Starting phenix.real_space_refine on Tue Aug 4 16:21:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9udi_64070/08_2026/9udi_64070_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9udi_64070/08_2026/9udi_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_64070/08_2026/9udi_64070_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9udi_64070/08_2026/9udi_64070_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9udi_64070/08_2026/9udi_64070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9udi_64070/08_2026/9udi_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-2.2rc3-6140/lib/python3.11/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: 1.26, per 1000 atoms: 0.25 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: 0.41 Conformation dependent library (CDL) restraints added in 65.2 milliseconds 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: 0.44 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: 0.86 Time building geometry restraints manager: 0.49 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=" C3' DA D -3 " pdb=" C2' DA D -3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.98e+00 bond pdb=" C3' DT C 19 " pdb=" C2' DT C 19 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.35e+00 bond pdb=" C3' DG C 11 " pdb=" C2' DG C 11 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.30e+00 bond pdb=" C3' DC C 14 " pdb=" C2' DC C 14 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.88e+00 bond pdb=" C3' DC C 9 " pdb=" C2' DC C 9 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.80e+00 ... (remaining 5379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 7510 2.08 - 4.16: 421 4.16 - 6.23: 10 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=" C2 C R -68 " pdb=" N1 C R -68 " pdb=" C6 C R -68 " ideal model delta sigma weight residual 120.30 118.25 2.05 4.00e-01 6.25e+00 2.62e+01 angle pdb=" N9 G R-162 " pdb=" C4 G R-162 " pdb=" N3 G R-162 " ideal model delta sigma weight residual 126.00 123.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT C 22 " pdb=" C4 DT C 22 " pdb=" O4 DT C 22 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT D -8 " pdb=" C4 DT D -8 " pdb=" O4 DT D -8 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 ... (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: 688 0.050 - 0.100: 148 0.100 - 0.150: 117 0.150 - 0.199: 9 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 2.47 2.27 0.20 2.00e-01 2.50e+01 9.92e-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: 1.150 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.060 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 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= 0.367 Angle : 0.848 10.391 7944 Z= 0.712 Chirality : 0.059 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 are 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/Z covalent geometry : bond 0.00440 / 0.37 ( 5384) covalent geometry : angle 0.84793 / 0.71 ( 7944) hydrogen bonds : bond 0.09851 / 6.13 ( 200) hydrogen bonds : angle 5.06153 / 3.71 ( 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 : 0.116 Fit side-chains REVERT: A 191 LYS cc_start: 0.6735 (mppt) cc_final: 0.6451 (mppt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0959 time to fit residues: 2.4307 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 : 0.063 ------------------------------------------------------------------------------- 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: 9.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.277829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.238930 restraints weight = 4625.548| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 1.10 r_work: 0.4208 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5384 Z= 0.226 Angle : 0.694 6.942 7944 Z= 0.400 Chirality : 0.044 0.243 963 Planarity : 0.007 0.090 503 Dihedral : 25.785 175.149 2296 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.37 % Favored : 88.24 % Rotamer: Outliers : 0.51 % Allowed : 7.18 % Favored : 92.31 % 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 are not related in a simple way. whole: -2.17 (0.51), residues: 255 helix: -0.09 (0.49), residues: 123 sheet: -1.52 (0.87), residues: 44 loop : -3.34 (0.46), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 228 TYR 0.023 0.003 TYR A 195 PHE 0.017 0.002 PHE A 184 TRP 0.010 0.002 TRP A 133 HIS 0.005 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.23 ( 5384) covalent geometry : angle 0.69363 / 0.40 ( 7944) hydrogen bonds : bond 0.09043 / 5.75 ( 200) hydrogen bonds : angle 4.98063 / 3.85 ( 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 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.070 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.1039 time to fit residues: 2.7356 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 : 0.065 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.259173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.214158 restraints weight = 4458.402| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 1.34 r_work: 0.4101 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.127 5384 Z= 0.506 Angle : 1.151 11.788 7944 Z= 0.603 Chirality : 0.068 0.315 963 Planarity : 0.011 0.098 503 Dihedral : 26.025 179.763 2296 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.78 % Allowed : 13.73 % Favored : 85.49 % Rotamer: Outliers : 2.05 % Allowed : 14.36 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.47), residues: 255 helix: -1.36 (0.45), residues: 121 sheet: -1.76 (0.93), residues: 35 loop : -3.51 (0.47), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG A 54 TYR 0.041 0.006 TYR A 206 PHE 0.031 0.005 PHE A 184 TRP 0.017 0.005 TRP A 133 HIS 0.012 0.003 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.01056 / 0.51 ( 5384) covalent geometry : angle 1.15122 / 0.60 ( 7944) hydrogen bonds : bond 0.14928 / 9.38 ( 200) hydrogen bonds : angle 6.15292 / 4.67 ( 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 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.079 Fit side-chains REVERT: A 192 MET cc_start: 0.7029 (ptt) cc_final: 0.6739 (ptt) outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 0.0736 time to fit residues: 2.0924 Evaluate side-chains 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 19 optimal weight: 0.0370 chunk 25 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.278521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.250038 restraints weight = 4577.229| |-----------------------------------------------------------------------------| r_work (start): 0.4829 rms_B_bonded: 0.87 r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5384 Z= 0.163 Angle : 0.628 5.986 7944 Z= 0.375 Chirality : 0.039 0.251 963 Planarity : 0.006 0.067 503 Dihedral : 25.746 176.799 2296 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.59 % Favored : 89.02 % Rotamer: Outliers : 1.03 % Allowed : 16.41 % Favored : 82.56 % 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 are not related in a simple way. whole: -2.26 (0.51), residues: 255 helix: -0.04 (0.50), residues: 120 sheet: -1.59 (0.87), residues: 43 loop : -3.45 (0.44), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 220 TYR 0.020 0.002 TYR A 195 PHE 0.007 0.002 PHE A 93 TRP 0.017 0.001 TRP A 133 HIS 0.009 0.002 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 ( 5384) covalent geometry : angle 0.62803 / 0.38 ( 7944) hydrogen bonds : bond 0.08158 / 5.14 ( 200) hydrogen bonds : angle 5.02390 / 3.92 ( 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 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.065 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.0721 time to fit residues: 1.9625 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 : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 0.0570 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.274814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.245514 restraints weight = 4628.338| |-----------------------------------------------------------------------------| r_work (start): 0.4718 rms_B_bonded: 0.90 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5384 Z= 0.212 Angle : 0.675 6.127 7944 Z= 0.391 Chirality : 0.042 0.255 963 Planarity : 0.006 0.063 503 Dihedral : 25.692 174.848 2296 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.16 % Favored : 87.45 % Rotamer: Outliers : 1.54 % Allowed : 17.44 % Favored : 81.03 % 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 are not related in a simple way. whole: -2.33 (0.51), residues: 255 helix: -0.07 (0.49), residues: 123 sheet: -1.65 (0.86), residues: 43 loop : -3.62 (0.44), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 247 TYR 0.022 0.003 TYR A 195 PHE 0.014 0.002 PHE A 184 TRP 0.014 0.002 TRP A 133 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 ( 5384) covalent geometry : angle 0.67509 / 0.39 ( 7944) hydrogen bonds : bond 0.08742 / 5.60 ( 200) hydrogen bonds : angle 4.98738 / 3.87 ( 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: 3 poor density : 21 time to evaluate : 0.064 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.0969 time to fit residues: 2.7491 Evaluate side-chains 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR 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: 9.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 50.0000 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 chunk 37 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.279638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.258158 restraints weight = 4655.139| |-----------------------------------------------------------------------------| r_work (start): 0.4902 rms_B_bonded: 0.75 r_work: 0.4513 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5384 Z= 0.149 Angle : 0.581 6.389 7944 Z= 0.348 Chirality : 0.037 0.256 963 Planarity : 0.005 0.053 503 Dihedral : 25.621 172.596 2296 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % 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 are not related in a simple way. whole: -1.79 (0.52), residues: 255 helix: 0.49 (0.51), residues: 121 sheet: -1.68 (0.84), residues: 44 loop : -3.31 (0.46), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 210 TYR 0.019 0.002 TYR A 195 PHE 0.010 0.001 PHE A 184 TRP 0.013 0.001 TRP A 133 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 ( 5384) covalent geometry : angle 0.58055 / 0.35 ( 7944) hydrogen bonds : bond 0.06886 / 4.49 ( 200) hydrogen bonds : angle 4.63728 / 3.61 ( 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 : 0.113 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.0873 time to fit residues: 2.4652 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 : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR 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: 0.9980 chunk 28 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 30.0000 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5076 r_free = 0.5076 target = 0.279639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.255979 restraints weight = 4658.219| |-----------------------------------------------------------------------------| r_work (start): 0.4888 rms_B_bonded: 0.67 r_work: 0.4515 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.1414 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= 0.155 Angle : 0.573 6.721 7944 Z= 0.341 Chirality : 0.036 0.258 963 Planarity : 0.005 0.052 503 Dihedral : 25.585 171.794 2296 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 2.56 % Allowed : 18.46 % 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 are not related in a simple way. whole: -1.68 (0.52), residues: 255 helix: 0.61 (0.50), residues: 121 sheet: -1.68 (0.84), residues: 44 loop : -3.26 (0.47), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 247 TYR 0.019 0.002 TYR A 195 PHE 0.009 0.001 PHE A 184 TRP 0.011 0.001 TRP A 133 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 ( 5384) covalent geometry : angle 0.57293 / 0.34 ( 7944) hydrogen bonds : bond 0.06627 / 4.38 ( 200) hydrogen bonds : angle 4.49205 / 3.49 ( 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 27 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.063 Fit side-chains REVERT: A 42 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6001 (ptp) outliers start: 5 outliers final: 2 residues processed: 25 average time/residue: 0.0642 time to fit residues: 2.0513 Evaluate side-chains 25 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.099 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 40.0000 chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.280528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.255792 restraints weight = 4604.458| |-----------------------------------------------------------------------------| r_work (start): 0.4886 rms_B_bonded: 0.67 r_work: 0.4555 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.1451 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= 0.144 Angle : 0.559 6.707 7944 Z= 0.335 Chirality : 0.036 0.258 963 Planarity : 0.005 0.051 503 Dihedral : 25.582 171.308 2296 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.80 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 are not related in a simple way. whole: -1.58 (0.52), residues: 255 helix: 0.68 (0.50), residues: 121 sheet: -1.57 (0.84), residues: 44 loop : -3.23 (0.47), 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 0.011 0.001 TRP A 133 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 ( 5384) covalent geometry : angle 0.55946 / 0.33 ( 7944) hydrogen bonds : bond 0.06259 / 4.16 ( 200) hydrogen bonds : angle 4.44622 / 3.47 ( 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 : 0.063 Fit side-chains REVERT: A 42 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6092 (ptp) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.0741 time to fit residues: 2.0856 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 : 0.105 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.280582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.254328 restraints weight = 4595.716| |-----------------------------------------------------------------------------| r_work (start): 0.4874 rms_B_bonded: 0.70 r_work: 0.4530 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5384 Z= 0.146 Angle : 0.561 6.674 7944 Z= 0.334 Chirality : 0.036 0.258 963 Planarity : 0.005 0.051 503 Dihedral : 25.583 171.063 2296 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % 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 are not related in a simple way. whole: -1.49 (0.53), residues: 255 helix: 0.76 (0.50), residues: 121 sheet: -1.50 (0.84), residues: 44 loop : -3.21 (0.48), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.018 0.002 TYR A 195 PHE 0.009 0.001 PHE A 184 TRP 0.010 0.001 TRP A 133 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 ( 5384) covalent geometry : angle 0.56088 / 0.33 ( 7944) hydrogen bonds : bond 0.06172 / 4.10 ( 200) hydrogen bonds : angle 4.41781 / 3.44 ( 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 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.105 Fit side-chains REVERT: A 42 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6115 (ptp) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.0748 time to fit residues: 1.9209 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 : 0.125 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 50.0000 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5091 r_free = 0.5091 target = 0.281874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.255150 restraints weight = 4608.740| |-----------------------------------------------------------------------------| r_work (start): 0.4879 rms_B_bonded: 0.72 r_work: 0.4485 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5384 Z= 0.134 Angle : 0.542 6.621 7944 Z= 0.326 Chirality : 0.035 0.257 963 Planarity : 0.005 0.051 503 Dihedral : 25.578 170.788 2296 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % 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 are not related in a simple way. whole: -1.38 (0.52), residues: 255 helix: 0.86 (0.50), residues: 121 sheet: -1.42 (0.84), residues: 44 loop : -3.20 (0.47), residues: 90 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 0.007 0.001 PHE A 184 TRP 0.010 0.001 TRP A 133 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 ( 5384) covalent geometry : angle 0.54186 / 0.33 ( 7944) hydrogen bonds : bond 0.05816 / 3.89 ( 200) hydrogen bonds : angle 4.34681 / 3.39 ( 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 : 0.072 Fit side-chains REVERT: A 42 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6140 (ptp) outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 0.0894 time to fit residues: 2.3752 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 : 0.099 ------------------------------------------------------------------------------- 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: 0.0970 chunk 25 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.280478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.256945 restraints weight = 4662.621| |-----------------------------------------------------------------------------| r_work (start): 0.4895 rms_B_bonded: 0.71 r_work: 0.4537 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.1589 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= 0.149 Angle : 0.557 6.604 7944 Z= 0.331 Chirality : 0.036 0.258 963 Planarity : 0.005 0.052 503 Dihedral : 25.585 170.853 2296 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % 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 are not related in a simple way. whole: -1.44 (0.52), residues: 255 helix: 0.83 (0.50), residues: 121 sheet: -1.46 (0.84), residues: 44 loop : -3.24 (0.46), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.019 0.002 TYR A 195 PHE 0.010 0.002 PHE A 184 TRP 0.009 0.001 TRP A 133 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 ( 5384) covalent geometry : angle 0.55735 / 0.33 ( 7944) hydrogen bonds : bond 0.06205 / 4.11 ( 200) hydrogen bonds : angle 4.37264 / 3.41 ( 472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1071.65 seconds wall clock time: 18 minutes 56.49 seconds (1136.49 seconds total)