Starting phenix.real_space_refine on Wed Sep 17 02:57:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbo_61321/09_2025/9jbo_61321_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbo_61321/09_2025/9jbo_61321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jbo_61321/09_2025/9jbo_61321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbo_61321/09_2025/9jbo_61321.map" model { file = "/net/cci-nas-00/data/ceres_data/9jbo_61321/09_2025/9jbo_61321_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbo_61321/09_2025/9jbo_61321_neut.cif" } resolution = 3.39 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= 0.005 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 6 5.16 5 C 1170 2.51 5 N 321 2.21 5 O 375 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1872 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 624 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Restraints were copied for chains: B, A Time building chain proxies: 0.41, per 1000 atoms: 0.22 Number of scatterers: 1872 At special positions: 0 Unit cell: (62.32, 103.36, 35.72, 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 6 16.00 O 375 8.00 N 321 7.00 C 1170 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: 0.07 Conformation dependent library (CDL) restraints added in 43.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 438 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 7 through 10 Processing sheet with id=AA2, first strand: chain 'C' and resid 14 through 23 removed outlier: 6.864A pdb=" N GLN C 15 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY B 16 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLN B 15 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY A 16 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 29 through 31 removed outlier: 5.912A pdb=" N LYS C 30 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LYS B 30 " --> pdb=" O VAL A 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 35 through 39 removed outlier: 6.037A pdb=" N LYS C 36 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR B 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 38 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS B 36 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N THR A 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 38 " --> pdb=" O THR A 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.495A pdb=" N VAL C 87 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 87 " --> pdb=" O THR A 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.130A pdb=" N SER C 98 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER B 98 " --> pdb=" O ILE A 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.081A pdb=" N VAL C 103 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL B 103 " --> pdb=" O ILE A 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.900A pdb=" N ILE C 112 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE B 112 " --> pdb=" O ILE A 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 118 through 120 24 hydrogen bonds defined for protein. 72 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: 0.12 Time building geometry restraints manager: 0.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 639 1.34 - 1.46: 304 1.46 - 1.58: 944 1.58 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 1893 Sorted by residual: bond pdb=" N ILE A 18 " pdb=" CA ILE A 18 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.54e+00 bond pdb=" N ILE B 18 " pdb=" CA ILE B 18 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.45e+00 bond pdb=" N ILE C 18 " pdb=" CA ILE C 18 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 8.27e+00 bond pdb=" N ASP C 92 " pdb=" CA ASP C 92 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.43e+00 bond pdb=" N ASP B 92 " pdb=" CA ASP B 92 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.37e+00 ... (remaining 1888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 2337 1.26 - 2.52: 181 2.52 - 3.78: 32 3.78 - 5.04: 3 5.04 - 6.31: 3 Bond angle restraints: 2556 Sorted by residual: angle pdb=" CA ASP A 92 " pdb=" CB ASP A 92 " pdb=" CG ASP A 92 " ideal model delta sigma weight residual 112.60 116.20 -3.60 1.00e+00 1.00e+00 1.30e+01 angle pdb=" CA ASP C 92 " pdb=" CB ASP C 92 " pdb=" CG ASP C 92 " ideal model delta sigma weight residual 112.60 116.19 -3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" CA ASP B 92 " pdb=" CB ASP B 92 " pdb=" CG ASP B 92 " ideal model delta sigma weight residual 112.60 116.19 -3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" CA LYS C 91 " pdb=" C LYS C 91 " pdb=" O LYS C 91 " ideal model delta sigma weight residual 121.23 118.20 3.03 1.07e+00 8.73e-01 8.01e+00 angle pdb=" CA LYS B 91 " pdb=" C LYS B 91 " pdb=" O LYS B 91 " ideal model delta sigma weight residual 121.23 118.21 3.02 1.07e+00 8.73e-01 7.96e+00 ... (remaining 2551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.66: 865 12.66 - 25.32: 137 25.32 - 37.98: 63 37.98 - 50.63: 18 50.63 - 63.29: 21 Dihedral angle restraints: 1104 sinusoidal: 414 harmonic: 690 Sorted by residual: dihedral pdb=" CA GLU B 24 " pdb=" CB GLU B 24 " pdb=" CG GLU B 24 " pdb=" CD GLU B 24 " ideal model delta sinusoidal sigma weight residual 60.00 117.33 -57.33 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA GLU C 24 " pdb=" CB GLU C 24 " pdb=" CG GLU C 24 " pdb=" CD GLU C 24 " ideal model delta sinusoidal sigma weight residual 60.00 117.32 -57.32 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA GLU A 24 " pdb=" CB GLU A 24 " pdb=" CG GLU A 24 " pdb=" CD GLU A 24 " ideal model delta sinusoidal sigma weight residual 60.00 117.30 -57.30 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 132 0.024 - 0.047: 78 0.047 - 0.071: 31 0.071 - 0.094: 26 0.094 - 0.118: 39 Chirality restraints: 306 Sorted by residual: chirality pdb=" CA ILE B 113 " pdb=" N ILE B 113 " pdb=" C ILE B 113 " pdb=" CB ILE B 113 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE A 99 " pdb=" N ILE A 99 " pdb=" C ILE A 99 " pdb=" CB ILE A 99 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA ILE B 99 " pdb=" N ILE B 99 " pdb=" C ILE B 99 " pdb=" CB ILE B 99 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 303 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 32 " -0.005 2.00e-02 2.50e+03 1.55e-02 5.99e+00 pdb=" CG TRP B 32 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 32 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 32 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 32 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 32 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 32 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 32 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 32 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 32 " -0.005 2.00e-02 2.50e+03 1.54e-02 5.95e+00 pdb=" CG TRP C 32 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 32 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 32 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 32 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 32 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 32 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 32 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 32 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 32 " -0.006 2.00e-02 2.50e+03 1.54e-02 5.89e+00 pdb=" CG TRP A 32 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 32 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 32 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 32 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 32 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 32 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 32 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 32 " -0.000 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.94: 813 2.94 - 3.43: 1631 3.43 - 3.92: 2943 3.92 - 4.41: 2829 4.41 - 4.90: 5748 Nonbonded interactions: 13964 Sorted by model distance: nonbonded pdb=" ND2 ASN C 19 " pdb=" OD1 ASN B 19 " model vdw 2.444 3.120 nonbonded pdb=" OD1 ASP B 96 " pdb=" N VAL B 97 " model vdw 2.506 3.120 nonbonded pdb=" OD1 ASP C 96 " pdb=" N VAL C 97 " model vdw 2.506 3.120 nonbonded pdb=" OD1 ASP A 96 " pdb=" N VAL A 97 " model vdw 2.506 3.120 nonbonded pdb=" O SER C 25 " pdb=" N ASN B 26 " model vdw 2.507 3.120 ... (remaining 13959 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 'B' selection = chain 'A' } 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.240 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 1893 Z= 0.289 Angle : 0.760 6.305 2556 Z= 0.474 Chirality : 0.053 0.118 306 Planarity : 0.003 0.023 330 Dihedral : 18.285 63.293 666 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 36.23 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.45), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 115 PHE 0.007 0.001 PHE C 20 TRP 0.036 0.010 TRP B 32 HIS 0.001 0.000 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 1893) covalent geometry : angle 0.76039 ( 2556) hydrogen bonds : bond 0.17798 ( 24) hydrogen bonds : angle 9.36950 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.039 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0389 time to fit residues: 1.7394 Evaluate side-chains 31 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.185869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.168965 restraints weight = 3062.877| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.85 r_work: 0.4178 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1893 Z= 0.091 Angle : 0.532 5.510 2556 Z= 0.276 Chirality : 0.052 0.173 306 Planarity : 0.002 0.020 330 Dihedral : 4.066 12.829 255 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 6.76 % Allowed : 32.85 % Favored : 60.39 % 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 aren not related in a simple way. whole: -2.67 (0.46), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 115 PHE 0.004 0.001 PHE C 45 TRP 0.018 0.003 TRP C 32 HIS 0.001 0.000 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 1893) covalent geometry : angle 0.53250 ( 2556) hydrogen bonds : bond 0.02419 ( 24) hydrogen bonds : angle 7.27567 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.041 Fit side-chains REVERT: C 3 LYS cc_start: 0.7539 (tttt) cc_final: 0.7158 (tttm) REVERT: C 91 LYS cc_start: 0.4051 (tppt) cc_final: 0.3548 (tppt) REVERT: A 92 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6927 (t0) outliers start: 14 outliers final: 6 residues processed: 43 average time/residue: 0.0377 time to fit residues: 1.8855 Evaluate side-chains 33 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.180759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.162433 restraints weight = 3042.105| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.90 r_work: 0.4112 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1893 Z= 0.119 Angle : 0.608 6.013 2556 Z= 0.312 Chirality : 0.052 0.151 306 Planarity : 0.004 0.032 330 Dihedral : 5.000 14.779 255 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 5.80 % Allowed : 32.37 % Favored : 61.84 % 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 aren not related in a simple way. whole: -2.56 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 115 PHE 0.005 0.001 PHE C 45 TRP 0.009 0.002 TRP B 32 HIS 0.001 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 1893) covalent geometry : angle 0.60762 ( 2556) hydrogen bonds : bond 0.02866 ( 24) hydrogen bonds : angle 6.56649 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.041 Fit side-chains REVERT: C 3 LYS cc_start: 0.7568 (tttt) cc_final: 0.7208 (tttm) REVERT: A 92 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7232 (t0) outliers start: 12 outliers final: 5 residues processed: 48 average time/residue: 0.0311 time to fit residues: 1.7772 Evaluate side-chains 40 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.180049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.161848 restraints weight = 2990.360| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.78 r_work: 0.4103 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1893 Z= 0.120 Angle : 0.602 5.628 2556 Z= 0.310 Chirality : 0.053 0.146 306 Planarity : 0.003 0.024 330 Dihedral : 5.008 14.988 255 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 5.80 % Allowed : 34.78 % Favored : 59.42 % 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 aren not related in a simple way. whole: -2.52 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 115 PHE 0.005 0.001 PHE B 45 TRP 0.010 0.002 TRP A 32 HIS 0.001 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 1893) covalent geometry : angle 0.60175 ( 2556) hydrogen bonds : bond 0.02631 ( 24) hydrogen bonds : angle 6.33371 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.049 Fit side-chains REVERT: C 3 LYS cc_start: 0.7583 (tttt) cc_final: 0.7245 (tttm) outliers start: 12 outliers final: 7 residues processed: 45 average time/residue: 0.0597 time to fit residues: 3.1599 Evaluate side-chains 44 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 8 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 0.4980 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4473 r_free = 0.4473 target = 0.184096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.165832 restraints weight = 2971.289| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.88 r_work: 0.4137 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1893 Z= 0.083 Angle : 0.526 5.750 2556 Z= 0.269 Chirality : 0.051 0.143 306 Planarity : 0.003 0.022 330 Dihedral : 4.583 14.476 255 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.38 % Allowed : 37.68 % Favored : 58.94 % 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 aren not related in a simple way. whole: -2.41 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 115 PHE 0.003 0.001 PHE A 45 TRP 0.009 0.002 TRP B 32 HIS 0.001 0.000 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 1893) covalent geometry : angle 0.52598 ( 2556) hydrogen bonds : bond 0.02166 ( 24) hydrogen bonds : angle 6.02207 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.056 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 0.0571 time to fit residues: 2.8787 Evaluate side-chains 38 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain A residue 8 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 16 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.4522 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.183987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.165198 restraints weight = 2987.304| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.92 r_work: 0.4132 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1893 Z= 0.092 Angle : 0.551 5.832 2556 Z= 0.279 Chirality : 0.052 0.141 306 Planarity : 0.003 0.024 330 Dihedral : 4.610 15.289 255 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.38 % Allowed : 36.71 % Favored : 59.90 % 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 aren not related in a simple way. whole: -2.29 (0.48), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 115 PHE 0.004 0.001 PHE C 45 TRP 0.007 0.002 TRP A 32 HIS 0.001 0.000 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 1893) covalent geometry : angle 0.55101 ( 2556) hydrogen bonds : bond 0.02200 ( 24) hydrogen bonds : angle 5.98335 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.077 Fit side-chains REVERT: B 92 ASP cc_start: 0.7678 (m-30) cc_final: 0.6502 (p0) outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.0533 time to fit residues: 2.6715 Evaluate side-chains 40 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain A residue 8 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.182115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.163473 restraints weight = 2911.001| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.78 r_work: 0.4120 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1893 Z= 0.102 Angle : 0.572 6.220 2556 Z= 0.289 Chirality : 0.052 0.140 306 Planarity : 0.003 0.024 330 Dihedral : 4.782 15.345 255 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 4.35 % Allowed : 35.27 % Favored : 60.39 % 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 aren not related in a simple way. whole: -2.25 (0.48), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 115 PHE 0.003 0.001 PHE C 45 TRP 0.007 0.002 TRP B 32 HIS 0.001 0.000 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 1893) covalent geometry : angle 0.57152 ( 2556) hydrogen bonds : bond 0.02480 ( 24) hydrogen bonds : angle 6.03447 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.097 Fit side-chains REVERT: B 92 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.6474 (p0) REVERT: A 90 ASP cc_start: 0.6574 (m-30) cc_final: 0.6183 (t0) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.0570 time to fit residues: 2.8684 Evaluate side-chains 39 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain A residue 8 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.183228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.164385 restraints weight = 2953.497| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.79 r_work: 0.4139 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1893 Z= 0.094 Angle : 0.563 6.174 2556 Z= 0.285 Chirality : 0.052 0.138 306 Planarity : 0.003 0.022 330 Dihedral : 4.680 15.205 255 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 3.38 % Allowed : 35.75 % Favored : 60.87 % 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 aren not related in a simple way. whole: -2.16 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 115 PHE 0.003 0.001 PHE C 45 TRP 0.008 0.002 TRP A 32 HIS 0.001 0.000 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 1893) covalent geometry : angle 0.56347 ( 2556) hydrogen bonds : bond 0.02257 ( 24) hydrogen bonds : angle 5.95911 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.075 Fit side-chains REVERT: B 92 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.6441 (p0) REVERT: A 90 ASP cc_start: 0.6412 (m-30) cc_final: 0.6208 (t0) outliers start: 7 outliers final: 4 residues processed: 37 average time/residue: 0.0509 time to fit residues: 2.2775 Evaluate side-chains 36 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain A residue 8 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 0.0570 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.1102 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.184534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.165705 restraints weight = 2963.814| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.81 r_work: 0.4134 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1893 Z= 0.113 Angle : 0.602 6.760 2556 Z= 0.304 Chirality : 0.053 0.150 306 Planarity : 0.003 0.026 330 Dihedral : 4.890 15.745 255 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 2.42 % Allowed : 38.16 % Favored : 59.42 % 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 aren not related in a simple way. whole: -2.12 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 115 PHE 0.006 0.001 PHE A 45 TRP 0.008 0.002 TRP A 32 HIS 0.001 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 1893) covalent geometry : angle 0.60192 ( 2556) hydrogen bonds : bond 0.02612 ( 24) hydrogen bonds : angle 6.10303 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.092 Fit side-chains REVERT: A 90 ASP cc_start: 0.6372 (m-30) cc_final: 0.5825 (t0) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 0.0608 time to fit residues: 2.5198 Evaluate side-chains 35 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain A residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.185077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.166092 restraints weight = 2948.376| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.81 r_work: 0.4141 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1893 Z= 0.109 Angle : 0.596 6.620 2556 Z= 0.300 Chirality : 0.052 0.148 306 Planarity : 0.003 0.021 330 Dihedral : 4.916 15.647 255 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.86 % Allowed : 36.71 % Favored : 59.42 % 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 aren not related in a simple way. whole: -2.08 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 115 PHE 0.005 0.001 PHE C 45 TRP 0.009 0.002 TRP A 32 HIS 0.001 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 1893) covalent geometry : angle 0.59614 ( 2556) hydrogen bonds : bond 0.02624 ( 24) hydrogen bonds : angle 6.10457 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.074 Fit side-chains REVERT: A 90 ASP cc_start: 0.6189 (m-30) cc_final: 0.5817 (t0) outliers start: 8 outliers final: 6 residues processed: 38 average time/residue: 0.0570 time to fit residues: 2.5625 Evaluate side-chains 37 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain A residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 0.0770 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 0.2980 overall best weight: 1.2278 ------------------------------------------------------------------------------- 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 = 0.4520 r_free = 0.4520 target = 0.187415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.168143 restraints weight = 2966.518| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.83 r_work: 0.4166 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1893 Z= 0.087 Angle : 0.553 6.651 2556 Z= 0.278 Chirality : 0.052 0.147 306 Planarity : 0.003 0.021 330 Dihedral : 4.590 14.203 255 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 2.90 % Allowed : 37.68 % Favored : 59.42 % 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 aren not related in a simple way. whole: -2.05 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 115 PHE 0.004 0.001 PHE C 45 TRP 0.009 0.002 TRP A 32 HIS 0.001 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 1893) covalent geometry : angle 0.55328 ( 2556) hydrogen bonds : bond 0.02181 ( 24) hydrogen bonds : angle 5.93446 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 617.89 seconds wall clock time: 11 minutes 26.51 seconds (686.51 seconds total)