Starting phenix.real_space_refine on Tue Aug 4 11:44:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1t_65556/08_2026/9w1t_65556.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1t_65556/08_2026/9w1t_65556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w1t_65556/08_2026/9w1t_65556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1t_65556/08_2026/9w1t_65556.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w1t_65556/08_2026/9w1t_65556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1t_65556/08_2026/9w1t_65556.map" } resolution = 3.0 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: 3 Type Number sf(0) Gaussians C 912 2.51 5 N 255 2.21 5 O 291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1458 Number of models: 1 Model: "" Number of chains: 2 Chain: "j" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 446 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Restraints were copied for chains: k, l, N, O Time building chain proxies: 0.40, per 1000 atoms: 0.27 Number of scatterers: 1458 At special positions: 0 Unit cell: (68.89, 67.23, 28.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 291 8.00 N 255 7.00 C 912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.10 Conformation dependent library (CDL) restraints added in 37.2 milliseconds 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 378 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'M' and resid 39 through 40 removed outlier: 5.964A pdb=" N TYR N 39 " --> pdb=" O VAL O 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 48 through 52 removed outlier: 6.736A pdb=" N VAL M 52 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL N 49 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL O 52 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY N 51 " --> pdb=" O VAL O 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 55 through 58 removed outlier: 6.240A pdb=" N VAL M 55 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LYS O 58 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU M 57 " --> pdb=" O LYS O 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.587A pdb=" N GLN M 62 " --> pdb=" O VAL O 63 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ASN O 65 " --> pdb=" O GLN M 62 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N THR M 64 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 69 through 71 removed outlier: 6.338A pdb=" N VAL N 70 " --> pdb=" O VAL O 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 77 through 83 removed outlier: 6.470A pdb=" N VAL M 77 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LYS O 80 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N GLN M 79 " --> pdb=" O LYS O 80 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL O 82 " --> pdb=" O GLN M 79 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N THR M 81 " --> pdb=" O VAL O 82 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR O 81 " --> pdb=" O LYS N 80 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL N 82 " --> pdb=" O THR O 81 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU O 83 " --> pdb=" O VAL N 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 91 through 96 removed outlier: 8.933A pdb=" N ALA M 91 " --> pdb=" O THR O 92 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE O 94 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY M 93 " --> pdb=" O PHE O 94 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS O 96 " --> pdb=" O GLY M 93 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL M 95 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA O 91 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR N 92 " --> pdb=" O ALA O 91 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY O 93 " --> pdb=" O THR N 92 " (cutoff:3.500A) 20 hydrogen bonds defined for protein. 60 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.11 Time building geometry restraints manager: 0.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 258 1.29 - 1.36: 231 1.36 - 1.42: 51 1.42 - 1.49: 257 1.49 - 1.55: 664 Bond restraints: 1461 Sorted by residual: bond pdb=" CA LYS O 97 " pdb=" C LYS O 97 " ideal model delta sigma weight residual 1.530 1.518 0.013 1.08e-02 8.57e+03 1.37e+00 bond pdb=" CA LYS M 97 " pdb=" CB LYS M 97 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.27e-02 6.20e+03 1.30e+00 bond pdb=" CA LYS O 97 " pdb=" CB LYS O 97 " ideal model delta sigma weight residual 1.522 1.535 -0.014 1.27e-02 6.20e+03 1.16e+00 bond pdb=" CA LYS N 97 " pdb=" C LYS N 97 " ideal model delta sigma weight residual 1.530 1.519 0.012 1.08e-02 8.57e+03 1.15e+00 bond pdb=" CA LYS M 97 " pdb=" C LYS M 97 " ideal model delta sigma weight residual 1.530 1.519 0.012 1.08e-02 8.57e+03 1.14e+00 ... (remaining 1456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 1703 1.06 - 2.13: 214 2.13 - 3.19: 48 3.19 - 4.26: 9 4.26 - 5.32: 3 Bond angle restraints: 1977 Sorted by residual: angle pdb=" N GLY O 47 " pdb=" CA GLY O 47 " pdb=" C GLY O 47 " ideal model delta sigma weight residual 113.18 107.86 5.32 2.37e+00 1.78e-01 5.05e+00 angle pdb=" N GLY M 47 " pdb=" CA GLY M 47 " pdb=" C GLY M 47 " ideal model delta sigma weight residual 113.18 107.86 5.32 2.37e+00 1.78e-01 5.04e+00 angle pdb=" N GLY N 47 " pdb=" CA GLY N 47 " pdb=" C GLY N 47 " ideal model delta sigma weight residual 113.18 107.92 5.26 2.37e+00 1.78e-01 4.92e+00 angle pdb=" C TYR O 39 " pdb=" N VAL O 40 " pdb=" CA VAL O 40 " ideal model delta sigma weight residual 122.90 120.11 2.79 1.28e+00 6.10e-01 4.77e+00 angle pdb=" C TYR N 39 " pdb=" N VAL N 40 " pdb=" CA VAL N 40 " ideal model delta sigma weight residual 122.90 120.12 2.78 1.28e+00 6.10e-01 4.72e+00 ... (remaining 1972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.67: 693 10.67 - 21.34: 117 21.34 - 32.01: 21 32.01 - 42.68: 24 42.68 - 53.35: 3 Dihedral angle restraints: 858 sinusoidal: 267 harmonic: 591 Sorted by residual: dihedral pdb=" CA GLY N 86 " pdb=" C GLY N 86 " pdb=" N SER N 87 " pdb=" CA SER N 87 " ideal model delta harmonic sigma weight residual -180.00 -166.75 -13.25 0 5.00e+00 4.00e-02 7.02e+00 dihedral pdb=" CA LEU N 100 " pdb=" CB LEU N 100 " pdb=" CG LEU N 100 " pdb=" CD1 LEU N 100 " ideal model delta sinusoidal sigma weight residual 60.00 99.57 -39.57 3 1.50e+01 4.44e-03 7.02e+00 dihedral pdb=" CA LEU M 100 " pdb=" CB LEU M 100 " pdb=" CG LEU M 100 " pdb=" CD1 LEU M 100 " ideal model delta sinusoidal sigma weight residual 60.00 99.56 -39.56 3 1.50e+01 4.44e-03 7.02e+00 ... (remaining 855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 127 0.027 - 0.054: 66 0.054 - 0.081: 36 0.081 - 0.108: 20 0.108 - 0.135: 15 Chirality restraints: 264 Sorted by residual: chirality pdb=" CA VAL N 48 " pdb=" N VAL N 48 " pdb=" C VAL N 48 " pdb=" CB VAL N 48 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL M 48 " pdb=" N VAL M 48 " pdb=" C VAL M 48 " pdb=" CB VAL M 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL O 48 " pdb=" N VAL O 48 " pdb=" C VAL O 48 " pdb=" CB VAL O 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 261 not shown) Planarity restraints: 246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS M 97 " 0.003 2.00e-02 2.50e+03 6.55e-03 4.29e-01 pdb=" C LYS M 97 " -0.011 2.00e-02 2.50e+03 pdb=" O LYS M 97 " 0.004 2.00e-02 2.50e+03 pdb=" N ASP M 98 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS O 97 " 0.003 2.00e-02 2.50e+03 6.41e-03 4.11e-01 pdb=" C LYS O 97 " -0.011 2.00e-02 2.50e+03 pdb=" O LYS O 97 " 0.004 2.00e-02 2.50e+03 pdb=" N ASP O 98 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS N 97 " 0.003 2.00e-02 2.50e+03 6.39e-03 4.08e-01 pdb=" C LYS N 97 " -0.011 2.00e-02 2.50e+03 pdb=" O LYS N 97 " 0.004 2.00e-02 2.50e+03 pdb=" N ASP N 98 " 0.004 2.00e-02 2.50e+03 ... (remaining 243 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.98: 723 2.98 - 3.46: 1267 3.46 - 3.94: 1992 3.94 - 4.42: 2184 4.42 - 4.90: 4859 Nonbonded interactions: 11025 Sorted by model distance: nonbonded pdb=" O TYR N 39 " pdb=" OG SER O 42 " model vdw 2.494 3.040 nonbonded pdb=" O ALA N 53 " pdb=" OG1 THR N 54 " model vdw 2.552 3.040 nonbonded pdb=" O ALA M 53 " pdb=" OG1 THR M 54 " model vdw 2.553 3.040 nonbonded pdb=" O ALA O 53 " pdb=" OG1 THR O 54 " model vdw 2.553 3.040 nonbonded pdb=" ND2 ASN N 65 " pdb=" OD1 ASN O 65 " model vdw 2.592 3.120 ... (remaining 11020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'j' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.510 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 1461 Z= 0.278 Angle : 0.818 5.323 1977 Z= 0.478 Chirality : 0.051 0.135 264 Planarity : 0.002 0.007 246 Dihedral : 13.708 53.353 480 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 15.22 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.44), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.33), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR M 39 PHE 0.010 0.003 PHE M 94 HIS 0.000 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.28 ( 1461) covalent geometry : angle 0.81784 / 0.48 ( 1977) hydrogen bonds : bond 0.17568 / 10.47 ( 20) hydrogen bonds : angle 8.77935 / 4.38 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.054 Fit side-chains REVERT: M 60 LYS cc_start: 0.7615 (mttp) cc_final: 0.6992 (mmmt) REVERT: M 99 GLN cc_start: 0.7721 (mm110) cc_final: 0.7475 (mp10) REVERT: N 60 LYS cc_start: 0.7737 (mttp) cc_final: 0.7219 (mmmt) REVERT: N 92 THR cc_start: 0.8439 (t) cc_final: 0.8174 (t) REVERT: O 60 LYS cc_start: 0.7578 (mttp) cc_final: 0.6914 (mmmt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.5906 time to fit residues: 16.1762 Evaluate side-chains 22 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.140673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.119836 restraints weight = 1508.134| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.26 r_work: 0.3687 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1461 Z= 0.161 Angle : 0.648 4.640 1977 Z= 0.357 Chirality : 0.053 0.138 264 Planarity : 0.002 0.008 246 Dihedral : 5.362 15.021 213 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.90 % Allowed : 18.84 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.48), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.36), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR M 39 PHE 0.008 0.002 PHE O 94 HIS 0.001 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 1461) covalent geometry : angle 0.64821 / 0.36 ( 1977) hydrogen bonds : bond 0.01998 / 1.28 ( 20) hydrogen bonds : angle 6.29883 / 3.21 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.056 Fit side-chains REVERT: M 60 LYS cc_start: 0.7897 (mttp) cc_final: 0.7087 (mmmt) REVERT: M 92 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8060 (t) REVERT: M 99 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7405 (mp10) REVERT: N 60 LYS cc_start: 0.8073 (mttp) cc_final: 0.7462 (mmmt) REVERT: O 60 LYS cc_start: 0.7890 (mttp) cc_final: 0.7132 (mmmt) REVERT: O 92 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.7946 (t) outliers start: 4 outliers final: 1 residues processed: 27 average time/residue: 0.6236 time to fit residues: 17.2770 Evaluate side-chains 21 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 0.0770 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.134977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.116169 restraints weight = 1685.764| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.26 r_work: 0.3699 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1461 Z= 0.114 Angle : 0.595 4.195 1977 Z= 0.331 Chirality : 0.053 0.128 264 Planarity : 0.002 0.013 246 Dihedral : 5.081 14.175 213 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.80 % Allowed : 19.57 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.49), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.37), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR M 39 PHE 0.006 0.002 PHE N 94 HIS 0.001 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 1461) covalent geometry : angle 0.59473 / 0.33 ( 1977) hydrogen bonds : bond 0.01725 / 1.10 ( 20) hydrogen bonds : angle 5.74904 / 2.93 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.054 Fit side-chains REVERT: M 60 LYS cc_start: 0.7844 (mttp) cc_final: 0.6995 (mmmt) REVERT: M 92 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.7985 (t) REVERT: M 99 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7159 (mp10) REVERT: N 60 LYS cc_start: 0.8049 (mttp) cc_final: 0.7399 (mmmt) REVERT: O 60 LYS cc_start: 0.7843 (mttp) cc_final: 0.7082 (mmmt) REVERT: O 92 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7827 (t) outliers start: 8 outliers final: 4 residues processed: 27 average time/residue: 0.5277 time to fit residues: 14.4813 Evaluate side-chains 25 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.0370 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.136433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.117779 restraints weight = 1707.126| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.28 r_work: 0.3773 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1461 Z= 0.107 Angle : 0.546 4.624 1977 Z= 0.301 Chirality : 0.052 0.126 264 Planarity : 0.002 0.013 246 Dihedral : 4.932 13.008 213 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 8.70 % Allowed : 17.39 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.51), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR M 39 PHE 0.006 0.002 PHE N 94 HIS 0.001 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 1461) covalent geometry : angle 0.54573 / 0.30 ( 1977) hydrogen bonds : bond 0.01559 / 0.99 ( 20) hydrogen bonds : angle 5.34604 / 2.71 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.054 Fit side-chains REVERT: M 60 LYS cc_start: 0.7865 (mttp) cc_final: 0.7017 (mmmt) REVERT: M 92 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.7986 (t) REVERT: M 99 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7136 (mp10) REVERT: N 60 LYS cc_start: 0.8085 (mttp) cc_final: 0.7427 (mmmt) REVERT: O 60 LYS cc_start: 0.7863 (mttp) cc_final: 0.7116 (mmmt) REVERT: O 92 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7904 (t) outliers start: 12 outliers final: 7 residues processed: 31 average time/residue: 0.4604 time to fit residues: 14.5358 Evaluate side-chains 29 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 17 optimal weight: 0.0970 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.134034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.115243 restraints weight = 1702.184| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.30 r_work: 0.3713 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1461 Z= 0.163 Angle : 0.662 5.270 1977 Z= 0.365 Chirality : 0.052 0.123 264 Planarity : 0.002 0.009 246 Dihedral : 5.166 13.216 213 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 10.14 % Allowed : 16.67 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.52), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR M 39 PHE 0.010 0.002 PHE N 94 HIS 0.001 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 1461) covalent geometry : angle 0.66224 / 0.37 ( 1977) hydrogen bonds : bond 0.01864 / 1.17 ( 20) hydrogen bonds : angle 5.44391 / 2.74 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.054 Fit side-chains REVERT: M 60 LYS cc_start: 0.7845 (mttp) cc_final: 0.7025 (mmmt) REVERT: M 92 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7928 (t) REVERT: M 99 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7211 (mp10) REVERT: N 60 LYS cc_start: 0.8103 (mttp) cc_final: 0.7443 (mmmt) REVERT: O 60 LYS cc_start: 0.7914 (mttp) cc_final: 0.7144 (mmmt) REVERT: O 79 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8382 (mt0) REVERT: O 92 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7890 (t) outliers start: 14 outliers final: 9 residues processed: 32 average time/residue: 0.4269 time to fit residues: 13.9232 Evaluate side-chains 34 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.0050 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.138897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.120798 restraints weight = 1639.315| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.25 r_work: 0.3772 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1461 Z= 0.092 Angle : 0.543 4.766 1977 Z= 0.303 Chirality : 0.052 0.129 264 Planarity : 0.002 0.013 246 Dihedral : 4.773 12.231 213 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 7.25 % Allowed : 20.29 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.52), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR M 39 PHE 0.005 0.001 PHE O 94 HIS 0.000 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.09 ( 1461) covalent geometry : angle 0.54284 / 0.30 ( 1977) hydrogen bonds : bond 0.01425 / 0.90 ( 20) hydrogen bonds : angle 5.07089 / 2.54 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.050 Fit side-chains REVERT: M 60 LYS cc_start: 0.7880 (mttp) cc_final: 0.7121 (mmmt) REVERT: M 92 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.7927 (t) REVERT: N 60 LYS cc_start: 0.8074 (mttp) cc_final: 0.7455 (mmmt) REVERT: O 60 LYS cc_start: 0.7901 (mttp) cc_final: 0.7219 (mmmt) REVERT: O 92 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7953 (t) outliers start: 10 outliers final: 6 residues processed: 29 average time/residue: 0.4838 time to fit residues: 14.3099 Evaluate side-chains 28 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.135306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.116579 restraints weight = 1707.014| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.34 r_work: 0.3766 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1461 Z= 0.133 Angle : 0.608 5.194 1977 Z= 0.337 Chirality : 0.051 0.119 264 Planarity : 0.003 0.018 246 Dihedral : 4.929 12.905 213 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 7.97 % Allowed : 21.01 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.52), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR M 39 PHE 0.007 0.002 PHE N 94 HIS 0.001 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 1461) covalent geometry : angle 0.60800 / 0.34 ( 1977) hydrogen bonds : bond 0.01608 / 1.00 ( 20) hydrogen bonds : angle 5.19831 / 2.59 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.053 Fit side-chains REVERT: M 60 LYS cc_start: 0.7805 (mttp) cc_final: 0.6969 (mmmt) REVERT: M 92 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7933 (t) REVERT: N 60 LYS cc_start: 0.8091 (mttp) cc_final: 0.7406 (mmmt) REVERT: O 60 LYS cc_start: 0.7860 (mttp) cc_final: 0.7077 (mmmt) REVERT: O 92 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7901 (t) outliers start: 11 outliers final: 8 residues processed: 31 average time/residue: 0.3847 time to fit residues: 12.1909 Evaluate side-chains 31 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 79 GLN ** 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 = 0.4014 r_free = 0.4014 target = 0.135116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.116214 restraints weight = 1676.216| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.41 r_work: 0.3744 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1461 Z= 0.138 Angle : 0.614 5.310 1977 Z= 0.339 Chirality : 0.051 0.122 264 Planarity : 0.003 0.020 246 Dihedral : 4.977 13.137 213 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 8.70 % Allowed : 22.46 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.53), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR M 39 PHE 0.007 0.002 PHE N 94 HIS 0.001 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 1461) covalent geometry : angle 0.61372 / 0.34 ( 1977) hydrogen bonds : bond 0.01674 / 1.03 ( 20) hydrogen bonds : angle 5.26080 / 2.61 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.051 Fit side-chains REVERT: M 60 LYS cc_start: 0.7786 (mttp) cc_final: 0.6945 (mmmt) REVERT: M 92 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7908 (t) REVERT: N 60 LYS cc_start: 0.8058 (mttp) cc_final: 0.7363 (mmmt) REVERT: O 60 LYS cc_start: 0.7843 (mttp) cc_final: 0.7050 (mmmt) REVERT: O 92 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7814 (t) outliers start: 12 outliers final: 8 residues processed: 33 average time/residue: 0.3930 time to fit residues: 13.2402 Evaluate side-chains 31 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 79 GLN N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.141714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.123262 restraints weight = 1618.085| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.29 r_work: 0.3789 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1461 Z= 0.096 Angle : 0.541 5.418 1977 Z= 0.302 Chirality : 0.051 0.126 264 Planarity : 0.003 0.021 246 Dihedral : 4.716 12.155 213 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 10.14 % Allowed : 20.29 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.53), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR M 39 PHE 0.005 0.001 PHE O 94 HIS 0.001 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.10 ( 1461) covalent geometry : angle 0.54075 / 0.30 ( 1977) hydrogen bonds : bond 0.01456 / 0.90 ( 20) hydrogen bonds : angle 5.04051 / 2.49 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 20 time to evaluate : 0.048 Fit side-chains REVERT: M 60 LYS cc_start: 0.7817 (mttp) cc_final: 0.6987 (mmmt) REVERT: M 92 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7853 (t) REVERT: N 60 LYS cc_start: 0.8056 (mttp) cc_final: 0.7353 (mmmt) REVERT: N 99 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.6127 (mp10) REVERT: O 60 LYS cc_start: 0.7831 (mttp) cc_final: 0.7050 (mmmt) REVERT: O 92 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7880 (t) outliers start: 14 outliers final: 8 residues processed: 32 average time/residue: 0.4302 time to fit residues: 14.0269 Evaluate side-chains 31 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.0050 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 79 GLN N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.140819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.122403 restraints weight = 1638.574| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.28 r_work: 0.3780 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1461 Z= 0.126 Angle : 0.581 5.426 1977 Z= 0.322 Chirality : 0.051 0.124 264 Planarity : 0.003 0.019 246 Dihedral : 4.898 12.886 213 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 10.87 % Allowed : 18.84 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.53), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR M 39 PHE 0.007 0.002 PHE N 94 HIS 0.001 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 1461) covalent geometry : angle 0.58081 / 0.32 ( 1977) hydrogen bonds : bond 0.01563 / 0.93 ( 20) hydrogen bonds : angle 5.20031 / 2.57 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 21 time to evaluate : 0.065 Fit side-chains REVERT: M 60 LYS cc_start: 0.7785 (mttp) cc_final: 0.6928 (mmmt) REVERT: M 92 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7899 (t) REVERT: N 60 LYS cc_start: 0.8048 (mttp) cc_final: 0.7376 (mmmt) REVERT: N 99 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.6136 (mp10) REVERT: O 60 LYS cc_start: 0.7877 (mttp) cc_final: 0.7086 (mmmt) REVERT: O 92 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7893 (t) outliers start: 15 outliers final: 9 residues processed: 33 average time/residue: 0.4359 time to fit residues: 14.7206 Evaluate side-chains 33 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 79 GLN M 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.145052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.127133 restraints weight = 1572.870| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.23 r_work: 0.3787 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1461 Z= 0.083 Angle : 0.508 5.444 1977 Z= 0.284 Chirality : 0.051 0.121 264 Planarity : 0.002 0.018 246 Dihedral : 4.609 14.701 213 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 8.70 % Allowed : 20.29 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.54), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR M 39 PHE 0.004 0.001 PHE O 94 HIS 0.001 0.000 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00157 / 0.08 ( 1461) covalent geometry : angle 0.50759 / 0.28 ( 1977) hydrogen bonds : bond 0.01290 / 0.77 ( 20) hydrogen bonds : angle 4.95511 / 2.46 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 859.38 seconds wall clock time: 15 minutes 33.39 seconds (933.39 seconds total)