Starting phenix.real_space_refine on Thu Jul 2 00:47:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9udi_64070/07_2026/9udi_64070_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9udi_64070/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9udi_64070/07_2026/9udi_64070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9udi_64070/07_2026/9udi_64070.map" model { file = "/net/cci-nas-00/data/ceres_data/9udi_64070/07_2026/9udi_64070_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9udi_64070/07_2026/9udi_64070_neut.cif" } 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-dev-6108/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: 1.28, per 1000 atoms: 0.26 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: 0.32 Conformation dependent library (CDL) restraints added in 56.9 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: 0.40 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: 0.68 Time building geometry restraints manager: 0.43 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: 7754 2.08 - 4.16: 178 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=" 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: 804 0.050 - 0.100: 135 0.100 - 0.150: 17 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.990 Find NCS groups from input model: 0.020 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.010 ------------------------------------------------------------------------------- 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= 0.358 Angle : 0.703 10.391 7944 Z= 0.604 Chirality : 0.039 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 0.00431 / 0.36 ( 5384) covalent geometry : angle 0.70285 / 0.60 ( 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 : 0.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0920 time to fit residues: 2.3418 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 : 0.064 ------------------------------------------------------------------------------- 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: 0.9980 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.5058 r_free = 0.5058 target = 0.277310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.253024 restraints weight = 4626.276| |-----------------------------------------------------------------------------| r_work (start): 0.4878 rms_B_bonded: 0.86 r_work: 0.4538 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5384 Z= 0.233 Angle : 0.678 6.814 7944 Z= 0.400 Chirality : 0.044 0.214 963 Planarity : 0.007 0.090 503 Dihedral : 25.799 173.552 2296 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.76 % Favored : 87.84 % 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: -2.19 (0.51), residues: 255 helix: -0.11 (0.49), residues: 123 sheet: -1.54 (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 0.011 0.002 TRP A 133 HIS 0.005 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.23 ( 5384) covalent geometry : angle 0.67788 / 0.40 ( 7944) hydrogen bonds : bond 0.08916 / 5.65 ( 200) hydrogen bonds : angle 5.00457 / 3.88 ( 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 : 0.108 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0839 time to fit residues: 2.2426 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 : 0.099 ------------------------------------------------------------------------------- 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: 0.7980 chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 40.0000 chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 overall best weight: 3.8586 ------------------------------------------------------------------------------- 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 = 0.4923 r_free = 0.4923 target = 0.262329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.218329 restraints weight = 4512.305| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 1.85 r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 5384 Z= 0.441 Angle : 0.964 10.622 7944 Z= 0.540 Chirality : 0.059 0.289 963 Planarity : 0.010 0.096 503 Dihedral : 26.034 178.245 2296 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.73 % Favored : 85.88 % 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: -3.17 (0.47), residues: 255 helix: -1.09 (0.45), residues: 124 sheet: -1.58 (0.99), residues: 33 loop : -3.63 (0.42), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 54 TYR 0.037 0.005 TYR A 206 PHE 0.027 0.005 PHE A 184 TRP 0.017 0.004 TRP A 133 HIS 0.011 0.003 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00901 / 0.44 ( 5384) covalent geometry : angle 0.96409 / 0.54 ( 7944) hydrogen bonds : bond 0.13208 / 8.35 ( 200) hydrogen bonds : angle 5.83889 / 4.45 ( 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 : 0.108 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 0.1121 time to fit residues: 3.1516 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 : 0.124 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 0.0040 chunk 25 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 = 0.5049 r_free = 0.5049 target = 0.276469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.250485 restraints weight = 4572.575| |-----------------------------------------------------------------------------| r_work (start): 0.4845 rms_B_bonded: 0.85 r_work (final): 0.4845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5384 Z= 0.185 Angle : 0.630 6.287 7944 Z= 0.381 Chirality : 0.042 0.212 963 Planarity : 0.006 0.071 503 Dihedral : 25.766 175.556 2296 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.98 % Favored : 88.63 % Rotamer: Outliers : 1.54 % Allowed : 16.41 % Favored : 82.05 % 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: -0.12 (0.49), residues: 123 sheet: -1.55 (0.87), residues: 43 loop : -3.59 (0.43), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 228 TYR 0.022 0.002 TYR A 195 PHE 0.010 0.002 PHE A 184 TRP 0.017 0.001 TRP A 133 HIS 0.007 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 5384) covalent geometry : angle 0.62956 / 0.38 ( 7944) hydrogen bonds : bond 0.08186 / 5.15 ( 200) hydrogen bonds : angle 5.02579 / 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: 3 poor density : 20 time to evaluate : 0.106 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1060 time to fit residues: 2.9132 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 : 0.103 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 0.0050 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.2798 ------------------------------------------------------------------------------- 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 = 0.5042 r_free = 0.5042 target = 0.275550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.246239 restraints weight = 4623.871| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 0.97 r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5384 Z= 0.199 Angle : 0.633 6.117 7944 Z= 0.378 Chirality : 0.042 0.213 963 Planarity : 0.006 0.061 503 Dihedral : 25.698 173.337 2296 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % 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: -2.17 (0.52), residues: 255 helix: 0.10 (0.50), residues: 123 sheet: -1.72 (0.85), residues: 44 loop : -3.53 (0.45), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 247 TYR 0.021 0.002 TYR A 195 PHE 0.015 0.002 PHE A 184 TRP 0.013 0.002 TRP A 133 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 ( 5384) covalent geometry : angle 0.63280 / 0.38 ( 7944) hydrogen bonds : bond 0.08131 / 5.21 ( 200) hydrogen bonds : angle 4.88391 / 3.80 ( 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 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 Fit side-chains REVERT: A 185 THR cc_start: 0.6250 (m) cc_final: 0.5919 (m) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.0931 time to fit residues: 2.6153 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 ------------------------------------------------------------------------------- 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: 6.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 40.0000 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 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 = 0.5072 r_free = 0.5072 target = 0.279538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.244611 restraints weight = 4643.930| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 1.12 r_work (final): 0.4692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.1339 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= 0.151 Angle : 0.566 5.813 7944 Z= 0.346 Chirality : 0.039 0.214 963 Planarity : 0.005 0.054 503 Dihedral : 25.625 171.940 2296 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % 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 are not related in a simple way. whole: -1.75 (0.52), residues: 255 helix: 0.53 (0.51), residues: 121 sheet: -1.68 (0.85), residues: 44 loop : -3.27 (0.46), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 210 TYR 0.019 0.002 TYR A 195 PHE 0.009 0.002 PHE A 184 TRP 0.012 0.001 TRP A 133 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 ( 5384) covalent geometry : angle 0.56569 / 0.35 ( 7944) hydrogen bonds : bond 0.06665 / 4.32 ( 200) hydrogen bonds : angle 4.62281 / 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 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.5911 (ptp) REVERT: A 185 THR cc_start: 0.6350 (m) cc_final: 0.6016 (m) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.0850 time to fit residues: 2.3550 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 : 0.062 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.5050 r_free = 0.5050 target = 0.276665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.249726 restraints weight = 4634.248| |-----------------------------------------------------------------------------| r_work (start): 0.4834 rms_B_bonded: 0.87 r_work: 0.4462 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5384 Z= 0.191 Angle : 0.608 5.750 7944 Z= 0.364 Chirality : 0.041 0.216 963 Planarity : 0.006 0.056 503 Dihedral : 25.634 172.044 2296 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 2.56 % Allowed : 17.44 % 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 are not related in a simple way. whole: -1.83 (0.52), residues: 255 helix: 0.46 (0.51), residues: 121 sheet: -1.71 (0.85), residues: 44 loop : -3.31 (0.47), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.021 0.002 TYR A 195 PHE 0.014 0.002 PHE A 184 TRP 0.011 0.002 TRP A 133 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 ( 5384) covalent geometry : angle 0.60753 / 0.36 ( 7944) hydrogen bonds : bond 0.07484 / 4.83 ( 200) hydrogen bonds : angle 4.70080 / 3.65 ( 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 : 0.071 Fit side-chains REVERT: A 42 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6134 (ptp) REVERT: A 185 THR cc_start: 0.6713 (m) cc_final: 0.6351 (m) outliers start: 5 outliers final: 2 residues processed: 25 average time/residue: 0.0687 time to fit residues: 2.1710 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 : 0.060 ------------------------------------------------------------------------------- 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: 1.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 36 optimal weight: 40.0000 chunk 10 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 11 optimal weight: 0.0040 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.280868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.254977 restraints weight = 4595.369| |-----------------------------------------------------------------------------| r_work (start): 0.4881 rms_B_bonded: 0.68 r_work: 0.4493 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5384 Z= 0.138 Angle : 0.548 5.858 7944 Z= 0.336 Chirality : 0.038 0.213 963 Planarity : 0.005 0.053 503 Dihedral : 25.588 170.705 2296 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.05 % Allowed : 19.49 % 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: -1.59 (0.53), residues: 255 helix: 0.68 (0.51), residues: 121 sheet: -1.60 (0.84), residues: 44 loop : -3.25 (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 93 TRP 0.012 0.001 TRP A 133 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 ( 5384) covalent geometry : angle 0.54771 / 0.34 ( 7944) hydrogen bonds : bond 0.06027 / 3.95 ( 200) hydrogen bonds : angle 4.48035 / 3.50 ( 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 : 0.062 Fit side-chains REVERT: A 42 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6130 (ptp) REVERT: A 185 THR cc_start: 0.6621 (m) cc_final: 0.6258 (m) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.0814 time to fit residues: 2.2707 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 : 0.075 ------------------------------------------------------------------------------- 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: 0.5980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 24 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 = 0.5076 r_free = 0.5076 target = 0.279983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.247999 restraints weight = 4598.967| |-----------------------------------------------------------------------------| r_work (start): 0.4728 rms_B_bonded: 1.03 r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5384 Z= 0.146 Angle : 0.550 5.986 7944 Z= 0.335 Chirality : 0.038 0.215 963 Planarity : 0.005 0.052 503 Dihedral : 25.577 170.338 2296 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % 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 are not related in a simple way. whole: -1.55 (0.52), residues: 255 helix: 0.74 (0.50), residues: 121 sheet: -1.56 (0.84), residues: 44 loop : -3.28 (0.47), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 210 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 0.001 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 ( 5384) covalent geometry : angle 0.54992 / 0.34 ( 7944) hydrogen bonds : bond 0.06103 / 4.01 ( 200) hydrogen bonds : angle 4.44382 / 3.47 ( 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 : 0.077 Fit side-chains REVERT: A 42 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.5930 (ptp) REVERT: A 185 THR cc_start: 0.6196 (m) cc_final: 0.5878 (m) outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 0.0813 time to fit residues: 2.1087 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 : 0.062 ------------------------------------------------------------------------------- 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: 0.7980 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 40.0000 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.5069 r_free = 0.5069 target = 0.279005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.258879 restraints weight = 4605.447| |-----------------------------------------------------------------------------| r_work (start): 0.4914 rms_B_bonded: 0.67 r_work: 0.4589 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.1493 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= 0.159 Angle : 0.565 5.930 7944 Z= 0.342 Chirality : 0.038 0.215 963 Planarity : 0.005 0.052 503 Dihedral : 25.596 170.580 2296 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % 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: -1.55 (0.52), residues: 255 helix: 0.74 (0.50), residues: 121 sheet: -1.61 (0.85), 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 0.011 0.002 PHE A 184 TRP 0.009 0.001 TRP A 133 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 ( 5384) covalent geometry : angle 0.56473 / 0.34 ( 7944) hydrogen bonds : bond 0.06392 / 4.17 ( 200) hydrogen bonds : angle 4.48858 / 3.51 ( 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 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.108 Fit side-chains REVERT: A 42 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.5995 (ptp) REVERT: A 185 THR cc_start: 0.6388 (m) cc_final: 0.6037 (m) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.0926 time to fit residues: 2.3524 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 : 0.098 ------------------------------------------------------------------------------- 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: 0.6980 chunk 25 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 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 = 0.5079 r_free = 0.5079 target = 0.280400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.249597 restraints weight = 4660.017| |-----------------------------------------------------------------------------| r_work (start): 0.4844 rms_B_bonded: 0.83 r_work: 0.4433 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.1547 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= 0.139 Angle : 0.542 5.993 7944 Z= 0.331 Chirality : 0.037 0.214 963 Planarity : 0.005 0.052 503 Dihedral : 25.587 170.318 2296 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % 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 are not related in a simple way. whole: -1.49 (0.52), residues: 255 helix: 0.80 (0.50), residues: 121 sheet: -1.51 (0.85), residues: 44 loop : -3.27 (0.45), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 247 TYR 0.018 0.002 TYR A 195 PHE 0.008 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 0.00256 / 0.14 ( 5384) covalent geometry : angle 0.54184 / 0.33 ( 7944) hydrogen bonds : bond 0.05858 / 3.85 ( 200) hydrogen bonds : angle 4.40626 / 3.44 ( 472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1033.66 seconds wall clock time: 18 minutes 22.84 seconds (1102.84 seconds total)