026/8eqf_28537.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8eqf_28537/07_2026/8eqf_28537.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eqf_28537/07_2026/8eqf_28537.cif" model { file = "/net/cci-nas-00/data/ceres_data/8eqf_28537/07_2026/8eqf_28537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqf_28537/07_2026/8eqf_28537.cif" } resolution = 3.16 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2133 2.51 5 N 556 2.21 5 O 644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3348 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.70, per 1000 atoms: 0.21 Number of scatterers: 3348 At special positions: 0 Unit cell: (54.516, 64.428, 108.206, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 644 8.00 N 556 7.00 C 2133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 336 " Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 74.4 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 9.5% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.772A pdb=" N VAL A 334 " --> pdb=" O PRO A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.509A pdb=" N TRP A 346 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 removed outlier: 4.421A pdb=" N ARG A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 415 removed outlier: 3.529A pdb=" N TYR A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.980A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.986A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.083A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 351 Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 355 removed outlier: 6.928A pdb=" N CYS A 354 " --> pdb=" O CYS A 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.837A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.062A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.510A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 243 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: 0.37 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1058 1.34 - 1.46: 917 1.46 - 1.58: 1445 1.58 - 1.70: 0 1.70 - 1.81: 18 Bond restraints: 3438 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" CA ASN A 433 " pdb=" CB ASN A 433 " ideal model delta sigma weight residual 1.530 1.514 0.015 1.43e-02 4.89e+03 1.14e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.05e+00 ... (remaining 3433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 4397 1.09 - 2.18: 227 2.18 - 3.27: 34 3.27 - 4.36: 15 4.36 - 5.45: 1 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.17 110.43 3.74 1.14e+00 7.69e-01 1.07e+01 angle pdb=" C ASP A 357 " pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " ideal model delta sigma weight residual 110.78 114.52 -3.74 1.60e+00 3.91e-01 5.45e+00 angle pdb=" N LEU A 434 " pdb=" CA LEU A 434 " pdb=" CB LEU A 434 " ideal model delta sigma weight residual 114.27 110.50 3.77 1.64e+00 3.72e-01 5.30e+00 angle pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " pdb=" CG ASP A 357 " ideal model delta sigma weight residual 112.60 114.65 -2.05 1.00e+00 1.00e+00 4.21e+00 angle pdb=" C ASN A 433 " pdb=" CA ASN A 433 " pdb=" CB ASN A 433 " ideal model delta sigma weight residual 109.75 112.89 -3.14 1.65e+00 3.67e-01 3.62e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 1813 17.04 - 34.07: 141 34.07 - 51.11: 32 51.11 - 68.15: 7 68.15 - 85.19: 2 Dihedral angle restraints: 1995 sinusoidal: 771 harmonic: 1224 Sorted by residual: dihedral pdb=" CB CYS A 384 " pdb=" SG CYS A 384 " pdb=" SG CYS A 518 " pdb=" CB CYS A 518 " ideal model delta sinusoidal sigma weight residual 93.00 133.02 -40.02 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 62.26 30.74 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 62.28 30.72 1 1.00e+01 1.00e-02 1.35e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 307 0.034 - 0.068: 143 0.068 - 0.102: 27 0.102 - 0.136: 19 0.136 - 0.170: 4 Chirality restraints: 500 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 336 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ILE A 427 " pdb=" N ILE A 427 " pdb=" C ILE A 427 " pdb=" CB ILE A 427 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 497 not shown) Planarity restraints: 602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 357 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" CG ASP A 357 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 357 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 357 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 336 " -0.013 2.00e-02 2.50e+03 1.27e-02 2.01e+00 pdb=" CG ASN A 336 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 336 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 336 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 357 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C ASP A 357 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP A 357 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR A 358 " 0.007 2.00e-02 2.50e+03 ... (remaining 599 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 30 2.58 - 3.16: 2736 3.16 - 3.74: 4913 3.74 - 4.32: 7512 4.32 - 4.90: 12547 Nonbonded interactions: 27738 Sorted by model distance: nonbonded pdb=" O4 NAG B 1 " pdb=" O6 NAG B 2 " model vdw 1.998 3.040 nonbonded pdb=" O3 NAG B 1 " pdb=" O7 NAG B 1 " model vdw 2.012 3.040 nonbonded pdb=" O ASP H 62 " pdb=" OG SER H 63 " model vdw 2.038 3.040 nonbonded pdb=" O ASP A 357 " pdb=" OD1 ASP A 357 " model vdw 2.142 3.040 nonbonded pdb=" OH TYR A 482 " pdb=" O TYR L 92 " model vdw 2.289 3.040 ... (remaining 27733 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: 8.920 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.340 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 3446 Z= 0.222 Angle : 0.598 7.350 4692 Z= 0.322 Chirality : 0.043 0.170 500 Planarity : 0.003 0.026 601 Dihedral : 13.040 85.187 1205 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.42), residues: 416 helix: -4.44 (0.43), residues: 27 sheet: -0.01 (0.44), residues: 136 loop : 0.23 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.011 0.001 TYR H 95 PHE 0.008 0.001 PHE A 393 TRP 0.011 0.002 TRP A 429 HIS 0.002 0.001 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 ( 3438) covalent geometry : angle 0.57064 / 0.32 ( 4674) SS BOND : bond 0.00297 / 0.15 ( 6) SS BOND : angle 0.73804 / 0.41 ( 12) hydrogen bonds : bond 0.15502 / 9.09 ( 100) hydrogen bonds : angle 7.83945 / 5.31 ( 243) link_BETA1-4 : bond 0.00357 / 0.19 ( 1) link_BETA1-4 : angle 4.39639 / 2.03 ( 3) link_NAG-ASN : bond 0.01145 / 0.60 ( 1) link_NAG-ASN : angle 5.54637 / 2.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.069 Fit side-chains REVERT: A 436 SER cc_start: 0.8113 (m) cc_final: 0.7883 (m) REVERT: A 488 TYR cc_start: 0.8303 (m-80) cc_final: 0.7914 (m-80) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0443 time to fit residues: 2.8606 Evaluate side-chains 50 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN H 57 ASN L 30 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.096138 restraints weight = 5253.661| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.97 r_work: 0.3058 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 3446 Z= 0.331 Angle : 0.721 9.380 4692 Z= 0.356 Chirality : 0.049 0.196 500 Planarity : 0.005 0.033 601 Dihedral : 4.626 15.250 471 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.10 % Allowed : 5.25 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.41), residues: 416 helix: -4.54 (0.41), residues: 27 sheet: 0.21 (0.45), residues: 134 loop : 0.13 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 87 TYR 0.015 0.002 TYR A 362 PHE 0.013 0.002 PHE A 393 TRP 0.015 0.002 TRP A 429 HIS 0.002 0.001 HIS L 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.33 ( 3438) covalent geometry : angle 0.69285 / 0.35 ( 4674) SS BOND : bond 0.00431 / 0.21 ( 6) SS BOND : angle 0.99987 / 0.56 ( 12) hydrogen bonds : bond 0.04428 / 2.78 ( 100) hydrogen bonds : angle 6.92732 / 4.62 ( 243) link_BETA1-4 : bond 0.01750 / 0.92 ( 1) link_BETA1-4 : angle 3.98924 / 1.83 ( 3) link_NAG-ASN : bond 0.01737 / 0.91 ( 1) link_NAG-ASN : angle 6.79048 / 3.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.073 Fit side-chains REVERT: A 488 TYR cc_start: 0.8504 (m-80) cc_final: 0.8058 (m-80) REVERT: H 115 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7976 (mm110) REVERT: L 81 GLU cc_start: 0.7673 (pm20) cc_final: 0.7468 (pm20) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.0490 time to fit residues: 3.5088 Evaluate side-chains 55 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.0050 chunk 3 optimal weight: 0.0870 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 39 optimal weight: 0.4980 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 0.1980 chunk 26 optimal weight: 0.3980 overall best weight: 0.1310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098458 restraints weight = 5169.829| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.97 r_work: 0.3100 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3446 Z= 0.129 Angle : 0.597 7.454 4692 Z= 0.291 Chirality : 0.043 0.144 500 Planarity : 0.003 0.031 601 Dihedral : 4.322 16.054 471 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.38 % Allowed : 5.52 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.41), residues: 416 helix: -4.47 (0.43), residues: 27 sheet: 0.06 (0.44), residues: 136 loop : 0.40 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.011 0.001 TYR A 501 PHE 0.008 0.001 PHE L 98 TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 3438) covalent geometry : angle 0.57058 / 0.29 ( 4674) SS BOND : bond 0.00175 / 0.09 ( 6) SS BOND : angle 0.67867 / 0.37 ( 12) hydrogen bonds : bond 0.03439 / 2.19 ( 100) hydrogen bonds : angle 6.57227 / 4.37 ( 243) link_BETA1-4 : bond 0.01370 / 0.72 ( 1) link_BETA1-4 : angle 4.19459 / 1.97 ( 3) link_NAG-ASN : bond 0.01364 / 0.72 ( 1) link_NAG-ASN : angle 5.57115 / 3.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.071 Fit side-chains REVERT: A 488 TYR cc_start: 0.8456 (m-80) cc_final: 0.8034 (m-80) outliers start: 5 outliers final: 4 residues processed: 62 average time/residue: 0.0377 time to fit residues: 2.9684 Evaluate side-chains 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 487 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.0050 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 40 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.0000 chunk 39 optimal weight: 0.2980 chunk 18 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN L 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098555 restraints weight = 5120.195| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.96 r_work: 0.3101 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3446 Z= 0.152 Angle : 0.592 7.050 4692 Z= 0.291 Chirality : 0.044 0.154 500 Planarity : 0.004 0.033 601 Dihedral : 4.277 16.159 471 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.66 % Allowed : 8.29 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.42), residues: 416 helix: -4.05 (0.69), residues: 20 sheet: 0.21 (0.45), residues: 136 loop : 0.46 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.013 0.001 TYR A 501 PHE 0.008 0.001 PHE L 98 TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 3438) covalent geometry : angle 0.56870 / 0.29 ( 4674) SS BOND : bond 0.00220 / 0.11 ( 6) SS BOND : angle 0.71115 / 0.39 ( 12) hydrogen bonds : bond 0.03371 / 2.16 ( 100) hydrogen bonds : angle 6.36712 / 4.22 ( 243) link_BETA1-4 : bond 0.01354 / 0.71 ( 1) link_BETA1-4 : angle 4.13688 / 1.94 ( 3) link_NAG-ASN : bond 0.01338 / 0.70 ( 1) link_NAG-ASN : angle 4.99403 / 2.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.118 Fit side-chains REVERT: A 488 TYR cc_start: 0.8454 (m-80) cc_final: 0.8023 (m-80) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.0624 time to fit residues: 4.5906 Evaluate side-chains 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.0570 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 21 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.0770 chunk 29 optimal weight: 0.0970 overall best weight: 0.0830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099612 restraints weight = 5141.751| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.05 r_work: 0.3116 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3446 Z= 0.102 Angle : 0.544 7.026 4692 Z= 0.268 Chirality : 0.043 0.141 500 Planarity : 0.003 0.034 601 Dihedral : 4.089 17.183 471 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.10 % Allowed : 9.12 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.42), residues: 416 helix: -4.03 (0.70), residues: 20 sheet: 0.37 (0.45), residues: 136 loop : 0.50 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.012 0.001 TYR A 501 PHE 0.006 0.001 PHE L 98 TRP 0.011 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 3438) covalent geometry : angle 0.52555 / 0.26 ( 4674) SS BOND : bond 0.00129 / 0.07 ( 6) SS BOND : angle 0.63121 / 0.34 ( 12) hydrogen bonds : bond 0.02999 / 1.95 ( 100) hydrogen bonds : angle 6.06886 / 4.01 ( 243) link_BETA1-4 : bond 0.01341 / 0.71 ( 1) link_BETA1-4 : angle 3.63347 / 1.71 ( 3) link_NAG-ASN : bond 0.01100 / 0.58 ( 1) link_NAG-ASN : angle 4.21617 / 2.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.107 Fit side-chains REVERT: A 348 ARG cc_start: 0.8572 (ttm170) cc_final: 0.8314 (ttm170) REVERT: A 488 TYR cc_start: 0.8402 (m-80) cc_final: 0.7917 (m-80) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.0526 time to fit residues: 3.3048 Evaluate side-chains 51 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 21 optimal weight: 0.0170 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 6 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 overall best weight: 0.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099284 restraints weight = 5099.994| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.99 r_work: 0.3113 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3446 Z= 0.146 Angle : 0.560 6.985 4692 Z= 0.279 Chirality : 0.043 0.144 500 Planarity : 0.004 0.034 601 Dihedral : 4.120 16.439 471 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.38 % Allowed : 10.22 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.42), residues: 416 helix: -4.02 (0.72), residues: 20 sheet: 0.38 (0.44), residues: 137 loop : 0.49 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.016 0.001 TYR A 501 PHE 0.008 0.001 PHE A 393 TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 3438) covalent geometry : angle 0.54349 / 0.28 ( 4674) SS BOND : bond 0.00234 / 0.12 ( 6) SS BOND : angle 0.70413 / 0.38 ( 12) hydrogen bonds : bond 0.03205 / 2.07 ( 100) hydrogen bonds : angle 6.04410 / 3.99 ( 243) link_BETA1-4 : bond 0.01274 / 0.67 ( 1) link_BETA1-4 : angle 3.63534 / 1.70 ( 3) link_NAG-ASN : bond 0.01173 / 0.62 ( 1) link_NAG-ASN : angle 3.89393 / 2.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.103 Fit side-chains REVERT: A 488 TYR cc_start: 0.8472 (m-80) cc_final: 0.8022 (m-80) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.0571 time to fit residues: 3.5616 Evaluate side-chains 49 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.1980 chunk 16 optimal weight: 0.2980 chunk 40 optimal weight: 0.0670 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 0.0770 chunk 0 optimal weight: 0.3980 overall best weight: 0.1414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099674 restraints weight = 5230.245| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.00 r_work: 0.3118 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3446 Z= 0.126 Angle : 0.552 6.950 4692 Z= 0.276 Chirality : 0.043 0.143 500 Planarity : 0.003 0.034 601 Dihedral : 4.085 16.592 471 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.10 % Allowed : 10.77 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.42), residues: 416 helix: -4.00 (0.74), residues: 20 sheet: 0.44 (0.44), residues: 137 loop : 0.47 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.015 0.001 TYR A 501 PHE 0.007 0.001 PHE L 98 TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 3438) covalent geometry : angle 0.53819 / 0.27 ( 4674) SS BOND : bond 0.00191 / 0.10 ( 6) SS BOND : angle 0.67775 / 0.37 ( 12) hydrogen bonds : bond 0.03094 / 2.01 ( 100) hydrogen bonds : angle 6.00063 / 3.96 ( 243) link_BETA1-4 : bond 0.01293 / 0.68 ( 1) link_BETA1-4 : angle 3.36950 / 1.58 ( 3) link_NAG-ASN : bond 0.01101 / 0.58 ( 1) link_NAG-ASN : angle 3.49560 / 1.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.071 Fit side-chains REVERT: A 348 ARG cc_start: 0.8594 (ttm170) cc_final: 0.8326 (ttm170) REVERT: A 488 TYR cc_start: 0.8467 (m-80) cc_final: 0.8111 (m-80) REVERT: L 56 SER cc_start: 0.8579 (t) cc_final: 0.8359 (p) outliers start: 4 outliers final: 4 residues processed: 52 average time/residue: 0.0409 time to fit residues: 2.6777 Evaluate side-chains 55 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 5 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 3 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN L 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098415 restraints weight = 5231.837| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.00 r_work: 0.3094 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3446 Z= 0.179 Angle : 0.574 6.862 4692 Z= 0.289 Chirality : 0.044 0.145 500 Planarity : 0.004 0.034 601 Dihedral : 4.213 16.835 471 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.66 % Allowed : 10.77 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.42), residues: 416 helix: -3.92 (0.80), residues: 20 sheet: 0.49 (0.45), residues: 130 loop : 0.36 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 87 TYR 0.018 0.001 TYR A 501 PHE 0.009 0.001 PHE A 393 TRP 0.013 0.002 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 3438) covalent geometry : angle 0.55972 / 0.29 ( 4674) SS BOND : bond 0.00267 / 0.14 ( 6) SS BOND : angle 0.72529 / 0.39 ( 12) hydrogen bonds : bond 0.03327 / 2.15 ( 100) hydrogen bonds : angle 6.07992 / 4.02 ( 243) link_BETA1-4 : bond 0.01212 / 0.64 ( 1) link_BETA1-4 : angle 3.43002 / 1.60 ( 3) link_NAG-ASN : bond 0.01197 / 0.63 ( 1) link_NAG-ASN : angle 3.57238 / 1.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.069 Fit side-chains REVERT: A 488 TYR cc_start: 0.8479 (m-80) cc_final: 0.8078 (m-80) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.0347 time to fit residues: 2.2785 Evaluate side-chains 50 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.0970 chunk 30 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 0.0770 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099195 restraints weight = 5155.282| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.98 r_work: 0.3109 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3446 Z= 0.155 Angle : 0.561 6.845 4692 Z= 0.282 Chirality : 0.043 0.146 500 Planarity : 0.003 0.034 601 Dihedral : 4.196 16.432 471 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.66 % Allowed : 11.33 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.42), residues: 416 helix: -3.93 (0.79), residues: 20 sheet: 0.49 (0.45), residues: 130 loop : 0.35 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 87 TYR 0.017 0.001 TYR A 501 PHE 0.008 0.001 PHE L 98 TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 3438) covalent geometry : angle 0.54842 / 0.28 ( 4674) SS BOND : bond 0.00219 / 0.11 ( 6) SS BOND : angle 0.70817 / 0.38 ( 12) hydrogen bonds : bond 0.03223 / 2.09 ( 100) hydrogen bonds : angle 6.04687 / 4.00 ( 243) link_BETA1-4 : bond 0.01349 / 0.71 ( 1) link_BETA1-4 : angle 3.17590 / 1.49 ( 3) link_NAG-ASN : bond 0.01145 / 0.60 ( 1) link_NAG-ASN : angle 3.35337 / 1.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.073 Fit side-chains REVERT: A 488 TYR cc_start: 0.8464 (m-80) cc_final: 0.8077 (m-80) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.0410 time to fit residues: 2.7112 Evaluate side-chains 51 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.0170 chunk 14 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 0.0060 chunk 35 optimal weight: 0.2980 chunk 16 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 overall best weight: 0.1632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN L 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099500 restraints weight = 5075.488| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.98 r_work: 0.3108 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3446 Z= 0.138 Angle : 0.548 6.850 4692 Z= 0.276 Chirality : 0.043 0.150 500 Planarity : 0.003 0.034 601 Dihedral : 4.138 16.332 471 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.38 % Allowed : 11.33 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.42), residues: 416 helix: -4.05 (0.59), residues: 33 sheet: 0.52 (0.45), residues: 130 loop : 0.38 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.018 0.001 TYR A 501 PHE 0.008 0.001 PHE L 98 TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 3438) covalent geometry : angle 0.53656 / 0.27 ( 4674) SS BOND : bond 0.00203 / 0.11 ( 6) SS BOND : angle 0.69803 / 0.37 ( 12) hydrogen bonds : bond 0.03138 / 2.05 ( 100) hydrogen bonds : angle 6.00901 / 3.97 ( 243) link_BETA1-4 : bond 0.01302 / 0.69 ( 1) link_BETA1-4 : angle 3.01141 / 1.41 ( 3) link_NAG-ASN : bond 0.01089 / 0.57 ( 1) link_NAG-ASN : angle 3.28783 / 1.78 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.078 Fit side-chains REVERT: A 488 TYR cc_start: 0.8469 (m-80) cc_final: 0.8090 (m-80) REVERT: H 34 MET cc_start: 0.8531 (mmt) cc_final: 0.8282 (mmt) outliers start: 5 outliers final: 5 residues processed: 52 average time/residue: 0.0494 time to fit residues: 3.2726 Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.0170 chunk 30 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.098390 restraints weight = 5179.915| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.00 r_work: 0.3092 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3446 Z= 0.206 Angle : 0.589 6.802 4692 Z= 0.298 Chirality : 0.044 0.154 500 Planarity : 0.004 0.047 601 Dihedral : 4.308 16.676 471 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.38 % Allowed : 12.43 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.42), residues: 416 helix: -3.70 (0.76), residues: 26 sheet: 0.45 (0.45), residues: 130 loop : 0.29 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 87 TYR 0.023 0.002 TYR A 501 PHE 0.010 0.001 PHE A 393 TRP 0.014 0.002 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 ( 3438) covalent geometry : angle 0.57633 / 0.29 ( 4674) SS BOND : bond 0.00292 / 0.15 ( 6) SS BOND : angle 0.80441 / 0.44 ( 12) hydrogen bonds : bond 0.03411 / 2.20 ( 100) hydrogen bonds : angle 6.13830 / 4.06 ( 243) link_BETA1-4 : bond 0.01220 / 0.64 ( 1) link_BETA1-4 : angle 3.18557 / 1.48 ( 3) link_NAG-ASN : bond 0.01217 / 0.64 ( 1) link_NAG-ASN : angle 3.49500 / 1.85 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1054.19 seconds wall clock time: 18 minutes 39.93 seconds (1119.93 seconds total)