Starting phenix.real_space_refine on Wed Jul 1 21:47:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wus_66269/07_2026/9wus_66269.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wus_66269/07_2026/9wus_66269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wus_66269/07_2026/9wus_66269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wus_66269/07_2026/9wus_66269.map" model { file = "/net/cci-nas-00/data/ceres_data/9wus_66269/07_2026/9wus_66269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wus_66269/07_2026/9wus_66269.cif" } resolution = 4.9 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= 0.003 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: 3 Type Number sf(0) Gaussians C 1974 2.51 5 N 552 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3168 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 528 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.63, per 1000 atoms: 0.20 Number of scatterers: 3168 At special positions: 0 Unit cell: (89.25, 82.95, 50.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 642 8.00 N 552 7.00 C 1974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 111.0 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 6 sheets defined 26.2% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'B' and resid 33 through 42 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'C' and resid 33 through 42 Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'D' and resid 33 through 42 Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'E' and resid 33 through 42 Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'F' and resid 33 through 42 Processing helix chain 'F' and resid 77 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 69 removed outlier: 7.500A pdb=" N GLU A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE A 51 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASN A 57 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 49 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 59 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 69 removed outlier: 7.501A pdb=" N GLU B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE B 51 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN B 57 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 49 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR B 59 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 69 removed outlier: 7.500A pdb=" N GLU C 55 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE C 51 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN C 57 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA C 49 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 59 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 69 removed outlier: 7.501A pdb=" N GLU D 55 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE D 51 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN D 57 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 49 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR D 59 " --> pdb=" O ARG D 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 65 through 69 removed outlier: 7.500A pdb=" N GLU E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE E 51 " --> pdb=" O GLU E 55 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASN E 57 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA E 49 " --> pdb=" O ASN E 57 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR E 59 " --> pdb=" O ARG E 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 65 through 69 removed outlier: 7.500A pdb=" N GLU F 55 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE F 51 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASN F 57 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA F 49 " --> pdb=" O ASN F 57 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR F 59 " --> pdb=" O ARG F 47 " (cutoff:3.500A) 108 hydrogen bonds defined for protein. 306 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: 0.39 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 582 1.29 - 1.36: 516 1.36 - 1.42: 174 1.42 - 1.48: 474 1.48 - 1.55: 1470 Bond restraints: 3216 Sorted by residual: bond pdb=" N ASN E 85 " pdb=" CA ASN E 85 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.42e-02 4.96e+03 5.46e-01 bond pdb=" N ASN A 85 " pdb=" CA ASN A 85 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.42e-02 4.96e+03 5.24e-01 bond pdb=" N ASN C 85 " pdb=" CA ASN C 85 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.42e-02 4.96e+03 5.03e-01 bond pdb=" N ASN D 85 " pdb=" CA ASN D 85 " ideal model delta sigma weight residual 1.460 1.469 -0.010 1.42e-02 4.96e+03 4.54e-01 bond pdb=" N ASN F 85 " pdb=" CA ASN F 85 " ideal model delta sigma weight residual 1.460 1.469 -0.009 1.42e-02 4.96e+03 4.46e-01 ... (remaining 3211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 4194 1.11 - 2.21: 120 2.21 - 3.32: 54 3.32 - 4.42: 0 4.42 - 5.53: 6 Bond angle restraints: 4374 Sorted by residual: angle pdb=" C LYS D 84 " pdb=" N ASN D 85 " pdb=" CA ASN D 85 " ideal model delta sigma weight residual 122.82 125.61 -2.79 1.42e+00 4.96e-01 3.87e+00 angle pdb=" C LYS F 84 " pdb=" N ASN F 85 " pdb=" CA ASN F 85 " ideal model delta sigma weight residual 122.82 125.61 -2.79 1.42e+00 4.96e-01 3.86e+00 angle pdb=" C LYS B 84 " pdb=" N ASN B 85 " pdb=" CA ASN B 85 " ideal model delta sigma weight residual 122.82 125.60 -2.78 1.42e+00 4.96e-01 3.83e+00 angle pdb=" C LYS C 84 " pdb=" N ASN C 85 " pdb=" CA ASN C 85 " ideal model delta sigma weight residual 122.82 125.58 -2.76 1.42e+00 4.96e-01 3.79e+00 angle pdb=" C LYS A 84 " pdb=" N ASN A 85 " pdb=" CA ASN A 85 " ideal model delta sigma weight residual 122.82 125.55 -2.73 1.42e+00 4.96e-01 3.69e+00 ... (remaining 4369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.24: 1703 10.24 - 20.49: 181 20.49 - 30.73: 96 30.73 - 40.98: 36 40.98 - 51.22: 12 Dihedral angle restraints: 2028 sinusoidal: 870 harmonic: 1158 Sorted by residual: dihedral pdb=" CB LYS D 84 " pdb=" CG LYS D 84 " pdb=" CD LYS D 84 " pdb=" CE LYS D 84 " ideal model delta sinusoidal sigma weight residual 180.00 131.12 48.88 3 1.50e+01 4.44e-03 8.70e+00 dihedral pdb=" CB LYS E 84 " pdb=" CG LYS E 84 " pdb=" CD LYS E 84 " pdb=" CE LYS E 84 " ideal model delta sinusoidal sigma weight residual 180.00 131.12 48.88 3 1.50e+01 4.44e-03 8.70e+00 dihedral pdb=" CB LYS C 84 " pdb=" CG LYS C 84 " pdb=" CD LYS C 84 " pdb=" CE LYS C 84 " ideal model delta sinusoidal sigma weight residual 180.00 131.14 48.86 3 1.50e+01 4.44e-03 8.70e+00 ... (remaining 2025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 211 0.023 - 0.045: 132 0.045 - 0.068: 73 0.068 - 0.090: 30 0.090 - 0.113: 58 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA ILE A 51 " pdb=" N ILE A 51 " pdb=" C ILE A 51 " pdb=" CB ILE A 51 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 chirality pdb=" CA VAL E 89 " pdb=" N VAL E 89 " pdb=" C VAL E 89 " pdb=" CB VAL E 89 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.16e-01 chirality pdb=" CA VAL A 89 " pdb=" N VAL A 89 " pdb=" C VAL A 89 " pdb=" CB VAL A 89 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 501 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 70 " 0.005 2.00e-02 2.50e+03 9.50e-03 9.02e-01 pdb=" C ILE F 70 " -0.016 2.00e-02 2.50e+03 pdb=" O ILE F 70 " 0.006 2.00e-02 2.50e+03 pdb=" N PRO F 71 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 52 " 0.005 2.00e-02 2.50e+03 9.45e-03 8.93e-01 pdb=" C ASN B 52 " -0.016 2.00e-02 2.50e+03 pdb=" O ASN B 52 " 0.006 2.00e-02 2.50e+03 pdb=" N GLY B 53 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 70 " -0.005 2.00e-02 2.50e+03 9.44e-03 8.92e-01 pdb=" C ILE D 70 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE D 70 " -0.006 2.00e-02 2.50e+03 pdb=" N PRO D 71 " -0.006 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1302 2.93 - 3.42: 2939 3.42 - 3.92: 4824 3.92 - 4.41: 4655 4.41 - 4.90: 8013 Nonbonded interactions: 21733 Sorted by model distance: nonbonded pdb=" O ASP B 33 " pdb=" OG1 THR B 36 " model vdw 2.441 3.040 nonbonded pdb=" O ASP A 33 " pdb=" OG1 THR A 36 " model vdw 2.441 3.040 nonbonded pdb=" O ASP F 33 " pdb=" OG1 THR F 36 " model vdw 2.441 3.040 nonbonded pdb=" O ASP E 33 " pdb=" OG1 THR E 36 " model vdw 2.441 3.040 nonbonded pdb=" O ASP D 33 " pdb=" OG1 THR D 36 " model vdw 2.442 3.040 ... (remaining 21728 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 4.210 Find NCS groups from input model: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 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 : 0.002 0.016 3216 Z= 0.106 Angle : 0.568 5.530 4374 Z= 0.306 Chirality : 0.048 0.113 504 Planarity : 0.003 0.012 588 Dihedral : 12.719 51.220 1272 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.42), residues: 378 helix: -0.40 (0.53), residues: 114 sheet: -0.97 (0.56), residues: 72 loop : -2.16 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 50 TYR 0.004 0.001 TYR A 66 PHE 0.003 0.001 PHE C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 3216) covalent geometry : angle 0.56754 / 0.31 ( 4374) hydrogen bonds : bond 0.15531 / 8.70 ( 108) hydrogen bonds : angle 5.61643 / 4.12 ( 306) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.026 Fit side-chains REVERT: A 44 ASP cc_start: 0.8025 (t0) cc_final: 0.7729 (t70) REVERT: A 66 TYR cc_start: 0.3311 (t80) cc_final: 0.2566 (t80) REVERT: A 69 TYR cc_start: 0.7538 (m-80) cc_final: 0.7059 (m-80) REVERT: A 84 LYS cc_start: 0.8755 (mttt) cc_final: 0.8502 (mtmt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0681 time to fit residues: 1.5199 Evaluate side-chains 15 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.0060 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0470 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 0.0060 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.193953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.158527 restraints weight = 872.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.162978 restraints weight = 628.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.167396 restraints weight = 489.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.170378 restraints weight = 390.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.172369 restraints weight = 320.524| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3216 Z= 0.096 Angle : 0.499 4.945 4374 Z= 0.255 Chirality : 0.047 0.110 504 Planarity : 0.002 0.010 588 Dihedral : 3.768 10.765 426 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.43), residues: 378 helix: -0.40 (0.52), residues: 114 sheet: 0.07 (0.67), residues: 72 loop : -1.98 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 54 TYR 0.004 0.001 TYR A 66 PHE 0.002 0.001 PHE B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 3216) covalent geometry : angle 0.49855 / 0.26 ( 4374) hydrogen bonds : bond 0.03706 / 2.15 ( 108) hydrogen bonds : angle 5.07622 / 3.74 ( 306) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.021 Fit side-chains REVERT: C 44 ASP cc_start: 0.7951 (t0) cc_final: 0.7546 (t70) REVERT: C 66 TYR cc_start: 0.3454 (t80) cc_final: 0.2043 (t80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0466 time to fit residues: 1.1436 Evaluate side-chains 17 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 0.0050 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.0060 chunk 33 optimal weight: 0.0030 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.3220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.196413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.160672 restraints weight = 851.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.165016 restraints weight = 629.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.167669 restraints weight = 498.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.171150 restraints weight = 418.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.172965 restraints weight = 347.401| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3216 Z= 0.095 Angle : 0.512 4.884 4374 Z= 0.262 Chirality : 0.048 0.109 504 Planarity : 0.002 0.009 588 Dihedral : 3.668 10.060 426 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.45), residues: 378 helix: -0.60 (0.51), residues: 114 sheet: 0.52 (0.60), residues: 102 loop : -2.03 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 54 TYR 0.003 0.001 TYR A 66 PHE 0.003 0.001 PHE B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 3216) covalent geometry : angle 0.51169 / 0.26 ( 4374) hydrogen bonds : bond 0.03332 / 1.97 ( 108) hydrogen bonds : angle 5.06584 / 3.76 ( 306) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.022 Fit side-chains REVERT: C 39 GLN cc_start: 0.7681 (pp30) cc_final: 0.7348 (pp30) REVERT: C 44 ASP cc_start: 0.7959 (t0) cc_final: 0.7569 (t70) REVERT: C 66 TYR cc_start: 0.3379 (t80) cc_final: 0.1993 (t80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0577 time to fit residues: 1.3491 Evaluate side-chains 18 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.192010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.161244 restraints weight = 858.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164948 restraints weight = 623.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167850 restraints weight = 489.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.170230 restraints weight = 400.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.171681 restraints weight = 339.573| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3216 Z= 0.125 Angle : 0.547 4.742 4374 Z= 0.286 Chirality : 0.049 0.118 504 Planarity : 0.002 0.011 588 Dihedral : 4.078 12.296 426 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.61 % Allowed : 4.84 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.50 (0.44), residues: 378 helix: -0.68 (0.50), residues: 114 sheet: 0.20 (0.60), residues: 102 loop : -1.99 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 54 TYR 0.007 0.001 TYR F 66 PHE 0.002 0.001 PHE F 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 3216) covalent geometry : angle 0.54679 / 0.29 ( 4374) hydrogen bonds : bond 0.03047 / 1.80 ( 108) hydrogen bonds : angle 5.18122 / 3.86 ( 306) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.020 Fit side-chains REVERT: C 44 ASP cc_start: 0.7901 (t0) cc_final: 0.7550 (t70) REVERT: C 66 TYR cc_start: 0.3977 (t80) cc_final: 0.2218 (t80) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0556 time to fit residues: 1.3081 Evaluate side-chains 18 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.187982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.157164 restraints weight = 885.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.162234 restraints weight = 591.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.166174 restraints weight = 434.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.169061 restraints weight = 338.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.170910 restraints weight = 273.948| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3216 Z= 0.101 Angle : 0.526 5.028 4374 Z= 0.271 Chirality : 0.049 0.114 504 Planarity : 0.002 0.010 588 Dihedral : 3.959 11.243 426 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.45), residues: 378 helix: -0.70 (0.50), residues: 114 sheet: 0.44 (0.61), residues: 102 loop : -1.87 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 50 TYR 0.004 0.001 TYR E 66 PHE 0.002 0.001 PHE B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 3216) covalent geometry : angle 0.52577 / 0.27 ( 4374) hydrogen bonds : bond 0.03013 / 1.83 ( 108) hydrogen bonds : angle 5.05022 / 3.74 ( 306) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.016 Fit side-chains REVERT: B 66 TYR cc_start: 0.3275 (t80) cc_final: 0.2723 (t80) REVERT: B 69 TYR cc_start: 0.7139 (m-80) cc_final: 0.6720 (m-80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0452 time to fit residues: 0.9689 Evaluate side-chains 18 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 0.0020 chunk 35 optimal weight: 0.0970 chunk 5 optimal weight: 0.0770 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.0050 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 6 optimal weight: 6.9990 overall best weight: 0.0496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.193687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.160151 restraints weight = 871.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.164270 restraints weight = 592.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.167356 restraints weight = 454.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.169787 restraints weight = 372.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.171714 restraints weight = 316.650| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3216 Z= 0.114 Angle : 0.536 4.885 4374 Z= 0.286 Chirality : 0.050 0.136 504 Planarity : 0.002 0.009 588 Dihedral : 3.708 9.452 426 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.45), residues: 378 helix: -0.55 (0.52), residues: 114 sheet: 0.55 (0.62), residues: 102 loop : -1.99 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 65 TYR 0.003 0.001 TYR F 66 PHE 0.002 0.001 PHE D 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 3216) covalent geometry : angle 0.53569 / 0.29 ( 4374) hydrogen bonds : bond 0.03104 / 1.87 ( 108) hydrogen bonds : angle 4.81189 / 3.57 ( 306) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.013 Fit side-chains REVERT: F 39 GLN cc_start: 0.7586 (pp30) cc_final: 0.7285 (pp30) REVERT: F 69 TYR cc_start: 0.7224 (m-80) cc_final: 0.6747 (m-80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0379 time to fit residues: 0.8880 Evaluate side-chains 19 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 0.0030 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 0.0470 chunk 27 optimal weight: 0.2980 chunk 2 optimal weight: 8.9990 overall best weight: 0.8490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.190156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.158970 restraints weight = 946.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.164431 restraints weight = 625.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.167791 restraints weight = 451.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.170186 restraints weight = 352.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.172033 restraints weight = 290.182| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3216 Z= 0.139 Angle : 0.628 5.052 4374 Z= 0.352 Chirality : 0.053 0.164 504 Planarity : 0.003 0.011 588 Dihedral : 4.136 12.158 426 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.44), residues: 378 helix: -0.74 (0.51), residues: 114 sheet: 0.41 (0.63), residues: 102 loop : -2.08 (0.41), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 47 TYR 0.004 0.001 TYR D 66 PHE 0.002 0.001 PHE B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 3216) covalent geometry : angle 0.62767 / 0.35 ( 4374) hydrogen bonds : bond 0.02918 / 1.78 ( 108) hydrogen bonds : angle 4.84802 / 3.60 ( 306) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.022 Fit side-chains REVERT: D 66 TYR cc_start: 0.3645 (t80) cc_final: 0.2834 (t80) REVERT: D 69 TYR cc_start: 0.7309 (m-80) cc_final: 0.6827 (m-80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0650 time to fit residues: 1.3873 Evaluate side-chains 17 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 33 optimal weight: 0.0570 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.191646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.161281 restraints weight = 947.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.166629 restraints weight = 601.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.170582 restraints weight = 419.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.173194 restraints weight = 317.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.174912 restraints weight = 254.647| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3216 Z= 0.113 Angle : 0.550 4.988 4374 Z= 0.293 Chirality : 0.051 0.131 504 Planarity : 0.002 0.011 588 Dihedral : 3.947 10.048 426 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.45), residues: 378 helix: -0.73 (0.51), residues: 114 sheet: 0.36 (0.63), residues: 102 loop : -2.11 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 54 TYR 0.004 0.001 TYR B 66 PHE 0.002 0.001 PHE D 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 3216) covalent geometry : angle 0.55047 / 0.29 ( 4374) hydrogen bonds : bond 0.02914 / 1.77 ( 108) hydrogen bonds : angle 4.74225 / 3.51 ( 306) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.023 Fit side-chains REVERT: D 66 TYR cc_start: 0.3544 (t80) cc_final: 0.2790 (t80) REVERT: D 69 TYR cc_start: 0.7358 (m-80) cc_final: 0.6824 (m-80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0637 time to fit residues: 1.3568 Evaluate side-chains 17 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 0.0070 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 27 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.190156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.157792 restraints weight = 969.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.162841 restraints weight = 640.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.166235 restraints weight = 461.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.168612 restraints weight = 361.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.169872 restraints weight = 300.824| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3216 Z= 0.116 Angle : 0.560 5.093 4374 Z= 0.298 Chirality : 0.052 0.128 504 Planarity : 0.002 0.010 588 Dihedral : 4.122 10.992 426 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.44), residues: 378 helix: -0.69 (0.51), residues: 114 sheet: 0.20 (0.61), residues: 102 loop : -2.05 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 65 TYR 0.007 0.001 TYR C 66 PHE 0.002 0.001 PHE B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 3216) covalent geometry : angle 0.55970 / 0.30 ( 4374) hydrogen bonds : bond 0.03185 / 1.86 ( 108) hydrogen bonds : angle 4.81678 / 3.50 ( 306) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.022 Fit side-chains REVERT: D 66 TYR cc_start: 0.4093 (t80) cc_final: 0.2952 (t80) REVERT: D 69 TYR cc_start: 0.7333 (m-80) cc_final: 0.6830 (m-80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0620 time to fit residues: 1.3208 Evaluate side-chains 18 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 0.0270 overall best weight: 2.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.179538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146409 restraints weight = 949.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152264 restraints weight = 620.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.156425 restraints weight = 449.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.158584 restraints weight = 350.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.161022 restraints weight = 296.015| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3216 Z= 0.169 Angle : 0.620 5.052 4374 Z= 0.334 Chirality : 0.052 0.127 504 Planarity : 0.003 0.017 588 Dihedral : 4.681 13.504 426 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.44), residues: 378 helix: -0.96 (0.50), residues: 114 sheet: -0.27 (0.58), residues: 102 loop : -1.85 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 50 TYR 0.009 0.002 TYR B 34 PHE 0.003 0.001 PHE B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 3216) covalent geometry : angle 0.61974 / 0.33 ( 4374) hydrogen bonds : bond 0.03438 / 2.01 ( 108) hydrogen bonds : angle 5.29029 / 3.84 ( 306) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.022 Fit side-chains REVERT: D 69 TYR cc_start: 0.7407 (m-80) cc_final: 0.6876 (m-80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0629 time to fit residues: 1.3410 Evaluate side-chains 17 residues out of total 62 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.0670 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.192087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.159423 restraints weight = 844.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.163377 restraints weight = 613.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.167000 restraints weight = 483.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.169093 restraints weight = 392.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.170859 restraints weight = 335.972| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3216 Z= 0.123 Angle : 0.569 5.043 4374 Z= 0.307 Chirality : 0.051 0.123 504 Planarity : 0.003 0.011 588 Dihedral : 4.277 12.123 426 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.42), residues: 378 helix: -1.23 (0.46), residues: 114 sheet: -0.31 (0.59), residues: 102 loop : -1.90 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 54 TYR 0.007 0.001 TYR E 66 PHE 0.002 0.001 PHE D 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 3216) covalent geometry : angle 0.56867 / 0.31 ( 4374) hydrogen bonds : bond 0.03178 / 1.91 ( 108) hydrogen bonds : angle 5.06517 / 3.67 ( 306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 660.55 seconds wall clock time: 12 minutes 2.06 seconds (722.06 seconds total)