Starting phenix.real_space_refine on Wed Sep 17 06:36:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rm9_19354/09_2025/8rm9_19354_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rm9_19354/09_2025/8rm9_19354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rm9_19354/09_2025/8rm9_19354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rm9_19354/09_2025/8rm9_19354.map" model { file = "/net/cci-nas-00/data/ceres_data/8rm9_19354/09_2025/8rm9_19354_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rm9_19354/09_2025/8rm9_19354_trim.cif" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 1950 2.51 5 N 570 2.21 5 O 630 1.98 5 H 2935 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 6095 Number of models: 1 Model: "" Number of chains: 6 Chain: "c" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 347 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 513 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 356 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: d, e, f, g, p, r, t, v, q, s, u, w Time building chain proxies: 0.74, per 1000 atoms: 0.12 Number of scatterers: 6095 At special positions: 0 Unit cell: (83.072, 67.584, 45.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 630 8.00 N 570 7.00 C 1950 6.00 H 2935 1.00 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=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 129.2 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'f' and resid 15 through 20 removed outlier: 6.506A pdb=" N LEU d 16 " --> pdb=" O VAL f 17 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N SER f 19 " --> pdb=" O LEU d 16 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS d 18 " --> pdb=" O SER f 19 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU c 16 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER d 19 " --> pdb=" O LEU c 16 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS c 18 " --> pdb=" O SER d 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 't' and resid 7 through 15 removed outlier: 4.639A pdb=" N ALA p 8 " --> pdb=" O ALA t 8 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N GLN t 10 " --> pdb=" O ALA p 8 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN p 10 " --> pdb=" O GLN t 10 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N LEU t 12 " --> pdb=" O GLN p 10 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU p 12 " --> pdb=" O LEU t 12 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASN t 14 " --> pdb=" O LEU p 12 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASN p 14 " --> pdb=" O ASN t 14 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA n 8 " --> pdb=" O ALA p 8 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N GLN p 10 " --> pdb=" O ALA n 8 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN n 10 " --> pdb=" O GLN p 10 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LEU p 12 " --> pdb=" O GLN n 10 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU n 12 " --> pdb=" O LEU p 12 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASN p 14 " --> pdb=" O LEU n 12 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ASN n 14 " --> pdb=" O ASN p 14 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA n 8 " --> pdb=" O ALA r 8 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN r 10 " --> pdb=" O ALA n 8 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN n 10 " --> pdb=" O GLN r 10 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU r 12 " --> pdb=" O GLN n 10 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU n 12 " --> pdb=" O LEU r 12 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASN r 14 " --> pdb=" O LEU n 12 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA r 8 " --> pdb=" O ALA v 8 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN v 10 " --> pdb=" O ALA r 8 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN r 10 " --> pdb=" O GLN v 10 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU v 12 " --> pdb=" O GLN r 10 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU r 12 " --> pdb=" O LEU v 12 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASN v 14 " --> pdb=" O LEU r 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 't' and resid 29 through 30 removed outlier: 6.650A pdb=" N SER n 29 " --> pdb=" O THR r 30 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER r 29 " --> pdb=" O THR v 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 't' and resid 34 through 35 removed outlier: 7.145A pdb=" N SER n 34 " --> pdb=" O ASN r 35 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER r 34 " --> pdb=" O ASN v 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'q' and resid 21 through 22 removed outlier: 3.588A pdb=" N ASN q 22 " --> pdb=" O ASN o 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN o 22 " --> pdb=" O ASN s 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'u' and resid 25 through 26 removed outlier: 6.672A pdb=" N ALA q 25 " --> pdb=" O ILE u 26 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA o 25 " --> pdb=" O ILE q 26 " (cutoff:3.500A) 18 hydrogen bonds defined for protein. 54 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: 1.06 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2935 1.03 - 1.23: 47 1.23 - 1.42: 1393 1.42 - 1.62: 1755 1.62 - 1.81: 10 Bond restraints: 6140 Sorted by residual: bond pdb=" CA ASN d 21 " pdb=" CB ASN d 21 " ideal model delta sigma weight residual 1.529 1.559 -0.030 1.62e-02 3.81e+03 3.37e+00 bond pdb=" CA ASN g 21 " pdb=" CB ASN g 21 " ideal model delta sigma weight residual 1.529 1.558 -0.029 1.62e-02 3.81e+03 3.31e+00 bond pdb=" CA ASN c 21 " pdb=" CB ASN c 21 " ideal model delta sigma weight residual 1.529 1.558 -0.029 1.62e-02 3.81e+03 3.29e+00 bond pdb=" N ASN d 14 " pdb=" CA ASN d 14 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" CA THR v 4 " pdb=" C THR v 4 " ideal model delta sigma weight residual 1.522 1.549 -0.027 1.51e-02 4.39e+03 3.20e+00 ... (remaining 6135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 9488 1.53 - 3.05: 1129 3.05 - 4.58: 221 4.58 - 6.11: 47 6.11 - 7.63: 10 Bond angle restraints: 10895 Sorted by residual: angle pdb=" C SER e 20 " pdb=" N ASN e 21 " pdb=" CA ASN e 21 " ideal model delta sigma weight residual 122.07 126.68 -4.61 1.43e+00 4.89e-01 1.04e+01 angle pdb=" C SER f 20 " pdb=" N ASN f 21 " pdb=" CA ASN f 21 " ideal model delta sigma weight residual 122.07 126.64 -4.57 1.43e+00 4.89e-01 1.02e+01 angle pdb=" C SER d 20 " pdb=" N ASN d 21 " pdb=" CA ASN d 21 " ideal model delta sigma weight residual 122.07 126.63 -4.56 1.43e+00 4.89e-01 1.02e+01 angle pdb=" C SER g 20 " pdb=" N ASN g 21 " pdb=" CA ASN g 21 " ideal model delta sigma weight residual 122.07 126.63 -4.56 1.43e+00 4.89e-01 1.02e+01 angle pdb=" CA ILE u 26 " pdb=" CB ILE u 26 " pdb=" CG1 ILE u 26 " ideal model delta sigma weight residual 110.40 115.78 -5.38 1.70e+00 3.46e-01 1.00e+01 ... (remaining 10890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.41: 2535 14.41 - 28.83: 318 28.83 - 43.24: 103 43.24 - 57.65: 34 57.65 - 72.07: 20 Dihedral angle restraints: 3010 sinusoidal: 1540 harmonic: 1470 Sorted by residual: dihedral pdb=" N ASN c 21 " pdb=" C ASN c 21 " pdb=" CA ASN c 21 " pdb=" CB ASN c 21 " ideal model delta harmonic sigma weight residual 122.80 129.73 -6.93 0 2.50e+00 1.60e-01 7.68e+00 dihedral pdb=" N ASN f 21 " pdb=" C ASN f 21 " pdb=" CA ASN f 21 " pdb=" CB ASN f 21 " ideal model delta harmonic sigma weight residual 122.80 129.66 -6.86 0 2.50e+00 1.60e-01 7.52e+00 dihedral pdb=" N ASN g 21 " pdb=" C ASN g 21 " pdb=" CA ASN g 21 " pdb=" CB ASN g 21 " ideal model delta harmonic sigma weight residual 122.80 129.64 -6.84 0 2.50e+00 1.60e-01 7.48e+00 ... (remaining 3007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 250 0.035 - 0.071: 161 0.071 - 0.106: 61 0.106 - 0.142: 38 0.142 - 0.177: 10 Chirality restraints: 520 Sorted by residual: chirality pdb=" CA ASN c 21 " pdb=" N ASN c 21 " pdb=" C ASN c 21 " pdb=" CB ASN c 21 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ASN f 21 " pdb=" N ASN f 21 " pdb=" C ASN f 21 " pdb=" CB ASN f 21 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA ASN e 21 " pdb=" N ASN e 21 " pdb=" C ASN e 21 " pdb=" CB ASN e 21 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 517 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE c 23 " 0.019 2.00e-02 2.50e+03 1.06e-02 3.39e+00 pdb=" CG PHE c 23 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE c 23 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE c 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE c 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE c 23 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE c 23 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE c 23 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE c 23 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE c 23 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE c 23 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE c 23 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE f 23 " 0.019 2.00e-02 2.50e+03 1.06e-02 3.38e+00 pdb=" CG PHE f 23 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE f 23 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE f 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE f 23 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE f 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE f 23 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE f 23 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE f 23 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE f 23 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE f 23 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE f 23 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE d 23 " 0.019 2.00e-02 2.50e+03 1.06e-02 3.36e+00 pdb=" CG PHE d 23 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE d 23 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE d 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE d 23 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE d 23 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE d 23 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE d 23 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE d 23 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE d 23 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE d 23 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE d 23 " 0.000 2.00e-02 2.50e+03 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1594 2.32 - 2.89: 12972 2.89 - 3.46: 15691 3.46 - 4.03: 22050 4.03 - 4.60: 31459 Nonbonded interactions: 83766 Sorted by model distance: nonbonded pdb=" HG SER o 19 " pdb=" O HIS q 18 " model vdw 1.749 2.450 nonbonded pdb=" H SER o 34 " pdb=" OG SER q 34 " model vdw 1.755 2.450 nonbonded pdb=" O HIS o 18 " pdb=" HG SER s 19 " model vdw 1.764 2.450 nonbonded pdb=" OG SER o 34 " pdb=" H SER s 34 " model vdw 1.769 2.450 nonbonded pdb=" HG SER c 29 " pdb=" O SER e 29 " model vdw 1.787 2.450 ... (remaining 83761 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' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'o' selection = chain 'q' selection = chain 's' selection = chain 'u' selection = chain 'w' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.330 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: 0.040 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5512 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 : 0.009 0.101 3220 Z= 0.753 Angle : 1.223 7.633 4375 Z= 0.730 Chirality : 0.059 0.177 520 Planarity : 0.006 0.033 575 Dihedral : 12.327 50.758 1035 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % 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: -4.54 (0.28), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.21), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG r 11 TYR 0.007 0.002 TYR v 37 PHE 0.031 0.006 PHE c 23 HIS 0.005 0.002 HIS d 18 Details of bonding type rmsd covalent geometry : bond 0.00642 ( 3205) covalent geometry : angle 1.22315 ( 4375) hydrogen bonds : bond 0.21193 ( 18) hydrogen bonds : angle 11.55934 ( 54) Misc. bond : bond 0.10037 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 20 SER cc_start: 0.7297 (t) cc_final: 0.6806 (t) REVERT: n 26 ILE cc_start: 0.7617 (mm) cc_final: 0.7270 (tp) REVERT: o 28 PRO cc_start: 0.7250 (Cg_exo) cc_final: 0.6973 (Cg_endo) REVERT: p 9 THR cc_start: 0.6716 (t) cc_final: 0.6460 (p) REVERT: p 26 ILE cc_start: 0.7530 (mm) cc_final: 0.7307 (tp) REVERT: r 11 ARG cc_start: 0.6854 (mtp180) cc_final: 0.6304 (tpp80) REVERT: r 15 PHE cc_start: 0.6873 (t80) cc_final: 0.5914 (t80) REVERT: r 26 ILE cc_start: 0.7619 (mm) cc_final: 0.7299 (tp) REVERT: v 4 THR cc_start: 0.7294 (m) cc_final: 0.7030 (m) REVERT: v 9 THR cc_start: 0.7029 (t) cc_final: 0.6629 (p) REVERT: v 11 ARG cc_start: 0.6790 (mtp180) cc_final: 0.6002 (ttm-80) REVERT: v 18 HIS cc_start: 0.6825 (t-90) cc_final: 0.6580 (t-90) REVERT: w 14 ASN cc_start: 0.7644 (p0) cc_final: 0.5694 (m-40) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0706 time to fit residues: 12.8037 Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.0270 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 31 ASN d 31 ASN e 31 ASN g 18 HIS g 31 ASN ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.201712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.182420 restraints weight = 13768.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.186960 restraints weight = 5250.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.190038 restraints weight = 2715.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.191654 restraints weight = 1544.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.192961 restraints weight = 1069.885| |-----------------------------------------------------------------------------| r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3220 Z= 0.139 Angle : 0.601 4.719 4375 Z= 0.336 Chirality : 0.047 0.157 520 Planarity : 0.003 0.028 575 Dihedral : 4.528 15.953 430 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.28 % Allowed : 4.17 % Favored : 95.56 % 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: -4.23 (0.30), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.23), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG v 11 TYR 0.006 0.002 TYR o 37 PHE 0.030 0.003 PHE v 23 HIS 0.003 0.001 HIS o 18 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3205) covalent geometry : angle 0.60118 ( 4375) hydrogen bonds : bond 0.05791 ( 18) hydrogen bonds : angle 9.85574 ( 54) Misc. bond : bond 0.00077 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 11 ARG cc_start: 0.6770 (mtp180) cc_final: 0.6367 (tpp80) REVERT: v 11 ARG cc_start: 0.6728 (mtp180) cc_final: 0.5469 (mmp-170) REVERT: w 14 ASN cc_start: 0.7666 (p0) cc_final: 0.5788 (m-40) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.0711 time to fit residues: 9.3821 Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 0 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 31 ASN g 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.193622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.175817 restraints weight = 14079.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.180496 restraints weight = 5682.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.183112 restraints weight = 2964.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.185065 restraints weight = 1892.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.186147 restraints weight = 1284.032| |-----------------------------------------------------------------------------| r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3220 Z= 0.175 Angle : 0.612 5.792 4375 Z= 0.337 Chirality : 0.049 0.184 520 Planarity : 0.004 0.037 575 Dihedral : 4.885 19.423 430 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -4.35 (0.29), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.22), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG v 11 TYR 0.009 0.002 TYR s 37 PHE 0.030 0.003 PHE v 23 HIS 0.004 0.001 HIS r 18 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 3205) covalent geometry : angle 0.61162 ( 4375) hydrogen bonds : bond 0.04337 ( 18) hydrogen bonds : angle 9.39574 ( 54) Misc. bond : bond 0.00029 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 11 ARG cc_start: 0.6793 (mtp180) cc_final: 0.6352 (tpp80) REVERT: v 9 THR cc_start: 0.6808 (m) cc_final: 0.6480 (p) REVERT: v 11 ARG cc_start: 0.6720 (mtp180) cc_final: 0.6322 (ttm-80) REVERT: w 14 ASN cc_start: 0.7881 (p0) cc_final: 0.6062 (m-40) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0759 time to fit residues: 8.4258 Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.4583 r_free = 0.4583 target = 0.186275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.165875 restraints weight = 14009.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.170422 restraints weight = 5535.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.173193 restraints weight = 2822.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.175115 restraints weight = 1750.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.176030 restraints weight = 1198.462| |-----------------------------------------------------------------------------| r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3220 Z= 0.199 Angle : 0.609 5.176 4375 Z= 0.337 Chirality : 0.047 0.157 520 Planarity : 0.004 0.040 575 Dihedral : 5.563 30.747 430 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.62 (0.26), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.20), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG v 11 TYR 0.009 0.002 TYR q 37 PHE 0.023 0.003 PHE v 23 HIS 0.006 0.002 HIS q 18 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 3205) covalent geometry : angle 0.60928 ( 4375) hydrogen bonds : bond 0.03442 ( 18) hydrogen bonds : angle 8.61251 ( 54) Misc. bond : bond 0.00031 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 11 ARG cc_start: 0.6525 (mtp180) cc_final: 0.6312 (ttm170) REVERT: p 15 PHE cc_start: 0.6211 (t80) cc_final: 0.5927 (t80) REVERT: r 11 ARG cc_start: 0.6857 (mtp180) cc_final: 0.6544 (tpp80) REVERT: v 9 THR cc_start: 0.7029 (m) cc_final: 0.6729 (p) REVERT: v 11 ARG cc_start: 0.6850 (mtp180) cc_final: 0.5598 (mmp-170) REVERT: w 14 ASN cc_start: 0.7907 (p0) cc_final: 0.6219 (m-40) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0881 time to fit residues: 9.5118 Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.184072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.162324 restraints weight = 14081.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.167288 restraints weight = 5537.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.170372 restraints weight = 2785.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.172210 restraints weight = 1671.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.173318 restraints weight = 1161.180| |-----------------------------------------------------------------------------| r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3220 Z= 0.197 Angle : 0.600 4.472 4375 Z= 0.334 Chirality : 0.046 0.155 520 Planarity : 0.005 0.059 575 Dihedral : 5.704 29.244 430 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: -4.78 (0.26), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.20), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG v 11 TYR 0.011 0.002 TYR t 37 PHE 0.021 0.003 PHE v 23 HIS 0.005 0.001 HIS p 18 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 3205) covalent geometry : angle 0.59952 ( 4375) hydrogen bonds : bond 0.03609 ( 18) hydrogen bonds : angle 8.65645 ( 54) Misc. bond : bond 0.00046 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 11 ARG cc_start: 0.6611 (mtp180) cc_final: 0.6356 (ttm170) REVERT: v 9 THR cc_start: 0.7108 (m) cc_final: 0.6863 (p) REVERT: v 11 ARG cc_start: 0.6941 (mtp180) cc_final: 0.5566 (tpp-160) REVERT: w 14 ASN cc_start: 0.7926 (p0) cc_final: 0.6223 (m-40) REVERT: w 15 PHE cc_start: 0.5511 (p90) cc_final: 0.5119 (p90) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0911 time to fit residues: 10.1967 Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.178639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.158606 restraints weight = 14348.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.163248 restraints weight = 5833.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.166265 restraints weight = 3047.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.168092 restraints weight = 1890.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.169210 restraints weight = 1355.584| |-----------------------------------------------------------------------------| r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3220 Z= 0.168 Angle : 0.547 4.010 4375 Z= 0.310 Chirality : 0.045 0.141 520 Planarity : 0.004 0.047 575 Dihedral : 5.489 27.628 430 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: -4.85 (0.26), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.20), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG n 11 TYR 0.012 0.002 TYR t 37 PHE 0.019 0.003 PHE n 23 HIS 0.004 0.001 HIS o 18 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3205) covalent geometry : angle 0.54698 ( 4375) hydrogen bonds : bond 0.03215 ( 18) hydrogen bonds : angle 8.31113 ( 54) Misc. bond : bond 0.00034 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: q 23 PHE cc_start: 0.8240 (m-80) cc_final: 0.8037 (m-80) REVERT: v 9 THR cc_start: 0.7084 (m) cc_final: 0.6841 (p) REVERT: v 11 ARG cc_start: 0.6844 (mtp180) cc_final: 0.5650 (tpp-160) REVERT: w 14 ASN cc_start: 0.7979 (p0) cc_final: 0.6259 (m-40) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0947 time to fit residues: 10.5397 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.179969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.160208 restraints weight = 14774.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.164498 restraints weight = 5963.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.167274 restraints weight = 3137.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.169024 restraints weight = 1969.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.170215 restraints weight = 1409.653| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3220 Z= 0.147 Angle : 0.539 4.236 4375 Z= 0.304 Chirality : 0.045 0.153 520 Planarity : 0.005 0.052 575 Dihedral : 5.359 27.932 430 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 0.28 % Allowed : 2.22 % Favored : 97.50 % 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: -4.77 (0.27), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.21), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG v 11 TYR 0.010 0.001 TYR t 37 PHE 0.018 0.002 PHE n 23 HIS 0.003 0.001 HIS s 18 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3205) covalent geometry : angle 0.53894 ( 4375) hydrogen bonds : bond 0.03137 ( 18) hydrogen bonds : angle 8.04267 ( 54) Misc. bond : bond 0.00026 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 9 THR cc_start: 0.7054 (m) cc_final: 0.6821 (p) REVERT: v 11 ARG cc_start: 0.6857 (mtp180) cc_final: 0.5695 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.0937 time to fit residues: 9.5882 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 18 HIS ** t 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.183890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.161812 restraints weight = 14286.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.166355 restraints weight = 5356.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.169168 restraints weight = 2655.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.170796 restraints weight = 1611.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.171938 restraints weight = 1140.724| |-----------------------------------------------------------------------------| r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.7309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3220 Z= 0.160 Angle : 0.543 3.829 4375 Z= 0.311 Chirality : 0.044 0.155 520 Planarity : 0.005 0.046 575 Dihedral : 5.487 28.050 430 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer: Outliers : 0.28 % Allowed : 1.67 % Favored : 98.06 % 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: -4.88 (0.27), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.20), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG n 11 TYR 0.013 0.002 TYR t 37 PHE 0.019 0.002 PHE n 23 HIS 0.004 0.001 HIS o 18 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3205) covalent geometry : angle 0.54336 ( 4375) hydrogen bonds : bond 0.02927 ( 18) hydrogen bonds : angle 7.85235 ( 54) Misc. bond : bond 0.00036 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 11 ARG cc_start: 0.5964 (tpp80) cc_final: 0.5657 (tpp80) REVERT: v 9 THR cc_start: 0.7042 (m) cc_final: 0.6787 (p) REVERT: v 11 ARG cc_start: 0.6922 (mtp180) cc_final: 0.5638 (tpp-160) REVERT: w 14 ASN cc_start: 0.7885 (p0) cc_final: 0.6097 (m-40) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.0904 time to fit residues: 9.3004 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 18 HIS e 22 ASN ** t 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.179089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.158025 restraints weight = 14896.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.162342 restraints weight = 6037.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.165208 restraints weight = 3201.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.166909 restraints weight = 2029.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.167998 restraints weight = 1469.598| |-----------------------------------------------------------------------------| r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.7381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3220 Z= 0.145 Angle : 0.528 3.921 4375 Z= 0.304 Chirality : 0.044 0.153 520 Planarity : 0.005 0.041 575 Dihedral : 5.387 26.888 430 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 0.28 % Allowed : 1.11 % Favored : 98.61 % 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: -4.89 (0.27), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.20), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG n 11 TYR 0.006 0.001 TYR q 37 PHE 0.019 0.003 PHE n 23 HIS 0.003 0.001 HIS o 18 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3205) covalent geometry : angle 0.52831 ( 4375) hydrogen bonds : bond 0.02867 ( 18) hydrogen bonds : angle 7.71739 ( 54) Misc. bond : bond 0.00028 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 9 THR cc_start: 0.7036 (m) cc_final: 0.6802 (p) REVERT: v 11 ARG cc_start: 0.6921 (mtp180) cc_final: 0.5634 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1007 time to fit residues: 9.6467 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 14 ASN ** t 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.179656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.158790 restraints weight = 14710.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.163322 restraints weight = 5822.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.166252 restraints weight = 3033.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.168062 restraints weight = 1898.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.169234 restraints weight = 1356.910| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3220 Z= 0.113 Angle : 0.511 3.905 4375 Z= 0.291 Chirality : 0.044 0.144 520 Planarity : 0.005 0.040 575 Dihedral : 5.143 26.875 430 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 0.28 % Allowed : 0.83 % Favored : 98.89 % 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: -4.83 (0.27), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.21), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG t 11 TYR 0.006 0.001 TYR c 37 PHE 0.021 0.002 PHE n 23 HIS 0.002 0.000 HIS n 18 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3205) covalent geometry : angle 0.51096 ( 4375) hydrogen bonds : bond 0.02583 ( 18) hydrogen bonds : angle 7.28582 ( 54) Misc. bond : bond 0.00016 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 11 ARG cc_start: 0.6178 (ttm170) cc_final: 0.5562 (tpp80) REVERT: v 9 THR cc_start: 0.7015 (m) cc_final: 0.6813 (p) REVERT: v 11 ARG cc_start: 0.6963 (mtp180) cc_final: 0.5460 (mmp80) REVERT: w 14 ASN cc_start: 0.7870 (p0) cc_final: 0.6126 (m-40) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1053 time to fit residues: 10.6472 Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 0.0470 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.179967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.159206 restraints weight = 14760.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.163597 restraints weight = 5870.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.166655 restraints weight = 3107.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.168245 restraints weight = 1920.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.169467 restraints weight = 1408.641| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3220 Z= 0.122 Angle : 0.505 4.122 4375 Z= 0.288 Chirality : 0.044 0.144 520 Planarity : 0.005 0.041 575 Dihedral : 5.104 25.841 430 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -4.86 (0.27), residues: 395 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.20), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG r 11 TYR 0.005 0.001 TYR q 37 PHE 0.026 0.003 PHE s 23 HIS 0.002 0.001 HIS o 18 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3205) covalent geometry : angle 0.50512 ( 4375) hydrogen bonds : bond 0.02520 ( 18) hydrogen bonds : angle 7.24390 ( 54) Misc. bond : bond 0.00022 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.41 seconds wall clock time: 29 minutes 37.13 seconds (1777.13 seconds total)