Starting phenix.real_space_refine on Wed Sep 17 05:12:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9udi_64070/09_2025/9udi_64070_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9udi_64070/09_2025/9udi_64070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9udi_64070/09_2025/9udi_64070_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9udi_64070/09_2025/9udi_64070_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9udi_64070/09_2025/9udi_64070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9udi_64070/09_2025/9udi_64070.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.105 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 139 5.49 5 S 2 5.16 5 C 2624 2.51 5 N 925 2.21 5 O 1296 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4986 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2025 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 247} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "R" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 2266 Inner-chain residues flagged as termini: ['pdbres=" A R-152 "'] Classifications: {'RNA': 106} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 1, 'rna3p_pur': 54, 'rna3p_pyr': 46} Link IDs: {'rna2p': 6, 'rna3p': 99} Chain breaks: 3 Time building chain proxies: 1.38, per 1000 atoms: 0.28 Number of scatterers: 4986 At special positions: 0 Unit cell: (83.52, 99.84, 90.24, 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 2 16.00 P 139 15.00 O 1296 8.00 N 925 7.00 C 2624 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: 0.47 Conformation dependent library (CDL) restraints added in 54.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 484 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 46.7% alpha, 11.7% beta 40 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 22 through 61 removed outlier: 3.866A pdb=" N ALA A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 78 removed outlier: 4.149A pdb=" N ILE A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 138 through 161 removed outlier: 3.690A pdb=" N GLY A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 removed outlier: 3.685A pdb=" N GLN A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 3.594A pdb=" N LEU A 263 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER A 248 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS A 265 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE A 246 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 100 hydrogen bonds defined for protein. 288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 858 1.33 - 1.45: 2119 1.45 - 1.57: 2130 1.57 - 1.69: 273 1.69 - 1.81: 4 Bond restraints: 5384 Sorted by residual: bond pdb=" CB PRO A 100 " pdb=" CG PRO A 100 " ideal model delta sigma weight residual 1.492 1.581 -0.089 5.00e-02 4.00e+02 3.16e+00 bond pdb=" CB VAL A 141 " pdb=" CG1 VAL A 141 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" O4' DG D -5 " pdb=" C1' DG D -5 " ideal model delta sigma weight residual 1.414 1.392 0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" N PRO A 100 " pdb=" CA PRO A 100 " ideal model delta sigma weight residual 1.472 1.457 0.014 1.34e-02 5.57e+03 1.13e+00 bond pdb=" CG PRO A 189 " pdb=" CD PRO A 189 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.60e-01 ... (remaining 5379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 7785 2.08 - 4.16: 147 4.16 - 6.23: 9 6.23 - 8.31: 2 8.31 - 10.39: 1 Bond angle restraints: 7944 Sorted by residual: angle pdb=" CA PRO A 100 " pdb=" N PRO A 100 " pdb=" CD PRO A 100 " ideal model delta sigma weight residual 112.00 101.61 10.39 1.40e+00 5.10e-01 5.51e+01 angle pdb=" C ALA A 188 " pdb=" N PRO A 189 " pdb=" CD PRO A 189 " ideal model delta sigma weight residual 120.60 113.24 7.36 2.20e+00 2.07e-01 1.12e+01 angle pdb=" C ALA A 188 " pdb=" N PRO A 189 " pdb=" CA PRO A 189 " ideal model delta sigma weight residual 127.00 134.46 -7.46 2.40e+00 1.74e-01 9.66e+00 angle pdb=" O3' C R-177 " pdb=" C3' C R-177 " pdb=" C2' C R-177 " ideal model delta sigma weight residual 113.70 118.13 -4.43 1.50e+00 4.44e-01 8.73e+00 angle pdb=" N MET A 42 " pdb=" CA MET A 42 " pdb=" CB MET A 42 " ideal model delta sigma weight residual 110.12 114.05 -3.93 1.47e+00 4.63e-01 7.14e+00 ... (remaining 7939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 2785 34.99 - 69.98: 410 69.98 - 104.97: 35 104.97 - 139.96: 1 139.96 - 174.95: 1 Dihedral angle restraints: 3232 sinusoidal: 2476 harmonic: 756 Sorted by residual: dihedral pdb=" O4' C R -68 " pdb=" C1' C R -68 " pdb=" N1 C R -68 " pdb=" C2 C R -68 " ideal model delta sinusoidal sigma weight residual 200.00 25.05 174.95 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" CA GLU A 49 " pdb=" C GLU A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 156.54 23.46 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA VAL A 169 " pdb=" C VAL A 169 " pdb=" N GLY A 170 " pdb=" CA GLY A 170 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 3229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 835 0.050 - 0.100: 107 0.100 - 0.150: 14 0.150 - 0.199: 6 0.199 - 0.249: 1 Chirality restraints: 963 Sorted by residual: chirality pdb=" CB THR A 99 " pdb=" CA THR A 99 " pdb=" OG1 THR A 99 " pdb=" CG2 THR A 99 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1' A R-105 " pdb=" O4' A R-105 " pdb=" C2' A R-105 " pdb=" N9 A R-105 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA THR A 99 " pdb=" N THR A 99 " pdb=" C THR A 99 " pdb=" CB THR A 99 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.98e-01 ... (remaining 960 not shown) Planarity restraints: 503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 99 " -0.100 5.00e-02 4.00e+02 1.45e-01 3.36e+01 pdb=" N PRO A 100 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G R 2 " -0.029 2.00e-02 2.50e+03 1.20e-02 4.30e+00 pdb=" N9 G R 2 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G R 2 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G R 2 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G R 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G R 2 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G R 2 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G R 2 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G R 2 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G R 2 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G R 2 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G R 2 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G R -72 " -0.020 2.00e-02 2.50e+03 1.11e-02 3.69e+00 pdb=" N9 G R -72 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G R -72 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G R -72 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G R -72 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G R -72 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G R -72 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G R -72 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G R -72 " 0.021 2.00e-02 2.50e+03 pdb=" N2 G R -72 " -0.011 2.00e-02 2.50e+03 pdb=" N3 G R -72 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G R -72 " -0.000 2.00e-02 2.50e+03 ... (remaining 500 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 246 2.68 - 3.23: 4057 3.23 - 3.79: 8797 3.79 - 4.34: 11261 4.34 - 4.90: 16296 Nonbonded interactions: 40657 Sorted by model distance: nonbonded pdb=" OG SER A 183 " pdb=" OP1 U R 3 " model vdw 2.120 3.040 nonbonded pdb=" O2 U R-144 " pdb=" O6 G R-104 " model vdw 2.146 2.432 nonbonded pdb=" NH1 ARG A 228 " pdb=" OP2 C R -70 " model vdw 2.205 3.120 nonbonded pdb=" ND2 ASN A 47 " pdb=" OE1 GLN A 87 " model vdw 2.235 3.120 nonbonded pdb=" O2' C R-177 " pdb=" OP1 G R-176 " model vdw 2.237 3.040 ... (remaining 40652 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.240 Find NCS groups from input model: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 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 : 0.004 0.089 5384 Z= 0.170 Angle : 0.659 10.391 7944 Z= 0.357 Chirality : 0.036 0.249 963 Planarity : 0.008 0.145 503 Dihedral : 24.508 174.949 2748 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.52), residues: 255 helix: -0.02 (0.50), residues: 120 sheet: -1.33 (0.87), residues: 44 loop : -3.04 (0.49), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.018 0.002 TYR A 195 PHE 0.010 0.002 PHE A 184 TRP 0.013 0.001 TRP A 157 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5384) covalent geometry : angle 0.65899 ( 7944) hydrogen bonds : bond 0.09851 ( 200) hydrogen bonds : angle 5.06153 ( 472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.120 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1325 time to fit residues: 3.3165 Evaluate side-chains 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.275768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.245132 restraints weight = 4625.374| |-----------------------------------------------------------------------------| r_work (start): 0.4710 rms_B_bonded: 1.02 r_work (final): 0.4710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5384 Z= 0.253 Angle : 0.767 6.776 7944 Z= 0.399 Chirality : 0.041 0.219 963 Planarity : 0.007 0.096 503 Dihedral : 25.598 176.977 2296 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.98 % Favored : 88.63 % Rotamer: Outliers : 1.03 % Allowed : 8.21 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.51), residues: 255 helix: -0.01 (0.49), residues: 124 sheet: -1.46 (0.86), residues: 43 loop : -3.45 (0.44), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.026 0.003 TYR A 195 PHE 0.016 0.002 PHE A 184 TRP 0.010 0.002 TRP A 133 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 5384) covalent geometry : angle 0.76748 ( 7944) hydrogen bonds : bond 0.07654 ( 200) hydrogen bonds : angle 4.86359 ( 472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.075 Fit side-chains REVERT: A 192 MET cc_start: 0.6715 (ptt) cc_final: 0.6514 (ptt) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.0952 time to fit residues: 2.8357 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.271815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.233856 restraints weight = 4502.446| |-----------------------------------------------------------------------------| r_work (start): 0.4591 rms_B_bonded: 1.23 r_work: 0.4174 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 5384 Z= 0.300 Angle : 0.848 6.636 7944 Z= 0.432 Chirality : 0.044 0.228 963 Planarity : 0.007 0.078 503 Dihedral : 25.662 178.132 2296 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.59 % Favored : 89.02 % Rotamer: Outliers : 2.05 % Allowed : 13.85 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.50), residues: 255 helix: -0.22 (0.49), residues: 123 sheet: -1.23 (1.02), residues: 33 loop : -3.54 (0.42), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.024 0.003 TYR A 195 PHE 0.018 0.003 PHE A 184 TRP 0.013 0.002 TRP A 133 HIS 0.005 0.002 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00630 ( 5384) covalent geometry : angle 0.84784 ( 7944) hydrogen bonds : bond 0.08984 ( 200) hydrogen bonds : angle 5.08258 ( 472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.117 Fit side-chains REVERT: A 49 GLU cc_start: 0.6734 (mp0) cc_final: 0.6220 (mm-30) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.1175 time to fit residues: 3.1751 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.273044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.237867 restraints weight = 4554.937| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 1.10 r_work (final): 0.4639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5384 Z= 0.258 Angle : 0.780 6.044 7944 Z= 0.401 Chirality : 0.042 0.212 963 Planarity : 0.006 0.067 503 Dihedral : 25.556 176.595 2296 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.98 % Favored : 88.63 % Rotamer: Outliers : 1.03 % Allowed : 17.44 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.51), residues: 255 helix: -0.01 (0.49), residues: 120 sheet: -1.68 (0.87), residues: 43 loop : -3.43 (0.45), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 247 TYR 0.023 0.003 TYR A 195 PHE 0.016 0.002 PHE A 184 TRP 0.013 0.002 TRP A 133 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 5384) covalent geometry : angle 0.78013 ( 7944) hydrogen bonds : bond 0.08014 ( 200) hydrogen bonds : angle 4.90337 ( 472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.115 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.1157 time to fit residues: 3.2920 Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.269867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.246625 restraints weight = 4588.832| |-----------------------------------------------------------------------------| r_work (start): 0.4738 rms_B_bonded: 0.75 r_work: 0.4349 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 5384 Z= 0.327 Angle : 0.889 7.183 7944 Z= 0.450 Chirality : 0.046 0.238 963 Planarity : 0.007 0.067 503 Dihedral : 25.741 178.753 2296 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.33 % Favored : 86.27 % Rotamer: Outliers : 2.05 % Allowed : 17.95 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.49), residues: 255 helix: -0.40 (0.48), residues: 123 sheet: -1.34 (1.00), residues: 33 loop : -3.61 (0.42), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 228 TYR 0.025 0.003 TYR A 206 PHE 0.019 0.003 PHE A 184 TRP 0.014 0.002 TRP A 133 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00689 ( 5384) covalent geometry : angle 0.88942 ( 7944) hydrogen bonds : bond 0.09601 ( 200) hydrogen bonds : angle 5.18921 ( 472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.117 Fit side-chains REVERT: A 139 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6487 (mm-40) outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 0.0933 time to fit residues: 2.7644 Evaluate side-chains 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.0470 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.279507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.257286 restraints weight = 4650.371| |-----------------------------------------------------------------------------| r_work (start): 0.4896 rms_B_bonded: 0.76 r_work: 0.4532 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5384 Z= 0.158 Angle : 0.650 6.017 7944 Z= 0.342 Chirality : 0.036 0.205 963 Planarity : 0.005 0.055 503 Dihedral : 25.461 172.608 2296 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 1.54 % Allowed : 18.97 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.53), residues: 255 helix: 0.54 (0.51), residues: 121 sheet: -1.62 (0.86), residues: 44 loop : -3.29 (0.46), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 247 TYR 0.018 0.002 TYR A 195 PHE 0.007 0.001 PHE A 184 TRP 0.014 0.001 TRP A 133 HIS 0.001 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5384) covalent geometry : angle 0.64994 ( 7944) hydrogen bonds : bond 0.05624 ( 200) hydrogen bonds : angle 4.46999 ( 472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.134 Fit side-chains REVERT: A 90 TYR cc_start: 0.5054 (p90) cc_final: 0.4299 (p90) REVERT: A 185 THR cc_start: 0.6324 (m) cc_final: 0.5965 (m) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.1109 time to fit residues: 3.0665 Evaluate side-chains 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.278945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.263841 restraints weight = 4641.597| |-----------------------------------------------------------------------------| r_work (start): 0.4950 rms_B_bonded: 0.51 r_work: 0.4681 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.4436 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5384 Z= 0.164 Angle : 0.641 5.959 7944 Z= 0.338 Chirality : 0.035 0.196 963 Planarity : 0.005 0.051 503 Dihedral : 25.427 172.748 2296 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 1.54 % Allowed : 19.49 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.52), residues: 255 helix: 0.73 (0.50), residues: 121 sheet: -1.56 (0.87), residues: 44 loop : -3.21 (0.46), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.018 0.002 TYR A 195 PHE 0.009 0.002 PHE A 184 TRP 0.010 0.001 TRP A 133 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5384) covalent geometry : angle 0.64138 ( 7944) hydrogen bonds : bond 0.05681 ( 200) hydrogen bonds : angle 4.39420 ( 472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.120 Fit side-chains REVERT: A 90 TYR cc_start: 0.4994 (p90) cc_final: 0.4197 (p90) REVERT: A 185 THR cc_start: 0.6492 (m) cc_final: 0.6132 (m) outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 0.1234 time to fit residues: 3.1769 Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 0.0000 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 0.0470 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.281802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.259673 restraints weight = 4618.181| |-----------------------------------------------------------------------------| r_work (start): 0.4920 rms_B_bonded: 0.73 r_work: 0.4564 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5384 Z= 0.139 Angle : 0.612 5.781 7944 Z= 0.325 Chirality : 0.034 0.195 963 Planarity : 0.005 0.051 503 Dihedral : 25.394 172.312 2296 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 2.05 % Allowed : 18.97 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.52), residues: 255 helix: 0.83 (0.49), residues: 121 sheet: -1.39 (0.85), residues: 44 loop : -3.12 (0.47), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.020 0.002 TYR A 38 PHE 0.006 0.001 PHE A 184 TRP 0.010 0.001 TRP A 133 HIS 0.002 0.000 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5384) covalent geometry : angle 0.61205 ( 7944) hydrogen bonds : bond 0.04992 ( 200) hydrogen bonds : angle 4.27146 ( 472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.081 Fit side-chains REVERT: A 185 THR cc_start: 0.6559 (m) cc_final: 0.6157 (m) outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 0.1031 time to fit residues: 2.9988 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 192 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 0.0570 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.282513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.250086 restraints weight = 4626.095| |-----------------------------------------------------------------------------| r_work (start): 0.4842 rms_B_bonded: 1.03 r_work: 0.4445 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5384 Z= 0.139 Angle : 0.598 5.740 7944 Z= 0.319 Chirality : 0.033 0.190 963 Planarity : 0.005 0.052 503 Dihedral : 25.330 171.092 2296 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 1.54 % Allowed : 18.97 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.52), residues: 255 helix: 1.34 (0.50), residues: 114 sheet: -1.29 (0.86), residues: 44 loop : -3.08 (0.46), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.017 0.002 TYR A 195 PHE 0.011 0.002 PHE A 156 TRP 0.008 0.001 TRP A 133 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5384) covalent geometry : angle 0.59828 ( 7944) hydrogen bonds : bond 0.04840 ( 200) hydrogen bonds : angle 4.13135 ( 472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.111 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1057 time to fit residues: 2.9304 Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 218 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.0770 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.278507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.254759 restraints weight = 4624.885| |-----------------------------------------------------------------------------| r_work (start): 0.4881 rms_B_bonded: 0.71 r_work: 0.4514 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5384 Z= 0.170 Angle : 0.638 5.694 7944 Z= 0.336 Chirality : 0.035 0.184 963 Planarity : 0.005 0.050 503 Dihedral : 25.383 172.835 2296 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 1.54 % Allowed : 20.00 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.53), residues: 255 helix: 0.92 (0.49), residues: 121 sheet: -1.39 (0.86), residues: 44 loop : -3.02 (0.49), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.019 0.002 TYR A 195 PHE 0.009 0.002 PHE A 184 TRP 0.008 0.001 TRP A 133 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5384) covalent geometry : angle 0.63758 ( 7944) hydrogen bonds : bond 0.05684 ( 200) hydrogen bonds : angle 4.27910 ( 472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.118 Fit side-chains REVERT: A 42 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.6416 (ptp) REVERT: A 185 THR cc_start: 0.6281 (m) cc_final: 0.5835 (m) outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 0.1338 time to fit residues: 3.4370 Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.280403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.247243 restraints weight = 4691.582| |-----------------------------------------------------------------------------| r_work (start): 0.4818 rms_B_bonded: 1.19 r_work (final): 0.4818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5384 Z= 0.153 Angle : 0.616 5.806 7944 Z= 0.326 Chirality : 0.034 0.182 963 Planarity : 0.005 0.051 503 Dihedral : 25.353 172.034 2296 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.05 % Allowed : 18.97 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.52), residues: 255 helix: 0.96 (0.49), residues: 121 sheet: -1.33 (0.86), residues: 44 loop : -2.99 (0.49), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.018 0.002 TYR A 195 PHE 0.008 0.001 PHE A 184 TRP 0.009 0.001 TRP A 133 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5384) covalent geometry : angle 0.61600 ( 7944) hydrogen bonds : bond 0.05228 ( 200) hydrogen bonds : angle 4.22657 ( 472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1289.55 seconds wall clock time: 22 minutes 46.48 seconds (1366.48 seconds total)