Starting phenix.real_space_refine on Thu Mar 13 02:26:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j89_6123/03_2025/3j89_6123.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j89_6123/03_2025/3j89_6123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j89_6123/03_2025/3j89_6123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j89_6123/03_2025/3j89_6123.map" model { file = "/net/cci-nas-00/data/ceres_data/3j89_6123/03_2025/3j89_6123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j89_6123/03_2025/3j89_6123.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.047 sd= 0.273 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 C 2755 2.51 5 N 855 2.21 5 O 817 1.98 5 H 4598 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9025 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R Time building chain proxies: 1.96, per 1000 atoms: 0.22 Number of scatterers: 9025 At special positions: 0 Unit cell: (90.78, 90.78, 67.32, 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) O 817 8.00 N 855 7.00 C 2755 6.00 H 4598 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=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 668.2 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 96.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.543A pdb=" N ALA A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA J 7 " --> pdb=" O ARG J 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA K 7 " --> pdb=" O ARG K 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA O 7 " --> pdb=" O ARG O 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA P 7 " --> pdb=" O ARG P 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA Q 7 " --> pdb=" O ARG Q 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA R 7 " --> pdb=" O ARG R 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA S 7 " --> pdb=" O ARG S 3 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1314 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: 3.06 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.08: 1102 1.08 - 1.19: 3496 1.19 - 1.31: 928 1.31 - 1.43: 1005 1.43 - 1.54: 2513 Bond restraints: 9044 Sorted by residual: bond pdb=" N ALA P 7 " pdb=" H ALA P 7 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.39e+01 bond pdb=" N ALA D 7 " pdb=" H ALA D 7 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" N ALA J 7 " pdb=" H ALA J 7 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.35e+01 bond pdb=" N ALA E 7 " pdb=" H ALA E 7 " ideal model delta sigma weight residual 0.860 1.031 -0.171 2.00e-02 2.50e+03 7.35e+01 bond pdb=" N ALA F 7 " pdb=" H ALA F 7 " ideal model delta sigma weight residual 0.860 1.031 -0.171 2.00e-02 2.50e+03 7.35e+01 ... (remaining 9039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 12390 1.65 - 3.30: 2619 3.30 - 4.95: 588 4.95 - 6.60: 648 6.60 - 8.25: 95 Bond angle restraints: 16340 Sorted by residual: angle pdb=" N ILE R 4 " pdb=" CA ILE R 4 " pdb=" C ILE R 4 " ideal model delta sigma weight residual 112.83 108.63 4.20 9.90e-01 1.02e+00 1.80e+01 angle pdb=" N ILE C 4 " pdb=" CA ILE C 4 " pdb=" C ILE C 4 " ideal model delta sigma weight residual 112.83 108.67 4.16 9.90e-01 1.02e+00 1.76e+01 angle pdb=" N ILE Q 4 " pdb=" CA ILE Q 4 " pdb=" C ILE Q 4 " ideal model delta sigma weight residual 112.83 108.70 4.13 9.90e-01 1.02e+00 1.74e+01 angle pdb=" N ILE H 4 " pdb=" CA ILE H 4 " pdb=" C ILE H 4 " ideal model delta sigma weight residual 112.83 108.70 4.13 9.90e-01 1.02e+00 1.74e+01 angle pdb=" N ILE K 4 " pdb=" CA ILE K 4 " pdb=" C ILE K 4 " ideal model delta sigma weight residual 112.83 108.71 4.12 9.90e-01 1.02e+00 1.73e+01 ... (remaining 16335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.65: 3769 11.65 - 23.30: 221 23.30 - 34.95: 38 34.95 - 46.59: 19 46.59 - 58.24: 19 Dihedral angle restraints: 4066 sinusoidal: 2280 harmonic: 1786 Sorted by residual: dihedral pdb=" CA ILE C 4 " pdb=" C ILE C 4 " pdb=" N LEU C 5 " pdb=" CA LEU C 5 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE F 4 " pdb=" C ILE F 4 " pdb=" N LEU F 5 " pdb=" CA LEU F 5 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE O 4 " pdb=" C ILE O 4 " pdb=" N LEU O 5 " pdb=" CA LEU O 5 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 119 0.040 - 0.079: 197 0.079 - 0.118: 208 0.118 - 0.157: 109 0.157 - 0.197: 70 Chirality restraints: 703 Sorted by residual: chirality pdb=" CA GLU N 10 " pdb=" N GLU N 10 " pdb=" C GLU N 10 " pdb=" CB GLU N 10 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA GLU B 10 " pdb=" N GLU B 10 " pdb=" C GLU B 10 " pdb=" CB GLU B 10 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA GLU O 10 " pdb=" N GLU O 10 " pdb=" C GLU O 10 " pdb=" CB GLU O 10 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 700 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 22 " 0.020 2.00e-02 2.50e+03 3.11e-02 2.18e+01 pdb=" CG HIS E 22 " 0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS E 22 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS E 22 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS E 22 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS E 22 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 HIS E 22 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 HIS E 22 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 HIS E 22 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 22 " 0.020 2.00e-02 2.50e+03 3.10e-02 2.17e+01 pdb=" CG HIS H 22 " 0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS H 22 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 HIS H 22 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS H 22 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS H 22 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 HIS H 22 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 HIS H 22 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 HIS H 22 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 22 " -0.019 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" CG HIS R 22 " -0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS R 22 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS R 22 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS R 22 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS R 22 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 HIS R 22 " 0.070 2.00e-02 2.50e+03 pdb=" HD2 HIS R 22 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 HIS R 22 " -0.018 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.29: 1304 2.29 - 2.84: 20083 2.84 - 3.40: 22086 3.40 - 3.95: 29734 3.95 - 4.50: 42641 Nonbonded interactions: 115848 Sorted by model distance: nonbonded pdb="HH22 ARG H 3 " pdb=" OE1 GLU H 6 " model vdw 1.738 2.450 nonbonded pdb="HH22 ARG S 3 " pdb=" OE1 GLU S 6 " model vdw 1.738 2.450 nonbonded pdb="HH22 ARG Q 3 " pdb=" OE1 GLU Q 6 " model vdw 1.738 2.450 nonbonded pdb="HH22 ARG N 3 " pdb=" OE1 GLU N 6 " model vdw 1.738 2.450 nonbonded pdb="HH22 ARG M 3 " pdb=" OE1 GLU M 6 " model vdw 1.738 2.450 ... (remaining 115843 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' } 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: 0.070 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: 0.170 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 19.480 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 : 0.022 0.065 4446 Z= 1.471 Angle : 1.639 5.689 5985 Z= 1.159 Chirality : 0.101 0.197 703 Planarity : 0.010 0.046 798 Dihedral : 11.967 58.243 1710 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.29), residues: 513 helix: -0.44 (0.18), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 22 TYR 0.015 0.006 TYR F 15 ARG 0.003 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.652 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.6353 time to fit residues: 102.5726 Evaluate side-chains 75 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093086 restraints weight = 28731.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096313 restraints weight = 14110.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098301 restraints weight = 9677.680| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4446 Z= 0.341 Angle : 0.675 5.492 5985 Z= 0.374 Chirality : 0.029 0.086 703 Planarity : 0.007 0.042 798 Dihedral : 4.874 16.651 646 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 2.51 % Allowed : 13.03 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.34), residues: 513 helix: 1.87 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 22 TYR 0.014 0.003 TYR E 15 ARG 0.008 0.002 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.639 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7469 (tt0) cc_final: 0.6905 (tt0) REVERT: D 24 GLU cc_start: 0.7949 (tt0) cc_final: 0.7641 (tt0) REVERT: E 10 GLU cc_start: 0.8244 (tt0) cc_final: 0.7978 (tt0) REVERT: J 10 GLU cc_start: 0.8512 (tt0) cc_final: 0.8271 (mt-10) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.7067 time to fit residues: 104.1262 Evaluate side-chains 110 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain N residue 8 ASP Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 26 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.111336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.090277 restraints weight = 29919.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093442 restraints weight = 14743.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095444 restraints weight = 10160.115| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4446 Z= 0.289 Angle : 0.568 4.878 5985 Z= 0.332 Chirality : 0.030 0.088 703 Planarity : 0.005 0.033 798 Dihedral : 4.647 16.722 646 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.01 % Allowed : 20.55 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.34), residues: 513 helix: 1.84 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS P 22 TYR 0.018 0.004 TYR M 15 ARG 0.005 0.001 ARG I 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.915 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: B 20 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7803 (mt-10) REVERT: I 10 GLU cc_start: 0.8419 (tt0) cc_final: 0.8153 (mt-10) outliers start: 16 outliers final: 11 residues processed: 115 average time/residue: 0.6795 time to fit residues: 88.6920 Evaluate side-chains 104 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.110848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089311 restraints weight = 29463.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092589 restraints weight = 14735.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094641 restraints weight = 10167.720| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4446 Z= 0.253 Angle : 0.517 4.278 5985 Z= 0.304 Chirality : 0.029 0.105 703 Planarity : 0.006 0.044 798 Dihedral : 4.445 17.322 646 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 5.01 % Allowed : 21.55 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.34), residues: 513 helix: 1.98 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS P 22 TYR 0.016 0.004 TYR M 15 ARG 0.005 0.001 ARG M 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 10 GLU cc_start: 0.8312 (tt0) cc_final: 0.8065 (mt-10) outliers start: 20 outliers final: 18 residues processed: 102 average time/residue: 0.7034 time to fit residues: 81.6826 Evaluate side-chains 107 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.4788 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.110379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088780 restraints weight = 29480.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091989 restraints weight = 14852.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094021 restraints weight = 10306.497| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4446 Z= 0.267 Angle : 0.515 4.553 5985 Z= 0.307 Chirality : 0.029 0.094 703 Planarity : 0.006 0.035 798 Dihedral : 4.494 18.784 646 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 5.01 % Allowed : 21.55 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.34), residues: 513 helix: 1.97 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS P 22 TYR 0.017 0.004 TYR M 15 ARG 0.005 0.001 ARG S 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.653 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: symmetry clash REVERT: I 10 GLU cc_start: 0.8333 (tt0) cc_final: 0.8112 (mt-10) outliers start: 20 outliers final: 18 residues processed: 96 average time/residue: 0.6997 time to fit residues: 75.8190 Evaluate side-chains 106 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 4 optimal weight: 10.9990 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.110897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088958 restraints weight = 29392.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.092309 restraints weight = 14821.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094370 restraints weight = 10256.530| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4446 Z= 0.240 Angle : 0.489 4.406 5985 Z= 0.290 Chirality : 0.029 0.129 703 Planarity : 0.006 0.050 798 Dihedral : 4.360 19.418 646 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 5.26 % Allowed : 21.80 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.34), residues: 513 helix: 2.16 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 22 TYR 0.014 0.004 TYR M 15 ARG 0.008 0.001 ARG P 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 10 GLU cc_start: 0.8338 (tt0) cc_final: 0.8131 (mt-10) REVERT: I 24 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7705 (tm-30) outliers start: 21 outliers final: 20 residues processed: 98 average time/residue: 0.7117 time to fit residues: 79.3062 Evaluate side-chains 111 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.110194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088053 restraints weight = 29827.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.091502 restraints weight = 14722.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093566 restraints weight = 10128.646| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4446 Z= 0.293 Angle : 0.534 5.120 5985 Z= 0.318 Chirality : 0.029 0.089 703 Planarity : 0.006 0.035 798 Dihedral : 4.504 21.528 646 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.76 % Allowed : 23.81 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.34), residues: 513 helix: 1.82 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS P 22 TYR 0.017 0.004 TYR M 15 ARG 0.007 0.001 ARG P 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 24 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7685 (tt0) outliers start: 19 outliers final: 16 residues processed: 93 average time/residue: 0.8643 time to fit residues: 91.6617 Evaluate side-chains 102 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.112369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.089890 restraints weight = 29617.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093392 restraints weight = 14635.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.095495 restraints weight = 9992.956| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 4446 Z= 0.167 Angle : 0.429 4.071 5985 Z= 0.256 Chirality : 0.028 0.145 703 Planarity : 0.004 0.042 798 Dihedral : 3.989 17.953 646 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.01 % Allowed : 24.56 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.34), residues: 513 helix: 2.51 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS P 22 TYR 0.010 0.003 TYR M 15 ARG 0.006 0.000 ARG P 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 15 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: I 24 GLU cc_start: 0.8068 (tt0) cc_final: 0.7850 (tm-30) outliers start: 16 outliers final: 14 residues processed: 108 average time/residue: 0.6999 time to fit residues: 86.8107 Evaluate side-chains 110 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.089229 restraints weight = 29523.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.092679 restraints weight = 14781.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094722 restraints weight = 10167.509| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4446 Z= 0.222 Angle : 0.479 4.011 5985 Z= 0.285 Chirality : 0.028 0.111 703 Planarity : 0.005 0.034 798 Dihedral : 4.265 26.102 646 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.76 % Allowed : 25.06 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.34), residues: 513 helix: 2.31 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 22 TYR 0.013 0.003 TYR M 15 ARG 0.006 0.001 ARG P 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 15 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7016 (m-80) outliers start: 15 outliers final: 14 residues processed: 98 average time/residue: 0.7209 time to fit residues: 80.4518 Evaluate side-chains 105 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087981 restraints weight = 28700.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.091297 restraints weight = 14381.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093316 restraints weight = 10034.727| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4446 Z= 0.285 Angle : 0.531 4.790 5985 Z= 0.316 Chirality : 0.030 0.126 703 Planarity : 0.006 0.032 798 Dihedral : 4.467 28.043 646 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.01 % Allowed : 24.56 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.34), residues: 513 helix: 1.98 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS P 22 TYR 0.015 0.004 TYR K 15 ARG 0.007 0.001 ARG M 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 15 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.6974 (m-80) outliers start: 16 outliers final: 15 residues processed: 95 average time/residue: 0.8192 time to fit residues: 88.9434 Evaluate side-chains 104 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.112245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.088709 restraints weight = 28700.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.092113 restraints weight = 14219.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.094160 restraints weight = 9916.011| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.6648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4446 Z= 0.209 Angle : 0.467 3.859 5985 Z= 0.278 Chirality : 0.028 0.123 703 Planarity : 0.005 0.034 798 Dihedral : 4.188 24.751 646 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 4.01 % Allowed : 24.81 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.34), residues: 513 helix: 2.27 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS P 22 TYR 0.012 0.003 TYR M 15 ARG 0.005 0.001 ARG M 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.58 seconds wall clock time: 54 minutes 19.13 seconds (3259.13 seconds total)