Starting phenix.real_space_refine on Wed Jul 1 22:20:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wr9_32719/07_2026/7wr9_32719.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wr9_32719/07_2026/7wr9_32719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wr9_32719/07_2026/7wr9_32719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wr9_32719/07_2026/7wr9_32719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wr9_32719/07_2026/7wr9_32719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wr9_32719/07_2026/7wr9_32719.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wr9_32719/07_2026/7wr9_32719.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wr9_32719/07_2026/7wr9_32719.cif" } resolution = 3.24 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= 0.032 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 2074 2.51 5 N 539 2.21 5 O 638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3266 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 780 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 9, 'TRANS': 94} Chain: "F" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1450 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.88, per 1000 atoms: 0.27 Number of scatterers: 3266 At special positions: 0 Unit cell: (90.48, 63.44, 74.88, 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 638 8.00 N 539 7.00 C 2074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 323 " - pdb=" SG CYS F 348 " distance=2.03 Simple disulfide: pdb=" SG CYS F 366 " - pdb=" SG CYS F 419 " distance=2.03 Simple disulfide: pdb=" SG CYS F 467 " - pdb=" SG CYS F 474 " 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 C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " NAG C 1 " - " FUC C 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN F 330 " " NAG F 601 " - " ASN F 357 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 115.7 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 3.9% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.057A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 397 Processing helix chain 'F' and resid 425 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.997A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.518A pdb=" N ALA A 92 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 34 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 59 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 20 Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.541A pdb=" N VAL B 10 " --> pdb=" O LYS B 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 47 removed outlier: 6.485A pdb=" N TRP B 34 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 341 through 345 removed outlier: 4.027A pdb=" N GLU F 341 " --> pdb=" O SER F 386 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN F 381 " --> pdb=" O GLU F 502 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 439 through 441 82 hydrogen bonds defined for protein. 207 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: 0.42 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 525 1.32 - 1.45: 1011 1.45 - 1.57: 1802 1.57 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3357 Sorted by residual: bond pdb=" C PRO A 102 " pdb=" O PRO A 102 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 9.14e+00 bond pdb=" CA TYR A 107 " pdb=" C TYR A 107 " ideal model delta sigma weight residual 1.529 1.498 0.031 1.04e-02 9.25e+03 9.05e+00 bond pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 1.469 1.432 0.036 1.28e-02 6.10e+03 8.02e+00 bond pdb=" N SER A 104 " pdb=" CA SER A 104 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.46e+00 bond pdb=" N ASP A 105 " pdb=" CA ASP A 105 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.41e-02 5.03e+03 6.45e+00 ... (remaining 3352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 4507 3.66 - 7.31: 64 7.31 - 10.97: 6 10.97 - 14.62: 1 14.62 - 18.28: 1 Bond angle restraints: 4579 Sorted by residual: angle pdb=" N PRO A 106 " pdb=" CA PRO A 106 " pdb=" CB PRO A 106 " ideal model delta sigma weight residual 103.25 92.17 11.08 1.05e+00 9.07e-01 1.11e+02 angle pdb=" C PRO A 106 " pdb=" CA PRO A 106 " pdb=" CB PRO A 106 " ideal model delta sigma weight residual 111.56 120.78 -9.22 1.65e+00 3.67e-01 3.12e+01 angle pdb=" CA LEU B 27 " pdb=" CB LEU B 27 " pdb=" CG LEU B 27 " ideal model delta sigma weight residual 116.30 134.58 -18.28 3.50e+00 8.16e-02 2.73e+01 angle pdb=" C ASP B 91 " pdb=" N ALA B 92 " pdb=" CA ALA B 92 " ideal model delta sigma weight residual 121.54 130.69 -9.15 1.91e+00 2.74e-01 2.30e+01 angle pdb=" C TYR A 107 " pdb=" CA TYR A 107 " pdb=" CB TYR A 107 " ideal model delta sigma weight residual 111.43 105.49 5.94 1.24e+00 6.50e-01 2.29e+01 ... (remaining 4574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 1728 17.01 - 34.02: 163 34.02 - 51.03: 34 51.03 - 68.04: 6 68.04 - 85.05: 3 Dihedral angle restraints: 1934 sinusoidal: 748 harmonic: 1186 Sorted by residual: dihedral pdb=" CA LEU B 27 " pdb=" C LEU B 27 " pdb=" N PRO B 28 " pdb=" CA PRO B 28 " ideal model delta harmonic sigma weight residual 180.00 145.93 34.07 0 5.00e+00 4.00e-02 4.64e+01 dihedral pdb=" CB CYS F 467 " pdb=" SG CYS F 467 " pdb=" SG CYS F 474 " pdb=" CB CYS F 474 " ideal model delta sinusoidal sigma weight residual -86.00 -130.82 44.82 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CA ALA B 92 " pdb=" C ALA B 92 " pdb=" N SER B 93 " pdb=" CA SER B 93 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 1931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 398 0.061 - 0.121: 86 0.121 - 0.181: 14 0.181 - 0.242: 4 0.242 - 0.302: 3 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ARG A 100 " pdb=" N ARG A 100 " pdb=" C ARG A 100 " pdb=" CB ARG A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TYR A 107 " pdb=" N TYR A 107 " pdb=" C TYR A 107 " pdb=" CB TYR A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 502 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 109 " 0.017 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP A 109 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A 109 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 109 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 109 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 109 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 109 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 109 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 109 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 109 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 105 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C ASP A 105 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP A 105 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO A 106 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 118 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C VAL A 118 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL A 118 " 0.023 2.00e-02 2.50e+03 pdb=" N TRP A 119 " 0.020 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1152 2.86 - 3.37: 2584 3.37 - 3.88: 5412 3.88 - 4.39: 6083 4.39 - 4.90: 10951 Nonbonded interactions: 26182 Sorted by model distance: nonbonded pdb=" O VAL A 108 " pdb=" OG SER A 111 " model vdw 2.350 3.040 nonbonded pdb=" O ALA F 430 " pdb=" OG1 THR F 485 " model vdw 2.389 3.040 nonbonded pdb=" OG SER B 93 " pdb=" OG1 THR B 95 " model vdw 2.408 3.040 nonbonded pdb=" O GLY B 76 " pdb=" NE2 GLN B 78 " model vdw 2.413 3.120 nonbonded pdb=" O SER B 62 " pdb=" OG SER B 62 " model vdw 2.421 3.040 ... (remaining 26177 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: 2.750 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.830 Find NCS groups from input model: 0.010 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.006 0.043 3367 Z= 0.282 Angle : 1.055 18.280 4604 Z= 0.592 Chirality : 0.058 0.302 505 Planarity : 0.009 0.075 585 Dihedral : 13.722 85.052 1171 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.63 % Favored : 89.88 % Rotamer: Outliers : 1.15 % Allowed : 0.86 % Favored : 97.99 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.72 (0.39), residues: 405 helix: -4.46 (0.69), residues: 25 sheet: -1.38 (0.43), residues: 131 loop : -1.78 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 100 TYR 0.040 0.002 TYR F 442 PHE 0.030 0.003 PHE F 364 TRP 0.072 0.004 TRP A 109 HIS 0.002 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.28 ( 3357) covalent geometry : angle 1.05147 / 0.59 ( 4579) SS BOND : bond 0.00362 / 0.20 ( 5) SS BOND : angle 1.29758 / 0.83 ( 10) hydrogen bonds : bond 0.26428 / 16.56 ( 82) hydrogen bonds : angle 9.68833 / 6.52 ( 207) link_BETA1-4 : bond 0.00863 / 0.42 ( 2) link_BETA1-4 : angle 1.85134 / 1.06 ( 6) link_BETA1-6 : bond 0.00513 / 0.27 ( 1) link_BETA1-6 : angle 1.12471 / 0.59 ( 3) link_NAG-ASN : bond 0.00121 / 0.06 ( 2) link_NAG-ASN : angle 1.65290 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 GLU cc_start: 0.6819 (pm20) cc_final: 0.6527 (pt0) outliers start: 4 outliers final: 1 residues processed: 66 average time/residue: 0.0775 time to fit residues: 6.1394 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0570 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122300 restraints weight = 3928.364| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.22 r_work: 0.3160 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 3367 Z= 0.167 Angle : 0.672 9.711 4604 Z= 0.342 Chirality : 0.046 0.148 505 Planarity : 0.008 0.117 585 Dihedral : 5.539 28.444 462 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.14 % Favored : 90.62 % Rotamer: Outliers : 1.44 % Allowed : 9.48 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.44 (0.41), residues: 405 helix: -4.71 (0.55), residues: 26 sheet: -1.23 (0.43), residues: 133 loop : -1.49 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 53 TYR 0.014 0.001 TYR F 356 PHE 0.016 0.002 PHE F 334 TRP 0.028 0.002 TRP A 109 HIS 0.004 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 3357) covalent geometry : angle 0.66750 / 0.34 ( 4579) SS BOND : bond 0.00307 / 0.18 ( 5) SS BOND : angle 0.96468 / 0.60 ( 10) hydrogen bonds : bond 0.04568 / 3.28 ( 82) hydrogen bonds : angle 6.99664 / 4.92 ( 207) link_BETA1-4 : bond 0.00602 / 0.29 ( 2) link_BETA1-4 : angle 1.65272 / 0.99 ( 6) link_BETA1-6 : bond 0.00268 / 0.14 ( 1) link_BETA1-6 : angle 0.92495 / 0.48 ( 3) link_NAG-ASN : bond 0.00136 / 0.07 ( 2) link_NAG-ASN : angle 1.35578 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6834 (p0) REVERT: B 78 GLN cc_start: 0.7515 (mp10) cc_final: 0.7176 (mp10) outliers start: 5 outliers final: 2 residues processed: 67 average time/residue: 0.0794 time to fit residues: 6.3919 Evaluate side-chains 62 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 36 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.149855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123984 restraints weight = 3900.399| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.24 r_work: 0.3192 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 3367 Z= 0.139 Angle : 0.607 7.473 4604 Z= 0.309 Chirality : 0.044 0.142 505 Planarity : 0.007 0.115 585 Dihedral : 4.988 24.943 459 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.40 % Favored : 91.36 % Rotamer: Outliers : 2.30 % Allowed : 11.49 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.23 (0.42), residues: 405 helix: -4.66 (0.54), residues: 27 sheet: -1.08 (0.44), residues: 133 loop : -1.31 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 100 TYR 0.013 0.001 TYR F 356 PHE 0.013 0.001 PHE A 101 TRP 0.017 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 3357) covalent geometry : angle 0.60434 / 0.31 ( 4579) SS BOND : bond 0.00376 / 0.24 ( 5) SS BOND : angle 0.65319 / 0.44 ( 10) hydrogen bonds : bond 0.03608 / 2.57 ( 82) hydrogen bonds : angle 6.36414 / 4.57 ( 207) link_BETA1-4 : bond 0.00530 / 0.26 ( 2) link_BETA1-4 : angle 1.49389 / 0.92 ( 6) link_BETA1-6 : bond 0.00316 / 0.17 ( 1) link_BETA1-6 : angle 0.88266 / 0.47 ( 3) link_NAG-ASN : bond 0.00125 / 0.06 ( 2) link_NAG-ASN : angle 0.95501 / 0.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 109 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.6826 (t60) REVERT: B 41 GLN cc_start: 0.7414 (pm20) cc_final: 0.7133 (pm20) outliers start: 8 outliers final: 6 residues processed: 69 average time/residue: 0.0747 time to fit residues: 6.2393 Evaluate side-chains 67 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.143057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117215 restraints weight = 3974.127| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.23 r_work: 0.3131 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 3367 Z= 0.218 Angle : 0.661 8.744 4604 Z= 0.336 Chirality : 0.046 0.141 505 Planarity : 0.007 0.116 585 Dihedral : 5.130 25.861 459 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.37 % Favored : 89.38 % Rotamer: Outliers : 2.87 % Allowed : 13.51 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.22 (0.43), residues: 405 helix: -4.89 (0.35), residues: 27 sheet: -1.09 (0.44), residues: 133 loop : -1.27 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 100 TYR 0.013 0.001 TYR F 356 PHE 0.017 0.002 PHE F 334 TRP 0.016 0.002 TRP F 423 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 ( 3357) covalent geometry : angle 0.65503 / 0.33 ( 4579) SS BOND : bond 0.00445 / 0.25 ( 5) SS BOND : angle 1.29906 / 1.09 ( 10) hydrogen bonds : bond 0.03620 / 2.58 ( 82) hydrogen bonds : angle 6.43071 / 4.61 ( 207) link_BETA1-4 : bond 0.00466 / 0.22 ( 2) link_BETA1-4 : angle 1.60594 / 0.98 ( 6) link_BETA1-6 : bond 0.00109 / 0.06 ( 1) link_BETA1-6 : angle 0.81200 / 0.44 ( 3) link_NAG-ASN : bond 0.00148 / 0.08 ( 2) link_NAG-ASN : angle 1.33178 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8739 (mtm180) cc_final: 0.8500 (mtm180) REVERT: A 109 TRP cc_start: 0.7945 (OUTLIER) cc_final: 0.6864 (t60) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.0736 time to fit residues: 6.1462 Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119782 restraints weight = 3872.353| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.20 r_work: 0.3183 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 3367 Z= 0.144 Angle : 0.632 12.212 4604 Z= 0.313 Chirality : 0.044 0.143 505 Planarity : 0.007 0.115 585 Dihedral : 4.933 24.735 459 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.14 % Favored : 90.62 % Rotamer: Outliers : 3.16 % Allowed : 14.94 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.10 (0.43), residues: 405 helix: -4.85 (0.37), residues: 27 sheet: -0.99 (0.44), residues: 133 loop : -1.19 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 100 TYR 0.013 0.001 TYR F 356 PHE 0.012 0.001 PHE A 101 TRP 0.014 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.14 ( 3357) covalent geometry : angle 0.62669 / 0.31 ( 4579) SS BOND : bond 0.00430 / 0.22 ( 5) SS BOND : angle 1.36152 / 1.05 ( 10) hydrogen bonds : bond 0.03167 / 2.30 ( 82) hydrogen bonds : angle 6.16410 / 4.45 ( 207) link_BETA1-4 : bond 0.00503 / 0.24 ( 2) link_BETA1-4 : angle 1.45401 / 0.91 ( 6) link_BETA1-6 : bond 0.00246 / 0.13 ( 1) link_BETA1-6 : angle 0.73764 / 0.39 ( 3) link_NAG-ASN : bond 0.00077 / 0.04 ( 2) link_NAG-ASN : angle 1.00083 / 0.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 109 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.6899 (t60) REVERT: B 78 GLN cc_start: 0.7313 (mp10) cc_final: 0.6893 (mp10) outliers start: 11 outliers final: 9 residues processed: 69 average time/residue: 0.0784 time to fit residues: 6.5166 Evaluate side-chains 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118588 restraints weight = 3949.540| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.21 r_work: 0.3166 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 3367 Z= 0.172 Angle : 0.639 10.456 4604 Z= 0.319 Chirality : 0.044 0.147 505 Planarity : 0.007 0.115 585 Dihedral : 4.836 24.502 459 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.88 % Favored : 89.88 % Rotamer: Outliers : 3.74 % Allowed : 16.38 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.09 (0.43), residues: 405 helix: -4.89 (0.34), residues: 27 sheet: -0.93 (0.44), residues: 133 loop : -1.21 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 100 TYR 0.012 0.001 TYR F 356 PHE 0.012 0.001 PHE A 101 TRP 0.015 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.17 ( 3357) covalent geometry : angle 0.63397 / 0.32 ( 4579) SS BOND : bond 0.00442 / 0.24 ( 5) SS BOND : angle 1.27184 / 1.01 ( 10) hydrogen bonds : bond 0.03128 / 2.26 ( 82) hydrogen bonds : angle 6.10885 / 4.42 ( 207) link_BETA1-4 : bond 0.00487 / 0.23 ( 2) link_BETA1-4 : angle 1.47654 / 0.92 ( 6) link_BETA1-6 : bond 0.00221 / 0.12 ( 1) link_BETA1-6 : angle 0.76291 / 0.41 ( 3) link_NAG-ASN : bond 0.00132 / 0.07 ( 2) link_NAG-ASN : angle 1.05844 / 0.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.120 Fit side-chains REVERT: A 56 ARG cc_start: 0.8756 (mtm180) cc_final: 0.8096 (mtm180) REVERT: A 109 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.6769 (t60) REVERT: F 366 CYS cc_start: 0.7429 (m) cc_final: 0.7045 (m) outliers start: 13 outliers final: 11 residues processed: 68 average time/residue: 0.0750 time to fit residues: 6.1663 Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.0040 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.148155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122071 restraints weight = 3960.907| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.25 r_work: 0.3186 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 3367 Z= 0.120 Angle : 0.608 10.180 4604 Z= 0.305 Chirality : 0.044 0.146 505 Planarity : 0.007 0.113 585 Dihedral : 4.655 24.285 459 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.15 % Favored : 91.60 % Rotamer: Outliers : 3.16 % Allowed : 17.82 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.43), residues: 405 helix: -4.90 (0.31), residues: 27 sheet: -0.86 (0.44), residues: 133 loop : -1.14 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 100 TYR 0.012 0.001 TYR F 356 PHE 0.011 0.001 PHE A 101 TRP 0.015 0.001 TRP A 109 HIS 0.002 0.000 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.12 ( 3357) covalent geometry : angle 0.60456 / 0.30 ( 4579) SS BOND : bond 0.00341 / 0.18 ( 5) SS BOND : angle 1.12014 / 0.89 ( 10) hydrogen bonds : bond 0.02834 / 2.07 ( 82) hydrogen bonds : angle 5.83676 / 4.25 ( 207) link_BETA1-4 : bond 0.00503 / 0.24 ( 2) link_BETA1-4 : angle 1.33137 / 0.85 ( 6) link_BETA1-6 : bond 0.00277 / 0.15 ( 1) link_BETA1-6 : angle 0.66784 / 0.35 ( 3) link_NAG-ASN : bond 0.00121 / 0.06 ( 2) link_NAG-ASN : angle 0.74664 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8667 (mtm180) cc_final: 0.8013 (mtm180) REVERT: A 109 TRP cc_start: 0.7855 (OUTLIER) cc_final: 0.6908 (t60) REVERT: B 80 GLU cc_start: 0.7267 (pm20) cc_final: 0.6839 (pt0) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.0900 time to fit residues: 7.2625 Evaluate side-chains 71 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.147153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121136 restraints weight = 3974.960| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.23 r_work: 0.3198 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 3367 Z= 0.141 Angle : 0.636 13.030 4604 Z= 0.313 Chirality : 0.044 0.147 505 Planarity : 0.007 0.113 585 Dihedral : 4.613 24.003 459 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.64 % Favored : 91.11 % Rotamer: Outliers : 2.87 % Allowed : 18.68 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.43), residues: 405 helix: -4.87 (0.33), residues: 27 sheet: -0.82 (0.44), residues: 133 loop : -1.08 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 100 TYR 0.012 0.001 TYR F 356 PHE 0.011 0.001 PHE A 101 TRP 0.014 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.14 ( 3357) covalent geometry : angle 0.63272 / 0.31 ( 4579) SS BOND : bond 0.00364 / 0.19 ( 5) SS BOND : angle 1.07022 / 0.85 ( 10) hydrogen bonds : bond 0.02874 / 2.10 ( 82) hydrogen bonds : angle 5.81276 / 4.24 ( 207) link_BETA1-4 : bond 0.00493 / 0.24 ( 2) link_BETA1-4 : angle 1.36711 / 0.87 ( 6) link_BETA1-6 : bond 0.00327 / 0.17 ( 1) link_BETA1-6 : angle 0.70859 / 0.37 ( 3) link_NAG-ASN : bond 0.00097 / 0.05 ( 2) link_NAG-ASN : angle 0.90036 / 0.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.126 Fit side-chains REVERT: A 56 ARG cc_start: 0.8677 (mtm180) cc_final: 0.8020 (mtm180) REVERT: A 109 TRP cc_start: 0.7905 (OUTLIER) cc_final: 0.6941 (t60) REVERT: B 80 GLU cc_start: 0.7185 (pm20) cc_final: 0.6725 (pt0) REVERT: F 366 CYS cc_start: 0.7389 (m) cc_final: 0.7001 (m) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.0618 time to fit residues: 4.9645 Evaluate side-chains 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.0270 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122232 restraints weight = 3937.359| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.23 r_work: 0.3183 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 3367 Z= 0.128 Angle : 0.608 11.600 4604 Z= 0.301 Chirality : 0.043 0.147 505 Planarity : 0.007 0.112 585 Dihedral : 4.540 23.958 459 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.90 % Favored : 91.85 % Rotamer: Outliers : 3.16 % Allowed : 18.39 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.43), residues: 405 helix: -4.87 (0.33), residues: 27 sheet: -0.80 (0.44), residues: 133 loop : -1.01 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.012 0.001 TYR F 356 PHE 0.011 0.001 PHE A 101 TRP 0.015 0.001 TRP A 109 HIS 0.002 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 ( 3357) covalent geometry : angle 0.60544 / 0.30 ( 4579) SS BOND : bond 0.00333 / 0.17 ( 5) SS BOND : angle 1.00688 / 0.80 ( 10) hydrogen bonds : bond 0.02818 / 2.06 ( 82) hydrogen bonds : angle 5.71850 / 4.17 ( 207) link_BETA1-4 : bond 0.00488 / 0.24 ( 2) link_BETA1-4 : angle 1.31378 / 0.84 ( 6) link_BETA1-6 : bond 0.00327 / 0.17 ( 1) link_BETA1-6 : angle 0.68796 / 0.36 ( 3) link_NAG-ASN : bond 0.00099 / 0.05 ( 2) link_NAG-ASN : angle 0.80670 / 0.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8705 (mtm180) cc_final: 0.8074 (mtm180) REVERT: A 109 TRP cc_start: 0.7920 (OUTLIER) cc_final: 0.6970 (t60) REVERT: F 366 CYS cc_start: 0.7429 (m) cc_final: 0.7041 (m) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.0751 time to fit residues: 5.8692 Evaluate side-chains 69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.0370 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.0670 chunk 34 optimal weight: 0.0000 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124735 restraints weight = 3886.134| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.23 r_work: 0.3218 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 3367 Z= 0.109 Angle : 0.601 13.597 4604 Z= 0.293 Chirality : 0.043 0.148 505 Planarity : 0.006 0.111 585 Dihedral : 4.375 23.668 459 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 2.87 % Allowed : 18.39 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.44), residues: 405 helix: -4.70 (0.44), residues: 20 sheet: -0.72 (0.44), residues: 133 loop : -1.05 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.012 0.001 TYR F 356 PHE 0.010 0.001 PHE A 101 TRP 0.016 0.001 TRP A 109 HIS 0.001 0.000 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.11 ( 3357) covalent geometry : angle 0.59897 / 0.29 ( 4579) SS BOND : bond 0.00265 / 0.14 ( 5) SS BOND : angle 0.84099 / 0.67 ( 10) hydrogen bonds : bond 0.02646 / 1.94 ( 82) hydrogen bonds : angle 5.56788 / 4.07 ( 207) link_BETA1-4 : bond 0.00490 / 0.24 ( 2) link_BETA1-4 : angle 1.25092 / 0.81 ( 6) link_BETA1-6 : bond 0.00350 / 0.18 ( 1) link_BETA1-6 : angle 0.68496 / 0.36 ( 3) link_NAG-ASN : bond 0.00145 / 0.07 ( 2) link_NAG-ASN : angle 0.66318 / 0.34 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8024 (mtm180) REVERT: A 109 TRP cc_start: 0.7710 (OUTLIER) cc_final: 0.6980 (t60) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.0717 time to fit residues: 5.7285 Evaluate side-chains 68 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.150578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124672 restraints weight = 3930.354| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.24 r_work: 0.3244 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 3367 Z= 0.112 Angle : 0.593 12.417 4604 Z= 0.290 Chirality : 0.043 0.148 505 Planarity : 0.007 0.111 585 Dihedral : 4.309 23.492 459 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.16 % Favored : 92.59 % Rotamer: Outliers : 3.16 % Allowed : 18.39 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.44), residues: 405 helix: -4.74 (0.41), residues: 20 sheet: -0.59 (0.44), residues: 133 loop : -0.98 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 67 TYR 0.011 0.001 TYR F 356 PHE 0.010 0.001 PHE A 101 TRP 0.016 0.001 TRP A 109 HIS 0.001 0.000 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.11 ( 3357) covalent geometry : angle 0.59048 / 0.29 ( 4579) SS BOND : bond 0.00269 / 0.14 ( 5) SS BOND : angle 0.81737 / 0.64 ( 10) hydrogen bonds : bond 0.02680 / 1.96 ( 82) hydrogen bonds : angle 5.52224 / 4.03 ( 207) link_BETA1-4 : bond 0.00466 / 0.23 ( 2) link_BETA1-4 : angle 1.24867 / 0.81 ( 6) link_BETA1-6 : bond 0.00407 / 0.21 ( 1) link_BETA1-6 : angle 0.73973 / 0.39 ( 3) link_NAG-ASN : bond 0.00139 / 0.07 ( 2) link_NAG-ASN : angle 0.69688 / 0.36 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1169.60 seconds wall clock time: 20 minutes 45.17 seconds (1245.17 seconds total)