Starting phenix.real_space_refine on Wed Jun 3 12:06:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9urm_64461/06_2026/9urm_64461.cif Found real_map, /net/cci-nas-00/data/ceres_data/9urm_64461/06_2026/9urm_64461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9urm_64461/06_2026/9urm_64461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9urm_64461/06_2026/9urm_64461.map" model { file = "/net/cci-nas-00/data/ceres_data/9urm_64461/06_2026/9urm_64461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9urm_64461/06_2026/9urm_64461.cif" } resolution = 4.24 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 15 5.16 5 C 2678 2.51 5 N 812 2.21 5 O 1142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4722 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1382 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "C" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "R" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1587 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 66} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.36, per 1000 atoms: 0.29 Number of scatterers: 4722 At special positions: 0 Unit cell: (92.16, 78.72, 127.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 75 15.00 O 1142 8.00 N 812 7.00 C 2678 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: 0.39 Conformation dependent library (CDL) restraints added in 133.7 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 47.2% beta 23 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.686A pdb=" N ILE A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.775A pdb=" N GLN A 145 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.559A pdb=" N TYR A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 178 " --> pdb=" O LYS A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.623A pdb=" N SER B 33 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B 34 " --> pdb=" O PHE B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 34' Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.643A pdb=" N ASP C 29 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.798A pdb=" N ASP C 81 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20 removed outlier: 3.519A pdb=" N LEU A 28 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 72 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 58 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP A 78 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 56 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 126 removed outlier: 6.980A pdb=" N MET A 120 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 135 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY A 122 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 133 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ARG A 133 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA A 171 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS A 160 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 150 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A 99 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 115 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER A 105 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 10 Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.098A pdb=" N ARG B 40 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 14 removed outlier: 4.339A pdb=" N VAL B 117 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 10 Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.847A pdb=" N TRP C 34 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 94 " --> pdb=" O ASP C 91 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1203 1.33 - 1.45: 1331 1.45 - 1.57: 2262 1.57 - 1.69: 148 1.69 - 1.81: 22 Bond restraints: 4966 Sorted by residual: bond pdb=" CA ARG A 84 " pdb=" C ARG A 84 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.24e-02 6.50e+03 1.16e+01 bond pdb=" N LYS C 102 " pdb=" CA LYS C 102 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.21e-02 6.83e+03 4.60e+00 bond pdb=" N LEU C 103 " pdb=" CA LEU C 103 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.21e-02 6.83e+03 4.28e+00 bond pdb=" O5' G R 9 " pdb=" C5' G R 9 " ideal model delta sigma weight residual 1.420 1.451 -0.031 1.50e-02 4.44e+03 4.15e+00 bond pdb=" C ARG A 84 " pdb=" N ASP A 85 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.44e-02 4.82e+03 4.07e+00 ... (remaining 4961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6596 1.71 - 3.41: 377 3.41 - 5.12: 65 5.12 - 6.83: 32 6.83 - 8.54: 9 Bond angle restraints: 7079 Sorted by residual: angle pdb=" O3' A R 6 " pdb=" P C R 7 " pdb=" O5' C R 7 " ideal model delta sigma weight residual 104.00 96.68 7.32 1.50e+00 4.44e-01 2.38e+01 angle pdb=" O3' A R 36 " pdb=" P U R 37 " pdb=" O5' U R 37 " ideal model delta sigma weight residual 104.00 98.30 5.70 1.50e+00 4.44e-01 1.44e+01 angle pdb=" C3' G R 9 " pdb=" C2' G R 9 " pdb=" C1' G R 9 " ideal model delta sigma weight residual 101.30 105.00 -3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" O3' A R 4 " pdb=" P A R 5 " pdb=" O5' A R 5 " ideal model delta sigma weight residual 104.00 98.80 5.20 1.50e+00 4.44e-01 1.20e+01 angle pdb=" O3' U R 14 " pdb=" C3' U R 14 " pdb=" C2' U R 14 " ideal model delta sigma weight residual 113.70 118.22 -4.52 1.50e+00 4.44e-01 9.10e+00 ... (remaining 7074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.91: 2655 22.91 - 45.83: 245 45.83 - 68.74: 135 68.74 - 91.65: 22 91.65 - 114.57: 1 Dihedral angle restraints: 3058 sinusoidal: 1901 harmonic: 1157 Sorted by residual: dihedral pdb=" O4' A R 59 " pdb=" C1' A R 59 " pdb=" N9 A R 59 " pdb=" C4 A R 59 " ideal model delta sinusoidal sigma weight residual 254.00 178.29 75.71 1 1.70e+01 3.46e-03 2.50e+01 dihedral pdb=" O4' U R 60 " pdb=" C1' U R 60 " pdb=" N1 U R 60 " pdb=" C2 U R 60 " ideal model delta sinusoidal sigma weight residual 232.00 178.73 53.27 1 1.70e+01 3.46e-03 1.34e+01 dihedral pdb=" O4' A R 4 " pdb=" C1' A R 4 " pdb=" N9 A R 4 " pdb=" C4 A R 4 " ideal model delta sinusoidal sigma weight residual -106.00 -154.63 48.63 1 1.70e+01 3.46e-03 1.13e+01 ... (remaining 3055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 705 0.110 - 0.219: 119 0.219 - 0.329: 17 0.329 - 0.439: 3 0.439 - 0.548: 13 Chirality restraints: 857 Sorted by residual: chirality pdb=" P C R 25 " pdb=" OP1 C R 25 " pdb=" OP2 C R 25 " pdb=" O5' C R 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.52e+00 chirality pdb=" P G R 9 " pdb=" OP1 G R 9 " pdb=" OP2 G R 9 " pdb=" O5' G R 9 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" P G R 12 " pdb=" OP1 G R 12 " pdb=" OP2 G R 12 " pdb=" O5' G R 12 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 854 not shown) Planarity restraints: 632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C PHE A 83 " -0.067 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 84 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 7 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO C 8 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 8 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 8 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 71 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C GLU A 71 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU A 71 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.010 2.00e-02 2.50e+03 ... (remaining 629 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 851 2.77 - 3.30: 3861 3.30 - 3.84: 7960 3.84 - 4.37: 9539 4.37 - 4.90: 15026 Nonbonded interactions: 37237 Sorted by model distance: nonbonded pdb=" O2' U R 14 " pdb=" OP1 G R 15 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR C 2 " pdb=" O ASP C 25 " model vdw 2.344 3.040 nonbonded pdb=" NH1 ARG B 69 " pdb=" O SER B 87 " model vdw 2.372 3.120 nonbonded pdb=" O SER B 54 " pdb=" NH1 ARG B 74 " model vdw 2.397 3.120 nonbonded pdb=" N ASP B 116 " pdb=" OD1 ASP B 116 " model vdw 2.426 3.120 ... (remaining 37232 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.030 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.300 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3402 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 : 0.006 0.042 4966 Z= 0.357 Angle : 0.949 8.537 7079 Z= 0.491 Chirality : 0.100 0.548 857 Planarity : 0.005 0.064 632 Dihedral : 20.314 114.566 2328 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % 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: 0.18 (0.43), residues: 405 helix: 1.98 (1.79), residues: 11 sheet: 1.08 (0.40), residues: 185 loop : -0.91 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.011 0.001 TYR B 97 PHE 0.011 0.001 PHE B 70 TRP 0.012 0.001 TRP C 90 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.36 ( 4966) covalent geometry : angle 0.94939 / 0.49 ( 7079) hydrogen bonds : bond 0.15143 / 9.37 ( 180) hydrogen bonds : angle 5.77581 / 4.08 ( 429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.144 Fit side-chains 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: 84 average time/residue: 0.1195 time to fit residues: 11.6486 Evaluate side-chains 33 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 145 GLN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN B 41 GLN B 59 ASN B 79 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.132352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.102685 restraints weight = 35277.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.102973 restraints weight = 32877.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.103433 restraints weight = 31698.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.103497 restraints weight = 30893.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.103509 restraints weight = 30633.670| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 4966 Z= 0.226 Angle : 0.736 6.407 7079 Z= 0.388 Chirality : 0.042 0.269 857 Planarity : 0.006 0.055 632 Dihedral : 21.359 122.811 1622 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.29 % Allowed : 3.21 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.40), residues: 405 helix: 2.95 (1.49), residues: 11 sheet: 0.85 (0.38), residues: 179 loop : -1.18 (0.38), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 33 TYR 0.033 0.003 TYR C 35 PHE 0.019 0.003 PHE A 108 TRP 0.022 0.003 TRP B 109 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 ( 4966) covalent geometry : angle 0.73642 / 0.39 ( 7079) hydrogen bonds : bond 0.05461 / 3.47 ( 180) hydrogen bonds : angle 4.85975 / 3.46 ( 429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8275 (mpt180) cc_final: 0.7264 (ptp90) REVERT: A 173 LEU cc_start: 0.6615 (tp) cc_final: 0.6290 (mt) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.1097 time to fit residues: 6.9172 Evaluate side-chains 35 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.111990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.083985 restraints weight = 33014.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.085058 restraints weight = 28977.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.086002 restraints weight = 27109.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.085944 restraints weight = 23099.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.085873 restraints weight = 23585.197| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.9067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 4966 Z= 0.318 Angle : 1.008 12.530 7079 Z= 0.528 Chirality : 0.050 0.299 857 Planarity : 0.008 0.097 632 Dihedral : 22.513 111.138 1622 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 33.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.69 % Favored : 95.06 % Rotamer: Outliers : 0.87 % Allowed : 4.08 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.40), residues: 405 helix: -0.34 (1.40), residues: 17 sheet: 0.03 (0.40), residues: 167 loop : -1.35 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG B 40 TYR 0.027 0.005 TYR B 55 PHE 0.024 0.003 PHE B 31 TRP 0.018 0.004 TRP B 109 HIS 0.010 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.32 ( 4966) covalent geometry : angle 1.00756 / 0.53 ( 7079) hydrogen bonds : bond 0.09358 / 5.96 ( 180) hydrogen bonds : angle 6.58509 / 4.67 ( 429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.140 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: A 166 ARG cc_start: 0.7929 (mpt180) cc_final: 0.6694 (mmp-170) REVERT: B 20 LEU cc_start: 0.9652 (pt) cc_final: 0.9298 (pt) REVERT: B 73 SER cc_start: 0.8299 (t) cc_final: 0.8045 (p) REVERT: B 100 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7669 (ptm160) outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 0.1111 time to fit residues: 6.6377 Evaluate side-chains 35 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.111768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.083708 restraints weight = 32621.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.084595 restraints weight = 29187.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.085436 restraints weight = 26996.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.085404 restraints weight = 23554.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.085404 restraints weight = 23797.674| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 1.0447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4966 Z= 0.239 Angle : 0.821 8.320 7079 Z= 0.424 Chirality : 0.043 0.242 857 Planarity : 0.006 0.071 632 Dihedral : 22.213 99.033 1622 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 27.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.29 % Allowed : 2.92 % Favored : 96.79 % 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: -1.30 (0.41), residues: 405 helix: -1.18 (1.25), residues: 17 sheet: -0.25 (0.40), residues: 168 loop : -1.32 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 100 TYR 0.029 0.004 TYR A 60 PHE 0.017 0.003 PHE B 31 TRP 0.020 0.003 TRP C 90 HIS 0.004 0.002 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.24 ( 4966) covalent geometry : angle 0.82136 / 0.42 ( 7079) hydrogen bonds : bond 0.07323 / 4.60 ( 180) hydrogen bonds : angle 6.26740 / 4.52 ( 429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7384 (mpt180) cc_final: 0.6677 (mmp-170) REVERT: B 73 SER cc_start: 0.9149 (t) cc_final: 0.8915 (p) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1170 time to fit residues: 6.1209 Evaluate side-chains 35 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 7.9990 chunk 23 optimal weight: 0.1980 chunk 2 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.117983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.088703 restraints weight = 32994.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.089274 restraints weight = 29875.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.089251 restraints weight = 27421.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.089251 restraints weight = 27458.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.089251 restraints weight = 27458.857| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 1.0250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4966 Z= 0.126 Angle : 0.643 9.684 7079 Z= 0.324 Chirality : 0.038 0.148 857 Planarity : 0.005 0.052 632 Dihedral : 21.399 95.765 1622 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.29 % Allowed : 2.04 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.42), residues: 405 helix: -0.64 (1.35), residues: 17 sheet: -0.03 (0.41), residues: 168 loop : -1.08 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 21 TYR 0.019 0.002 TYR A 60 PHE 0.016 0.002 PHE A 169 TRP 0.015 0.002 TRP B 118 HIS 0.009 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 4966) covalent geometry : angle 0.64320 / 0.32 ( 7079) hydrogen bonds : bond 0.05533 / 3.54 ( 180) hydrogen bonds : angle 5.52564 / 4.00 ( 429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.7425 (m-10) cc_final: 0.6856 (m-10) REVERT: A 166 ARG cc_start: 0.7396 (mpt180) cc_final: 0.6319 (mmp-170) REVERT: B 86 ASN cc_start: 0.6796 (t0) cc_final: 0.6143 (p0) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.1274 time to fit residues: 7.0560 Evaluate side-chains 38 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.115971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.086729 restraints weight = 33545.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.087454 restraints weight = 29989.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.088276 restraints weight = 28442.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.088253 restraints weight = 24899.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.088252 restraints weight = 25098.754| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 1.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4966 Z= 0.135 Angle : 0.648 7.771 7079 Z= 0.329 Chirality : 0.038 0.152 857 Planarity : 0.005 0.051 632 Dihedral : 21.334 97.145 1622 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: -0.84 (0.42), residues: 405 helix: -0.56 (1.40), residues: 17 sheet: 0.01 (0.42), residues: 160 loop : -0.96 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 21 TYR 0.021 0.002 TYR A 60 PHE 0.015 0.002 PHE A 169 TRP 0.017 0.002 TRP C 90 HIS 0.001 0.000 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 4966) covalent geometry : angle 0.64821 / 0.33 ( 7079) hydrogen bonds : bond 0.05478 / 3.41 ( 180) hydrogen bonds : angle 5.40798 / 3.87 ( 429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7351 (mpt180) cc_final: 0.6596 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1213 time to fit residues: 6.2057 Evaluate side-chains 32 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 17 optimal weight: 0.2980 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.0770 overall best weight: 4.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.106084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.078661 restraints weight = 33766.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.079666 restraints weight = 28778.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.080656 restraints weight = 26180.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.080589 restraints weight = 22039.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.080589 restraints weight = 22482.910| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 1.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 4966 Z= 0.314 Angle : 0.976 12.154 7079 Z= 0.505 Chirality : 0.050 0.244 857 Planarity : 0.007 0.067 632 Dihedral : 22.512 102.371 1622 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 38.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.15 % Favored : 91.60 % Rotamer: Outliers : 0.29 % Allowed : 4.37 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.41), residues: 405 helix: -2.57 (1.06), residues: 17 sheet: -0.19 (0.44), residues: 138 loop : -1.28 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 21 TYR 0.038 0.006 TYR A 60 PHE 0.020 0.003 PHE A 25 TRP 0.025 0.004 TRP C 90 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.31 ( 4966) covalent geometry : angle 0.97648 / 0.50 ( 7079) hydrogen bonds : bond 0.08901 / 5.55 ( 180) hydrogen bonds : angle 6.70697 / 4.79 ( 429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7115 (mpt180) cc_final: 0.6304 (mmp-170) REVERT: B 115 MET cc_start: 0.7679 (tpp) cc_final: 0.7477 (mmm) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1185 time to fit residues: 6.1467 Evaluate side-chains 32 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 42 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.107177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.081654 restraints weight = 36249.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.081654 restraints weight = 38081.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.081654 restraints weight = 38081.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.081654 restraints weight = 38081.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.081654 restraints weight = 38081.274| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 1.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4966 Z= 0.158 Angle : 0.723 9.592 7079 Z= 0.365 Chirality : 0.040 0.161 857 Planarity : 0.005 0.053 632 Dihedral : 21.845 96.455 1622 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.42), residues: 405 helix: -1.37 (1.33), residues: 17 sheet: -0.08 (0.42), residues: 145 loop : -0.96 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 74 TYR 0.029 0.003 TYR A 60 PHE 0.018 0.002 PHE A 169 TRP 0.018 0.002 TRP C 90 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 ( 4966) covalent geometry : angle 0.72339 / 0.37 ( 7079) hydrogen bonds : bond 0.06149 / 3.90 ( 180) hydrogen bonds : angle 5.76508 / 4.13 ( 429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7225 (mpt180) cc_final: 0.6191 (mmp-170) REVERT: B 20 LEU cc_start: 0.9664 (pt) cc_final: 0.9418 (pt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1106 time to fit residues: 6.0264 Evaluate side-chains 34 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.100728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.077478 restraints weight = 36277.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.077478 restraints weight = 36596.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.077478 restraints weight = 36596.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.077478 restraints weight = 36596.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.077478 restraints weight = 36596.031| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 1.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4966 Z= 0.297 Angle : 0.945 9.970 7079 Z= 0.488 Chirality : 0.048 0.267 857 Planarity : 0.007 0.057 632 Dihedral : 22.579 97.157 1622 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 37.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.41), residues: 405 helix: -2.80 (1.07), residues: 17 sheet: -0.54 (0.42), residues: 140 loop : -1.32 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 100 TYR 0.038 0.005 TYR A 60 PHE 0.024 0.004 PHE B 70 TRP 0.025 0.004 TRP C 90 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.30 ( 4966) covalent geometry : angle 0.94473 / 0.49 ( 7079) hydrogen bonds : bond 0.08466 / 5.28 ( 180) hydrogen bonds : angle 6.68414 / 4.82 ( 429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8333 (m-30) cc_final: 0.8116 (m-30) REVERT: B 20 LEU cc_start: 0.9596 (pt) cc_final: 0.9112 (pt) REVERT: B 115 MET cc_start: 0.7021 (mmm) cc_final: 0.6772 (mmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1331 time to fit residues: 6.2395 Evaluate side-chains 35 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.110485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.084037 restraints weight = 32851.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.084321 restraints weight = 29154.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.084931 restraints weight = 27080.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.084911 restraints weight = 23810.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.084911 restraints weight = 23958.732| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 1.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4966 Z= 0.167 Angle : 0.752 8.886 7079 Z= 0.380 Chirality : 0.041 0.205 857 Planarity : 0.005 0.051 632 Dihedral : 22.100 96.600 1622 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.42), residues: 405 helix: -1.78 (1.30), residues: 17 sheet: -0.14 (0.44), residues: 137 loop : -1.22 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 21 TYR 0.029 0.003 TYR A 60 PHE 0.021 0.002 PHE A 169 TRP 0.017 0.002 TRP C 90 HIS 0.002 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 ( 4966) covalent geometry : angle 0.75173 / 0.38 ( 7079) hydrogen bonds : bond 0.06576 / 4.22 ( 180) hydrogen bonds : angle 5.94464 / 4.31 ( 429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8335 (m-30) cc_final: 0.7931 (t70) REVERT: A 166 ARG cc_start: 0.6979 (mmt180) cc_final: 0.5900 (mmp-170) REVERT: B 20 LEU cc_start: 0.9706 (pt) cc_final: 0.9334 (pt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1223 time to fit residues: 6.1764 Evaluate side-chains 36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 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 = 0.4286 r_free = 0.4286 target = 0.122529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.106653 restraints weight = 48381.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.106653 restraints weight = 39142.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.107540 restraints weight = 39141.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.107540 restraints weight = 36932.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.107540 restraints weight = 36932.743| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 1.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 4966 Z= 0.328 Angle : 1.004 10.782 7079 Z= 0.518 Chirality : 0.050 0.326 857 Planarity : 0.007 0.078 632 Dihedral : 22.884 101.536 1622 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 41.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.41), residues: 405 helix: -2.65 (1.14), residues: 17 sheet: -0.93 (0.42), residues: 135 loop : -1.32 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 100 TYR 0.041 0.005 TYR A 60 PHE 0.027 0.004 PHE B 70 TRP 0.033 0.004 TRP C 90 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.33 ( 4966) covalent geometry : angle 1.00355 / 0.52 ( 7079) hydrogen bonds : bond 0.09245 / 5.83 ( 180) hydrogen bonds : angle 7.00115 / 5.09 ( 429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1421.73 seconds wall clock time: 25 minutes 10.43 seconds (1510.43 seconds total)