Starting phenix.real_space_refine on Thu Sep 10 20:10:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ag3_15414/09_2026/8ag3_15414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ag3_15414/09_2026/8ag3_15414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ag3_15414/09_2026/8ag3_15414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ag3_15414/09_2026/8ag3_15414.map" model { file = "/net/cci-nas-00/data/ceres_data/8ag3_15414/09_2026/8ag3_15414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ag3_15414/09_2026/8ag3_15414.cif" } resolution = 3.47 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= 0.001 sd= 0.015 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 20 5.16 5 C 1668 2.51 5 N 436 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2632 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1316 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "D" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1316 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Time building chain proxies: 0.78, per 1000 atoms: 0.30 Number of scatterers: 2632 At special positions: 0 Unit cell: (78.49, 64.295, 64.295, 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 20 16.00 O 508 8.00 N 436 7.00 C 1668 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: 0.13 Conformation dependent library (CDL) restraints added in 55.2 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 16.1% alpha, 52.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'C' and resid 20 through 31 removed outlier: 3.778A pdb=" N ASN C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 46 through 61 removed outlier: 4.125A pdb=" N ILE D 50 " --> pdb=" O ASN D 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 42 removed outlier: 7.238A pdb=" N THR C 72 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP C 155 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 149 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 103 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 149 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 69 removed outlier: 3.619A pdb=" N CYS C 66 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 103 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.897A pdb=" N PHE C 139 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP C 138 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 127 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.831A pdb=" N CYS D 112 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 145 " --> pdb=" O CYS D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 150 hydrogen bonds defined for protein. 423 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: 0.27 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 852 1.35 - 1.46: 557 1.46 - 1.58: 1237 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 2676 Sorted by residual: bond pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB PRO C 80 " pdb=" CG PRO C 80 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.38e-01 bond pdb=" CA GLU C 65 " pdb=" CB GLU C 65 " ideal model delta sigma weight residual 1.534 1.546 -0.013 1.45e-02 4.76e+03 7.44e-01 bond pdb=" CB MET D 43 " pdb=" CG MET D 43 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.20e-01 bond pdb=" CA LYS D 7 " pdb=" CB LYS D 7 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.68e-02 3.54e+03 4.56e-01 ... (remaining 2671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 3542 1.78 - 3.55: 58 3.55 - 5.33: 4 5.33 - 7.11: 5 7.11 - 8.88: 1 Bond angle restraints: 3610 Sorted by residual: angle pdb=" CA GLU C 65 " pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA MET D 43 " pdb=" CB MET D 43 " pdb=" CG MET D 43 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB MET D 43 " pdb=" CG MET D 43 " pdb=" SD MET D 43 " ideal model delta sigma weight residual 112.70 121.58 -8.88 3.00e+00 1.11e-01 8.77e+00 angle pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" CD PRO C 80 " ideal model delta sigma weight residual 112.00 108.65 3.35 1.40e+00 5.10e-01 5.73e+00 angle pdb=" C MET D 43 " pdb=" CA MET D 43 " pdb=" CB MET D 43 " ideal model delta sigma weight residual 110.19 114.05 -3.86 1.62e+00 3.81e-01 5.66e+00 ... (remaining 3605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1299 13.04 - 26.08: 225 26.08 - 39.11: 81 39.11 - 52.15: 37 52.15 - 65.19: 12 Dihedral angle restraints: 1654 sinusoidal: 694 harmonic: 960 Sorted by residual: dihedral pdb=" CA ASP C 128 " pdb=" CB ASP C 128 " pdb=" CG ASP C 128 " pdb=" OD1 ASP C 128 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 83 " pdb=" CB ASP C 83 " pdb=" CG ASP C 83 " pdb=" OD1 ASP C 83 " ideal model delta sinusoidal sigma weight residual -30.00 -87.13 57.13 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA LYS D 77 " pdb=" CB LYS D 77 " pdb=" CG LYS D 77 " pdb=" CD LYS D 77 " ideal model delta sinusoidal sigma weight residual 60.00 117.48 -57.48 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 238 0.028 - 0.057: 103 0.057 - 0.085: 37 0.085 - 0.113: 28 0.113 - 0.141: 6 Chirality restraints: 412 Sorted by residual: chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 409 not shown) Planarity restraints: 458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 79 " -0.088 5.00e-02 4.00e+02 1.33e-01 2.81e+01 pdb=" N PRO C 80 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 120 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO C 121 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 43 " -0.005 2.00e-02 2.50e+03 9.79e-03 9.58e-01 pdb=" C MET D 43 " 0.017 2.00e-02 2.50e+03 pdb=" O MET D 43 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU D 44 " -0.006 2.00e-02 2.50e+03 ... (remaining 455 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 59 2.69 - 3.25: 2329 3.25 - 3.80: 3801 3.80 - 4.35: 5021 4.35 - 4.90: 8610 Nonbonded interactions: 19820 Sorted by model distance: nonbonded pdb=" O ASP C 48 " pdb=" ND2 ASN C 52 " model vdw 2.143 3.120 nonbonded pdb=" O GLN C 10 " pdb=" OH TYR C 101 " model vdw 2.232 3.040 nonbonded pdb=" O GLN D 10 " pdb=" OH TYR D 101 " model vdw 2.294 3.040 nonbonded pdb=" N GLU C 44 " pdb=" OE1 GLU C 44 " model vdw 2.344 3.120 nonbonded pdb=" NH1 ARG D 23 " pdb=" O TYR D 106 " model vdw 2.350 3.120 ... (remaining 19815 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.960 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 0.048 2676 Z= 0.114 Angle : 0.600 8.883 3610 Z= 0.322 Chirality : 0.044 0.141 412 Planarity : 0.007 0.133 458 Dihedral : 17.158 65.191 1030 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 34.74 % Favored : 65.26 % 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: -1.45 (0.47), residues: 318 helix: 2.05 (0.79), residues: 50 sheet: -0.29 (0.51), residues: 112 loop : -2.61 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 27 TYR 0.009 0.001 TYR D 4 PHE 0.010 0.001 PHE D 15 TRP 0.003 0.001 TRP D 91 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 2676) covalent geometry : angle 0.60029 / 0.32 ( 3610) hydrogen bonds : bond 0.13884 / 8.21 ( 113) hydrogen bonds : angle 7.18697 / 5.09 ( 423) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.060 Fit side-chains revert: symmetry clash REVERT: D 106 TYR cc_start: 0.8501 (m-80) cc_final: 0.8225 (m-80) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0606 time to fit residues: 7.3414 Evaluate side-chains 105 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 ASN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108061 restraints weight = 3651.925| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.55 r_work: 0.3178 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2676 Z= 0.140 Angle : 0.555 5.950 3610 Z= 0.298 Chirality : 0.044 0.140 412 Planarity : 0.006 0.102 458 Dihedral : 4.442 12.599 350 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.95 % Allowed : 28.90 % Favored : 69.16 % 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: -1.28 (0.48), residues: 318 helix: 2.02 (0.80), residues: 50 sheet: 0.01 (0.54), residues: 102 loop : -2.46 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 60 TYR 0.010 0.002 TYR D 101 PHE 0.012 0.001 PHE C 133 TRP 0.005 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 2676) covalent geometry : angle 0.55466 / 0.30 ( 3610) hydrogen bonds : bond 0.04366 / 2.72 ( 113) hydrogen bonds : angle 4.81926 / 3.37 ( 423) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.104 Fit side-chains REVERT: C 52 ASN cc_start: 0.7859 (m-40) cc_final: 0.7646 (m110) REVERT: C 71 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7786 (p) REVERT: C 75 PHE cc_start: 0.8241 (m-80) cc_final: 0.7656 (m-80) REVERT: C 119 TYR cc_start: 0.8599 (m-80) cc_final: 0.8377 (m-80) REVERT: D 106 TYR cc_start: 0.8574 (m-80) cc_final: 0.8316 (m-80) REVERT: D 156 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8024 (mm) outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 0.0605 time to fit residues: 7.6574 Evaluate side-chains 111 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 4 optimal weight: 0.0870 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.133329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108422 restraints weight = 3710.688| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.68 r_work: 0.3156 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2676 Z= 0.136 Angle : 0.540 6.995 3610 Z= 0.290 Chirality : 0.043 0.142 412 Planarity : 0.005 0.086 458 Dihedral : 4.398 11.471 350 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.90 % Allowed : 26.95 % Favored : 69.16 % 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: -1.23 (0.48), residues: 318 helix: 2.03 (0.79), residues: 50 sheet: 0.03 (0.53), residues: 102 loop : -2.41 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 60 TYR 0.009 0.001 TYR C 101 PHE 0.013 0.001 PHE C 133 TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 2676) covalent geometry : angle 0.53994 / 0.29 ( 3610) hydrogen bonds : bond 0.04230 / 2.64 ( 113) hydrogen bonds : angle 4.62161 / 3.22 ( 423) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.7495 (mp0) cc_final: 0.6303 (mp0) REVERT: C 52 ASN cc_start: 0.7868 (m-40) cc_final: 0.7652 (m110) REVERT: C 71 SER cc_start: 0.8034 (OUTLIER) cc_final: 0.7735 (p) REVERT: C 75 PHE cc_start: 0.8134 (m-80) cc_final: 0.7527 (m-80) REVERT: C 119 TYR cc_start: 0.8530 (m-80) cc_final: 0.8245 (m-80) REVERT: D 101 TYR cc_start: 0.8513 (m-80) cc_final: 0.8151 (m-80) REVERT: D 106 TYR cc_start: 0.8577 (m-80) cc_final: 0.8292 (m-80) REVERT: D 156 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8007 (mm) outliers start: 12 outliers final: 6 residues processed: 112 average time/residue: 0.0577 time to fit residues: 7.6706 Evaluate side-chains 114 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.0070 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.132641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108248 restraints weight = 3704.922| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.58 r_work: 0.3185 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2676 Z= 0.118 Angle : 0.528 7.037 3610 Z= 0.283 Chirality : 0.044 0.142 412 Planarity : 0.005 0.083 458 Dihedral : 4.337 12.450 350 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.55 % Allowed : 25.65 % Favored : 69.81 % 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: -1.14 (0.48), residues: 318 helix: 2.22 (0.80), residues: 50 sheet: 0.06 (0.53), residues: 102 loop : -2.37 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 27 TYR 0.009 0.001 TYR C 101 PHE 0.011 0.001 PHE C 133 TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 2676) covalent geometry : angle 0.52775 / 0.28 ( 3610) hydrogen bonds : bond 0.03932 / 2.44 ( 113) hydrogen bonds : angle 4.43780 / 3.08 ( 423) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 52 ASN cc_start: 0.7880 (m-40) cc_final: 0.7660 (m-40) REVERT: C 71 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7766 (p) REVERT: C 75 PHE cc_start: 0.8132 (m-80) cc_final: 0.7572 (m-80) REVERT: C 119 TYR cc_start: 0.8509 (m-80) cc_final: 0.8263 (m-80) REVERT: D 13 LYS cc_start: 0.8550 (tptp) cc_final: 0.8220 (tptm) REVERT: D 101 TYR cc_start: 0.8478 (m-80) cc_final: 0.8088 (m-80) REVERT: D 106 TYR cc_start: 0.8582 (m-80) cc_final: 0.8319 (m-80) REVERT: D 119 TYR cc_start: 0.7651 (m-10) cc_final: 0.7188 (m-80) REVERT: D 129 LYS cc_start: 0.8263 (mmtm) cc_final: 0.8057 (mttm) REVERT: D 156 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8044 (mm) outliers start: 14 outliers final: 8 residues processed: 112 average time/residue: 0.0643 time to fit residues: 8.4667 Evaluate side-chains 116 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106064 restraints weight = 3652.053| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.53 r_work: 0.3144 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2676 Z= 0.214 Angle : 0.588 6.534 3610 Z= 0.319 Chirality : 0.045 0.148 412 Planarity : 0.005 0.081 458 Dihedral : 4.742 13.376 350 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.19 % Allowed : 26.30 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.32 (0.47), residues: 318 helix: 1.82 (0.78), residues: 50 sheet: -0.01 (0.52), residues: 102 loop : -2.43 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 27 TYR 0.014 0.002 TYR D 101 PHE 0.017 0.002 PHE C 133 TRP 0.009 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 ( 2676) covalent geometry : angle 0.58840 / 0.32 ( 3610) hydrogen bonds : bond 0.04907 / 3.03 ( 113) hydrogen bonds : angle 4.77159 / 3.31 ( 423) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 52 ASN cc_start: 0.7987 (m-40) cc_final: 0.7766 (m-40) REVERT: C 60 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7692 (mtp85) REVERT: C 65 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7110 (tm-30) REVERT: C 75 PHE cc_start: 0.8238 (m-80) cc_final: 0.7625 (m-80) REVERT: C 119 TYR cc_start: 0.8612 (m-80) cc_final: 0.8401 (m-80) REVERT: C 140 LYS cc_start: 0.8285 (tttp) cc_final: 0.7797 (tttp) REVERT: D 69 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7561 (mm) REVERT: D 77 LYS cc_start: 0.7802 (pttt) cc_final: 0.7211 (pttm) REVERT: D 156 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8115 (mm) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 0.0643 time to fit residues: 8.6354 Evaluate side-chains 124 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.131586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107479 restraints weight = 3675.146| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.57 r_work: 0.3165 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2676 Z= 0.141 Angle : 0.548 7.194 3610 Z= 0.294 Chirality : 0.044 0.141 412 Planarity : 0.005 0.080 458 Dihedral : 4.511 13.449 350 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.90 % Allowed : 27.60 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.21 (0.47), residues: 318 helix: 2.03 (0.78), residues: 50 sheet: 0.03 (0.53), residues: 102 loop : -2.38 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 27 TYR 0.013 0.002 TYR D 101 PHE 0.014 0.001 PHE C 133 TRP 0.007 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 2676) covalent geometry : angle 0.54757 / 0.29 ( 3610) hydrogen bonds : bond 0.04262 / 2.67 ( 113) hydrogen bonds : angle 4.56370 / 3.17 ( 423) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: C 43 MET cc_start: 0.4259 (tpp) cc_final: 0.3739 (tmm) REVERT: C 52 ASN cc_start: 0.7939 (m-40) cc_final: 0.7691 (m-40) REVERT: C 65 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7105 (tm-30) REVERT: C 71 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7866 (p) REVERT: C 75 PHE cc_start: 0.8227 (m-80) cc_final: 0.7584 (m-80) REVERT: C 119 TYR cc_start: 0.8583 (m-80) cc_final: 0.8332 (m-80) REVERT: C 140 LYS cc_start: 0.8267 (tttp) cc_final: 0.7723 (tttp) REVERT: D 19 PHE cc_start: 0.8519 (m-80) cc_final: 0.8317 (m-80) REVERT: D 70 ASP cc_start: 0.8170 (t70) cc_final: 0.7898 (t70) REVERT: D 77 LYS cc_start: 0.7784 (pttt) cc_final: 0.7195 (pttm) REVERT: D 156 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8130 (mm) outliers start: 12 outliers final: 7 residues processed: 110 average time/residue: 0.0697 time to fit residues: 8.9436 Evaluate side-chains 115 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.0010 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 29 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.7253 > 50:) chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.131954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107565 restraints weight = 3690.759| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.57 r_work: 0.3158 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2676 Z= 0.143 Angle : 0.569 6.783 3610 Z= 0.297 Chirality : 0.045 0.156 412 Planarity : 0.005 0.078 458 Dihedral : 4.515 14.855 350 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.57 % Allowed : 28.90 % Favored : 67.53 % 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: -1.13 (0.47), residues: 318 helix: 2.82 (0.78), residues: 46 sheet: 0.06 (0.53), residues: 102 loop : -2.45 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 60 TYR 0.013 0.002 TYR D 101 PHE 0.014 0.001 PHE C 133 TRP 0.007 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 2676) covalent geometry : angle 0.56878 / 0.30 ( 3610) hydrogen bonds : bond 0.04226 / 2.65 ( 113) hydrogen bonds : angle 4.43287 / 3.08 ( 423) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.7669 (mp0) cc_final: 0.6777 (mp0) REVERT: C 43 MET cc_start: 0.4331 (tpp) cc_final: 0.3856 (tmm) REVERT: C 52 ASN cc_start: 0.7943 (m-40) cc_final: 0.7690 (m-40) REVERT: C 65 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7097 (tm-30) REVERT: C 71 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7857 (p) REVERT: C 75 PHE cc_start: 0.8233 (m-80) cc_final: 0.7601 (m-80) REVERT: C 119 TYR cc_start: 0.8585 (m-80) cc_final: 0.8341 (m-80) REVERT: C 140 LYS cc_start: 0.8296 (tttp) cc_final: 0.7772 (tttp) REVERT: D 19 PHE cc_start: 0.8530 (m-80) cc_final: 0.8249 (m-80) REVERT: D 69 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7395 (mm) REVERT: D 77 LYS cc_start: 0.7757 (pttt) cc_final: 0.7152 (pttm) REVERT: D 156 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8098 (mm) outliers start: 11 outliers final: 6 residues processed: 113 average time/residue: 0.0595 time to fit residues: 7.8456 Evaluate side-chains 116 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 25 optimal weight: 0.0670 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 overall best weight: 0.3118 ------------------------------------------------------------------------------- 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 = 0.132580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108327 restraints weight = 3712.060| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.57 r_work: 0.3183 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2676 Z= 0.116 Angle : 0.537 5.668 3610 Z= 0.286 Chirality : 0.044 0.142 412 Planarity : 0.005 0.078 458 Dihedral : 4.391 14.517 350 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.92 % Allowed : 30.19 % Favored : 66.88 % 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: -1.05 (0.48), residues: 318 helix: 2.96 (0.78), residues: 46 sheet: 0.06 (0.53), residues: 102 loop : -2.37 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 60 TYR 0.012 0.001 TYR D 101 PHE 0.012 0.001 PHE C 133 TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 2676) covalent geometry : angle 0.53696 / 0.29 ( 3610) hydrogen bonds : bond 0.03870 / 2.43 ( 113) hydrogen bonds : angle 4.30179 / 2.99 ( 423) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.7697 (mp0) cc_final: 0.6826 (mp0) REVERT: C 43 MET cc_start: 0.4402 (tpp) cc_final: 0.3900 (tmm) REVERT: C 52 ASN cc_start: 0.7918 (m-40) cc_final: 0.7645 (m-40) REVERT: C 65 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7060 (tm-30) REVERT: C 71 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7806 (p) REVERT: C 75 PHE cc_start: 0.8249 (m-80) cc_final: 0.7625 (m-80) REVERT: C 119 TYR cc_start: 0.8570 (m-80) cc_final: 0.8342 (m-80) REVERT: C 140 LYS cc_start: 0.8305 (tttp) cc_final: 0.7775 (tttp) REVERT: D 19 PHE cc_start: 0.8544 (m-80) cc_final: 0.8292 (m-80) REVERT: D 69 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7175 (mm) REVERT: D 70 ASP cc_start: 0.8118 (t70) cc_final: 0.7831 (t70) REVERT: D 77 LYS cc_start: 0.7771 (pttt) cc_final: 0.7197 (pttm) REVERT: D 106 TYR cc_start: 0.8606 (m-80) cc_final: 0.8375 (m-80) REVERT: D 119 TYR cc_start: 0.7797 (m-10) cc_final: 0.7391 (m-80) REVERT: D 129 LYS cc_start: 0.8330 (mmtm) cc_final: 0.8119 (mttp) REVERT: D 156 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8079 (mm) outliers start: 9 outliers final: 5 residues processed: 109 average time/residue: 0.0627 time to fit residues: 8.0213 Evaluate side-chains 111 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 overall best weight: 0.3558 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.133045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108503 restraints weight = 3787.360| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.60 r_work: 0.3161 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2676 Z= 0.125 Angle : 0.546 5.144 3610 Z= 0.290 Chirality : 0.044 0.141 412 Planarity : 0.005 0.077 458 Dihedral : 4.387 14.519 350 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.92 % Allowed : 29.22 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.47), residues: 318 helix: 2.22 (0.79), residues: 50 sheet: 0.07 (0.53), residues: 102 loop : -2.35 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 60 TYR 0.011 0.001 TYR D 101 PHE 0.013 0.001 PHE C 133 TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 2676) covalent geometry : angle 0.54573 / 0.29 ( 3610) hydrogen bonds : bond 0.03951 / 2.47 ( 113) hydrogen bonds : angle 4.30498 / 2.97 ( 423) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: C 43 MET cc_start: 0.4445 (tpp) cc_final: 0.3963 (tmm) REVERT: C 52 ASN cc_start: 0.7964 (m-40) cc_final: 0.7701 (m-40) REVERT: C 60 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7903 (ttm-80) REVERT: C 65 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7129 (tm-30) REVERT: C 71 SER cc_start: 0.8168 (OUTLIER) cc_final: 0.7831 (p) REVERT: C 75 PHE cc_start: 0.8272 (m-80) cc_final: 0.7667 (m-80) REVERT: C 119 TYR cc_start: 0.8583 (m-80) cc_final: 0.8358 (m-80) REVERT: C 140 LYS cc_start: 0.8366 (tttp) cc_final: 0.7867 (tttp) REVERT: D 19 PHE cc_start: 0.8523 (m-80) cc_final: 0.8239 (m-80) REVERT: D 69 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7179 (mm) REVERT: D 106 TYR cc_start: 0.8619 (m-80) cc_final: 0.8393 (m-80) REVERT: D 119 TYR cc_start: 0.7790 (m-10) cc_final: 0.7389 (m-80) REVERT: D 129 LYS cc_start: 0.8341 (mmtm) cc_final: 0.8131 (mttp) REVERT: D 156 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8094 (mm) outliers start: 9 outliers final: 5 residues processed: 110 average time/residue: 0.0639 time to fit residues: 8.2090 Evaluate side-chains 111 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.0070 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.133275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108683 restraints weight = 3732.438| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.64 r_work: 0.3190 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2676 Z= 0.144 Angle : 0.557 5.089 3610 Z= 0.297 Chirality : 0.044 0.141 412 Planarity : 0.005 0.078 458 Dihedral : 4.446 14.169 350 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.60 % Allowed : 30.52 % Favored : 66.88 % 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: -1.09 (0.47), residues: 318 helix: 2.84 (0.77), residues: 46 sheet: 0.06 (0.53), residues: 102 loop : -2.40 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 60 TYR 0.014 0.002 TYR D 101 PHE 0.014 0.001 PHE C 133 TRP 0.007 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 2676) covalent geometry : angle 0.55702 / 0.30 ( 3610) hydrogen bonds : bond 0.04178 / 2.62 ( 113) hydrogen bonds : angle 4.40741 / 3.04 ( 423) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: C 43 MET cc_start: 0.4352 (tpp) cc_final: 0.3953 (tmm) REVERT: C 52 ASN cc_start: 0.7896 (m-40) cc_final: 0.7622 (m-40) REVERT: C 60 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7689 (ttm-80) REVERT: C 65 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6811 (tm-30) REVERT: C 71 SER cc_start: 0.8148 (OUTLIER) cc_final: 0.7819 (p) REVERT: C 75 PHE cc_start: 0.8139 (m-80) cc_final: 0.7497 (m-80) REVERT: C 119 TYR cc_start: 0.8503 (m-80) cc_final: 0.8264 (m-80) REVERT: C 140 LYS cc_start: 0.8229 (tttp) cc_final: 0.7700 (tttp) REVERT: D 19 PHE cc_start: 0.8508 (m-80) cc_final: 0.8225 (m-80) REVERT: D 69 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7070 (mm) REVERT: D 106 TYR cc_start: 0.8607 (m-80) cc_final: 0.8362 (m-80) REVERT: D 129 LYS cc_start: 0.8287 (mmtm) cc_final: 0.8081 (mttp) REVERT: D 156 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8027 (mm) outliers start: 8 outliers final: 5 residues processed: 110 average time/residue: 0.0576 time to fit residues: 7.4622 Evaluate side-chains 113 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 25 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.132437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108068 restraints weight = 3711.453| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.63 r_work: 0.3164 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2676 Z= 0.143 Angle : 0.558 5.028 3610 Z= 0.297 Chirality : 0.045 0.142 412 Planarity : 0.005 0.077 458 Dihedral : 4.448 13.921 350 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.60 % Allowed : 30.52 % Favored : 66.88 % 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: -1.11 (0.47), residues: 318 helix: 2.81 (0.77), residues: 46 sheet: 0.04 (0.53), residues: 102 loop : -2.39 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 60 TYR 0.012 0.002 TYR D 101 PHE 0.014 0.001 PHE C 133 TRP 0.007 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 2676) covalent geometry : angle 0.55833 / 0.30 ( 3610) hydrogen bonds : bond 0.04158 / 2.60 ( 113) hydrogen bonds : angle 4.42088 / 3.04 ( 423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 860.56 seconds wall clock time: 15 minutes 24.61 seconds (924.61 seconds total)