Starting phenix.real_space_refine on Wed Mar 5 16:12:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ag3_15414/03_2025/8ag3_15414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ag3_15414/03_2025/8ag3_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_15414/03_2025/8ag3_15414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ag3_15414/03_2025/8ag3_15414.map" model { file = "/net/cci-nas-00/data/ceres_data/8ag3_15414/03_2025/8ag3_15414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ag3_15414/03_2025/8ag3_15414.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.86, per 1000 atoms: 1.09 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: 0.63 Conformation dependent library (CDL) restraints added in 326.9 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: 0.43 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: 0.77 Time building geometry restraints manager: 0.77 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: 0.01 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: 0.010 Normalize map: mean=0, sd=1: 1.120 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.730 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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= 0.167 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.001 TRP D 91 HIS 0.002 0.001 HIS C 32 PHE 0.010 0.001 PHE D 15 TYR 0.009 0.001 TYR D 4 ARG 0.001 0.000 ARG D 27 *********************** 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 : 0.307 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: 0.1712 time to fit residues: 20.5344 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3693 r_free = 0.3693 target = 0.135375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110599 restraints weight = 3585.024| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.59 r_work: 0.3194 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0923 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= 0.197 Angle : 0.549 5.819 3610 Z= 0.295 Chirality : 0.044 0.141 412 Planarity : 0.006 0.102 458 Dihedral : 4.394 12.484 350 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.48), residues: 318 helix: 2.05 (0.80), residues: 50 sheet: 0.01 (0.53), residues: 102 loop : -2.45 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.012 0.001 PHE C 133 TYR 0.010 0.002 TYR D 101 ARG 0.001 0.000 ARG D 60 *********************** 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 : 0.283 Fit side-chains REVERT: C 71 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7795 (p) REVERT: C 75 PHE cc_start: 0.8261 (m-80) cc_final: 0.7661 (m-80) REVERT: C 119 TYR cc_start: 0.8605 (m-80) cc_final: 0.8378 (m-80) REVERT: D 106 TYR cc_start: 0.8576 (m-80) cc_final: 0.8320 (m-80) REVERT: D 156 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8032 (mm) outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 0.1675 time to fit residues: 21.0108 Evaluate side-chains 110 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106735 restraints weight = 3682.366| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.49 r_work: 0.3148 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2676 Z= 0.330 Angle : 0.605 7.010 3610 Z= 0.327 Chirality : 0.045 0.154 412 Planarity : 0.006 0.088 458 Dihedral : 4.794 12.504 350 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.19 % Allowed : 25.32 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.47), residues: 318 helix: 1.64 (0.77), residues: 50 sheet: -0.04 (0.53), residues: 102 loop : -2.50 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.017 0.002 PHE C 133 TYR 0.013 0.002 TYR D 101 ARG 0.003 0.000 ARG C 60 *********************** 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 126 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.7732 (mp0) cc_final: 0.6599 (mp0) REVERT: C 65 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7119 (tm-30) REVERT: C 75 PHE cc_start: 0.8221 (m-80) cc_final: 0.7644 (m-80) REVERT: D 156 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8147 (mm) outliers start: 16 outliers final: 10 residues processed: 117 average time/residue: 0.1677 time to fit residues: 22.6656 Evaluate side-chains 120 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 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 85 LYS 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 17 optimal weight: 0.1980 chunk 27 optimal weight: 0.1980 chunk 29 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 20 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108140 restraints weight = 3694.125| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.70 r_work: 0.3167 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2676 Z= 0.135 Angle : 0.521 6.908 3610 Z= 0.279 Chirality : 0.044 0.153 412 Planarity : 0.005 0.083 458 Dihedral : 4.349 12.981 350 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.22 % Allowed : 26.95 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.47), residues: 318 helix: 2.15 (0.79), residues: 50 sheet: 0.06 (0.53), residues: 102 loop : -2.44 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 91 HIS 0.001 0.001 HIS C 120 PHE 0.010 0.001 PHE D 15 TYR 0.009 0.001 TYR C 119 ARG 0.001 0.000 ARG D 27 *********************** 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: 13 poor density : 106 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 52 ASN cc_start: 0.7883 (m-40) cc_final: 0.7678 (m110) REVERT: C 71 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7765 (p) REVERT: C 75 PHE cc_start: 0.8111 (m-80) cc_final: 0.7505 (m-80) REVERT: C 119 TYR cc_start: 0.8527 (m-80) cc_final: 0.8301 (m-80) REVERT: C 140 LYS cc_start: 0.8167 (tttp) cc_final: 0.7594 (tttp) REVERT: D 13 LYS cc_start: 0.8584 (tptp) cc_final: 0.8231 (tptm) REVERT: D 106 TYR cc_start: 0.8562 (m-80) cc_final: 0.8320 (m-80) REVERT: D 119 TYR cc_start: 0.7654 (m-10) cc_final: 0.7251 (m-80) REVERT: D 156 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8063 (mm) outliers start: 13 outliers final: 9 residues processed: 111 average time/residue: 0.1678 time to fit residues: 21.7891 Evaluate side-chains 116 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 C residue 158 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 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109408 restraints weight = 3638.529| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.63 r_work: 0.3139 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2676 Z= 0.268 Angle : 0.561 6.738 3610 Z= 0.304 Chirality : 0.044 0.143 412 Planarity : 0.005 0.080 458 Dihedral : 4.599 13.100 350 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.19 % Allowed : 25.97 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.47), residues: 318 helix: 1.91 (0.78), residues: 50 sheet: 0.03 (0.53), residues: 102 loop : -2.48 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.015 0.001 PHE C 133 TYR 0.014 0.002 TYR D 101 ARG 0.001 0.000 ARG D 27 *********************** 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 123 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 52 ASN cc_start: 0.7932 (m-40) cc_final: 0.7717 (m-40) REVERT: C 65 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6839 (tm-30) REVERT: C 71 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7820 (p) REVERT: C 75 PHE cc_start: 0.8114 (m-80) cc_final: 0.7519 (m-80) REVERT: C 140 LYS cc_start: 0.8188 (tttp) cc_final: 0.7661 (tttp) REVERT: D 156 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8037 (mm) outliers start: 16 outliers final: 10 residues processed: 115 average time/residue: 0.1765 time to fit residues: 23.2001 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 : 0.305 ------------------------------------------------------------------------------- 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 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 48 ASP 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 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109769 restraints weight = 3623.567| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.62 r_work: 0.3148 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2676 Z= 0.263 Angle : 0.562 7.033 3610 Z= 0.303 Chirality : 0.045 0.159 412 Planarity : 0.005 0.080 458 Dihedral : 4.621 14.486 350 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.57 % Allowed : 27.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.47), residues: 318 helix: 1.99 (0.78), residues: 50 sheet: 0.04 (0.52), residues: 102 loop : -2.47 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.015 0.001 PHE C 133 TYR 0.017 0.002 TYR D 101 ARG 0.006 0.000 ARG C 60 *********************** 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 122 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.7514 (mp0) cc_final: 0.6589 (mp0) REVERT: C 43 MET cc_start: 0.4271 (tpp) cc_final: 0.3826 (tmm) REVERT: C 52 ASN cc_start: 0.7906 (m-40) cc_final: 0.7694 (m-40) REVERT: C 65 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6819 (tm-30) REVERT: C 75 PHE cc_start: 0.8124 (m-80) cc_final: 0.7527 (m-80) REVERT: C 140 LYS cc_start: 0.8200 (tttp) cc_final: 0.7650 (tttp) REVERT: D 156 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8144 (mm) outliers start: 11 outliers final: 10 residues processed: 115 average time/residue: 0.1649 time to fit residues: 21.8651 Evaluate side-chains 122 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105601 restraints weight = 3874.821| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.64 r_work: 0.3166 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2676 Z= 0.296 Angle : 0.582 5.778 3610 Z= 0.315 Chirality : 0.045 0.156 412 Planarity : 0.006 0.079 458 Dihedral : 4.756 15.046 350 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.90 % Allowed : 28.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.47), residues: 318 helix: 1.94 (0.78), residues: 50 sheet: 0.05 (0.52), residues: 102 loop : -2.48 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.016 0.001 PHE C 133 TYR 0.011 0.002 TYR C 119 ARG 0.013 0.001 ARG C 60 *********************** 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 121 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 MET cc_start: 0.4352 (tpp) cc_final: 0.3946 (tmm) REVERT: C 52 ASN cc_start: 0.7926 (m-40) cc_final: 0.7690 (m-40) REVERT: C 60 ARG cc_start: 0.7957 (ttm110) cc_final: 0.7731 (ttm-80) REVERT: C 65 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6834 (tm-30) REVERT: C 75 PHE cc_start: 0.8122 (m-80) cc_final: 0.7529 (m-80) REVERT: C 140 LYS cc_start: 0.8243 (tttp) cc_final: 0.7716 (tttp) REVERT: D 156 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8107 (mm) outliers start: 12 outliers final: 11 residues processed: 113 average time/residue: 0.1669 time to fit residues: 21.7374 Evaluate side-chains 120 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 26 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106167 restraints weight = 3675.559| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.64 r_work: 0.3130 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2676 Z= 0.345 Angle : 0.607 5.038 3610 Z= 0.328 Chirality : 0.046 0.157 412 Planarity : 0.006 0.080 458 Dihedral : 4.897 14.919 350 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.87 % Allowed : 28.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.46), residues: 318 helix: 1.77 (0.78), residues: 50 sheet: 0.04 (0.52), residues: 102 loop : -2.54 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.018 0.002 PHE C 133 TYR 0.015 0.002 TYR D 101 ARG 0.010 0.001 ARG C 60 *********************** 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 124 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 MET cc_start: 0.4345 (tpp) cc_final: 0.3959 (tmm) REVERT: C 52 ASN cc_start: 0.7920 (m-40) cc_final: 0.7675 (m-40) REVERT: C 60 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7744 (ttm-80) REVERT: C 65 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6834 (tm-30) REVERT: C 75 PHE cc_start: 0.8135 (m-80) cc_final: 0.7528 (m-80) REVERT: C 140 LYS cc_start: 0.8182 (tttp) cc_final: 0.7638 (tttp) REVERT: D 156 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8096 (mm) outliers start: 15 outliers final: 12 residues processed: 115 average time/residue: 0.1815 time to fit residues: 24.0592 Evaluate side-chains 121 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 26 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109733 restraints weight = 3600.657| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.60 r_work: 0.3146 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2676 Z= 0.236 Angle : 0.559 5.200 3610 Z= 0.302 Chirality : 0.044 0.146 412 Planarity : 0.005 0.079 458 Dihedral : 4.698 14.600 350 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.22 % Allowed : 27.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.47), residues: 318 helix: 2.74 (0.78), residues: 46 sheet: 0.07 (0.52), residues: 102 loop : -2.55 (0.42), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.015 0.001 PHE C 133 TYR 0.011 0.002 TYR D 101 ARG 0.010 0.001 ARG C 60 *********************** 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 119 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: C 43 MET cc_start: 0.4349 (tpp) cc_final: 0.3928 (tmm) REVERT: C 52 ASN cc_start: 0.7938 (m-40) cc_final: 0.7690 (m-40) REVERT: C 60 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7901 (ttm-80) REVERT: C 65 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7120 (tm-30) REVERT: C 75 PHE cc_start: 0.8225 (m-80) cc_final: 0.7589 (m-80) REVERT: C 140 LYS cc_start: 0.8283 (tttp) cc_final: 0.7732 (tttp) REVERT: D 156 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8149 (mm) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.1747 time to fit residues: 22.2091 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 : 0.317 ------------------------------------------------------------------------------- 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 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 26 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 9 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107071 restraints weight = 3667.208| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.67 r_work: 0.3142 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2676 Z= 0.248 Angle : 0.565 5.169 3610 Z= 0.306 Chirality : 0.045 0.144 412 Planarity : 0.005 0.079 458 Dihedral : 4.687 14.543 350 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.90 % Allowed : 28.90 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.47), residues: 318 helix: 2.02 (0.78), residues: 50 sheet: 0.08 (0.52), residues: 102 loop : -2.49 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.015 0.001 PHE C 133 TYR 0.012 0.002 TYR D 101 ARG 0.009 0.000 ARG C 60 ********************** 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 125 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: C 43 MET cc_start: 0.4347 (tpp) cc_final: 0.3974 (tmm) REVERT: C 52 ASN cc_start: 0.7885 (m-40) cc_final: 0.7627 (m-40) REVERT: C 60 ARG cc_start: 0.7941 (ttm110) cc_final: 0.7737 (ttm-80) REVERT: C 65 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6820 (tm-30) REVERT: C 75 PHE cc_start: 0.8111 (m-80) cc_final: 0.7464 (m-80) REVERT: C 117 LYS cc_start: 0.7909 (tttt) cc_final: 0.7678 (ttmm) REVERT: C 140 LYS cc_start: 0.8192 (tttp) cc_final: 0.7661 (tttp) REVERT: D 156 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8077 (mm) outliers start: 12 outliers final: 11 residues processed: 117 average time/residue: 0.1622 time to fit residues: 22.0335 Evaluate side-chains 124 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 26 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106567 restraints weight = 3687.863| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.55 r_work: 0.3179 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2676 Z= 0.240 Angle : 0.576 7.363 3610 Z= 0.306 Chirality : 0.045 0.144 412 Planarity : 0.005 0.079 458 Dihedral : 4.653 14.426 350 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.22 % Allowed : 28.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.47), residues: 318 helix: 2.07 (0.78), residues: 50 sheet: 0.12 (0.53), residues: 102 loop : -2.50 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.015 0.001 PHE C 133 TYR 0.011 0.002 TYR D 101 ARG 0.009 0.000 ARG C 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1832.04 seconds wall clock time: 32 minutes 9.04 seconds (1929.04 seconds total)