Starting phenix.real_space_refine on Tue Mar 3 10:56:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y13_33555/03_2026/7y13_33555.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y13_33555/03_2026/7y13_33555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y13_33555/03_2026/7y13_33555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y13_33555/03_2026/7y13_33555.map" model { file = "/net/cci-nas-00/data/ceres_data/7y13_33555/03_2026/7y13_33555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y13_33555/03_2026/7y13_33555.cif" } resolution = 3.1 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= 0.070 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 1479 2.51 5 N 342 2.21 5 O 356 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2199 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2071 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 253} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 128 Unusual residues: {'PLM': 7} Classifications: {'undetermined': 7, 'water': 2} Link IDs: {None: 8} Time building chain proxies: 0.72, per 1000 atoms: 0.33 Number of scatterers: 2199 At special positions: 0 Unit cell: (56.7, 66.825, 68.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 356 8.00 N 342 7.00 C 1479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 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: 0.15 Conformation dependent library (CDL) restraints added in 51.6 milliseconds 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 512 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'R' and resid 22 through 53 removed outlier: 3.575A pdb=" N LEU R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 86 removed outlier: 3.750A pdb=" N ILE R 65 " --> pdb=" O PHE R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 129 removed outlier: 3.538A pdb=" N LEU R 100 " --> pdb=" O LYS R 96 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 140 through 165 Processing helix chain 'R' and resid 172 through 209 removed outlier: 3.512A pdb=" N PHE R 176 " --> pdb=" O GLU R 172 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG R 177 " --> pdb=" O ASP R 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA R 184 " --> pdb=" O MET R 180 " (cutoff:3.500A) Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 216 through 245 removed outlier: 4.240A pdb=" N LEU R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) Proline residue: R 236 - end of helix removed outlier: 3.800A pdb=" N TRP R 241 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE R 242 " --> pdb=" O SER R 238 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 277 Proline residue: R 273 - end of helix 166 hydrogen bonds defined for protein. 498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.31 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 629 1.35 - 1.46: 570 1.46 - 1.58: 1014 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 2246 Sorted by residual: bond pdb=" C2 PLM R 407 " pdb=" C3 PLM R 407 " ideal model delta sigma weight residual 1.522 1.493 0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C2 PLM R 405 " pdb=" C3 PLM R 405 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C2 PLM R 403 " pdb=" C3 PLM R 403 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C2 PLM R 406 " pdb=" C3 PLM R 406 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C2 PLM R 401 " pdb=" C3 PLM R 401 " ideal model delta sigma weight residual 1.522 1.497 0.025 2.00e-02 2.50e+03 1.60e+00 ... (remaining 2241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 2912 1.66 - 3.32: 90 3.32 - 4.98: 14 4.98 - 6.64: 2 6.64 - 8.30: 1 Bond angle restraints: 3019 Sorted by residual: angle pdb=" CA LEU R 52 " pdb=" CB LEU R 52 " pdb=" CG LEU R 52 " ideal model delta sigma weight residual 116.30 124.60 -8.30 3.50e+00 8.16e-02 5.62e+00 angle pdb=" C LYS R 166 " pdb=" N PHE R 167 " pdb=" CA PHE R 167 " ideal model delta sigma weight residual 120.17 123.62 -3.45 1.54e+00 4.22e-01 5.01e+00 angle pdb=" C ALA R 143 " pdb=" N TRP R 144 " pdb=" CA TRP R 144 " ideal model delta sigma weight residual 121.14 117.38 3.76 1.75e+00 3.27e-01 4.62e+00 angle pdb=" CA TRP R 144 " pdb=" CB TRP R 144 " pdb=" CG TRP R 144 " ideal model delta sigma weight residual 113.60 117.63 -4.03 1.90e+00 2.77e-01 4.49e+00 angle pdb=" N PHE R 167 " pdb=" CA PHE R 167 " pdb=" C PHE R 167 " ideal model delta sigma weight residual 113.50 110.22 3.28 1.65e+00 3.67e-01 3.94e+00 ... (remaining 3014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.54: 1117 11.54 - 23.08: 142 23.08 - 34.63: 59 34.63 - 46.17: 23 46.17 - 57.71: 4 Dihedral angle restraints: 1345 sinusoidal: 563 harmonic: 782 Sorted by residual: dihedral pdb=" CG ARG R 103 " pdb=" CD ARG R 103 " pdb=" NE ARG R 103 " pdb=" CZ ARG R 103 " ideal model delta sinusoidal sigma weight residual -90.00 -134.56 44.56 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA HIS R 57 " pdb=" C HIS R 57 " pdb=" N ARG R 58 " pdb=" CA ARG R 58 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CB MET R 35 " pdb=" CG MET R 35 " pdb=" SD MET R 35 " pdb=" CE MET R 35 " ideal model delta sinusoidal sigma weight residual 60.00 117.71 -57.71 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 219 0.031 - 0.062: 103 0.062 - 0.092: 20 0.092 - 0.123: 8 0.123 - 0.154: 1 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA MET R 79 " pdb=" N MET R 79 " pdb=" C MET R 79 " pdb=" CB MET R 79 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA PRO R 236 " pdb=" N PRO R 236 " pdb=" C PRO R 236 " pdb=" CB PRO R 236 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 348 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 235 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO R 236 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 236 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 236 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 144 " -0.015 2.00e-02 2.50e+03 1.27e-02 4.06e+00 pdb=" CG TRP R 144 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP R 144 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 144 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 144 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 144 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 144 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET R 187 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C MET R 187 " 0.030 2.00e-02 2.50e+03 pdb=" O MET R 187 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY R 188 " -0.010 2.00e-02 2.50e+03 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 134 2.74 - 3.28: 2109 3.28 - 3.82: 3736 3.82 - 4.36: 4123 4.36 - 4.90: 7542 Nonbonded interactions: 17644 Sorted by model distance: nonbonded pdb=" NH2 ARG R 137 " pdb=" OG SER R 142 " model vdw 2.195 3.120 nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.211 3.040 nonbonded pdb=" O ARG R 55 " pdb=" ND1 HIS R 57 " model vdw 2.411 3.120 nonbonded pdb=" OG1 THR R 22 " pdb=" N VAL R 23 " model vdw 2.435 3.120 nonbonded pdb=" O SER R 78 " pdb=" OG SER R 81 " model vdw 2.436 3.040 ... (remaining 17639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 max=1.00 mean=0.99 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.860 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2247 Z= 0.240 Angle : 0.677 8.296 3021 Z= 0.339 Chirality : 0.038 0.154 351 Planarity : 0.005 0.075 350 Dihedral : 13.192 57.709 830 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.56), residues: 262 helix: 1.91 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.24 (0.94), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 262 TYR 0.007 0.001 TYR R 109 PHE 0.014 0.001 PHE R 202 TRP 0.035 0.002 TRP R 144 HIS 0.001 0.000 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 2246) covalent geometry : angle 0.67624 ( 3019) SS BOND : bond 0.00430 ( 1) SS BOND : angle 1.21361 ( 2) hydrogen bonds : bond 0.09114 ( 166) hydrogen bonds : angle 6.38148 ( 498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.055 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0473 time to fit residues: 1.9377 Evaluate side-chains 30 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.183171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141604 restraints weight = 2156.638| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.80 r_work: 0.3254 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2247 Z= 0.148 Angle : 0.583 7.725 3021 Z= 0.292 Chirality : 0.038 0.170 351 Planarity : 0.005 0.074 350 Dihedral : 8.075 45.079 382 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.43 % Allowed : 8.19 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.56), residues: 262 helix: 2.09 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.23 (0.95), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 262 TYR 0.006 0.001 TYR R 109 PHE 0.015 0.002 PHE R 202 TRP 0.028 0.002 TRP R 144 HIS 0.004 0.001 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2246) covalent geometry : angle 0.58223 ( 3019) SS BOND : bond 0.00209 ( 1) SS BOND : angle 1.19829 ( 2) hydrogen bonds : bond 0.03447 ( 166) hydrogen bonds : angle 5.02900 ( 498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.067 Fit side-chains REVERT: R 95 ASP cc_start: 0.7306 (t0) cc_final: 0.6924 (t0) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.0415 time to fit residues: 1.8484 Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.183381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140947 restraints weight = 2179.365| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.88 r_work: 0.3249 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2247 Z= 0.138 Angle : 0.574 10.815 3021 Z= 0.286 Chirality : 0.037 0.165 351 Planarity : 0.005 0.073 350 Dihedral : 8.417 46.960 382 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.86 % Allowed : 12.07 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.57), residues: 262 helix: 2.26 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.28 (0.97), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 262 TYR 0.007 0.001 TYR R 109 PHE 0.014 0.001 PHE R 202 TRP 0.021 0.001 TRP R 144 HIS 0.003 0.001 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2246) covalent geometry : angle 0.57329 ( 3019) SS BOND : bond 0.00296 ( 1) SS BOND : angle 0.88993 ( 2) hydrogen bonds : bond 0.03308 ( 166) hydrogen bonds : angle 4.85912 ( 498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.061 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 0.0439 time to fit residues: 1.9257 Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.182802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.141292 restraints weight = 2163.410| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.82 r_work: 0.3239 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2247 Z= 0.139 Angle : 0.572 11.028 3021 Z= 0.285 Chirality : 0.037 0.165 351 Planarity : 0.005 0.074 350 Dihedral : 9.072 49.846 382 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.86 % Allowed : 14.22 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.56), residues: 262 helix: 2.35 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.24 (0.96), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 262 TYR 0.007 0.001 TYR R 109 PHE 0.013 0.001 PHE R 202 TRP 0.019 0.001 TRP R 144 HIS 0.003 0.001 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 2246) covalent geometry : angle 0.57140 ( 3019) SS BOND : bond 0.00179 ( 1) SS BOND : angle 0.91131 ( 2) hydrogen bonds : bond 0.03309 ( 166) hydrogen bonds : angle 4.78781 ( 498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.083 Fit side-chains REVERT: R 95 ASP cc_start: 0.7409 (t0) cc_final: 0.6993 (t0) REVERT: R 185 LEU cc_start: 0.7920 (tt) cc_final: 0.7483 (tp) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 0.0370 time to fit residues: 1.6977 Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.183458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141129 restraints weight = 2151.815| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.87 r_work: 0.3243 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2247 Z= 0.128 Angle : 0.555 10.816 3021 Z= 0.277 Chirality : 0.036 0.162 351 Planarity : 0.005 0.073 350 Dihedral : 9.228 54.403 382 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.86 % Allowed : 15.09 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.57), residues: 262 helix: 2.51 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.20 (0.97), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 262 TYR 0.007 0.001 TYR R 109 PHE 0.015 0.001 PHE R 75 TRP 0.017 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2246) covalent geometry : angle 0.55436 ( 3019) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.86850 ( 2) hydrogen bonds : bond 0.03195 ( 166) hydrogen bonds : angle 4.71134 ( 498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.080 Fit side-chains REVERT: R 185 LEU cc_start: 0.7891 (tt) cc_final: 0.7447 (tp) outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.0401 time to fit residues: 1.7096 Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 0.0040 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.182994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.140809 restraints weight = 2115.195| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.86 r_work: 0.3234 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2247 Z= 0.129 Angle : 0.555 10.679 3021 Z= 0.277 Chirality : 0.036 0.160 351 Planarity : 0.005 0.073 350 Dihedral : 9.527 59.722 382 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.86 % Allowed : 15.95 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.57), residues: 262 helix: 2.59 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.18 (0.97), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 262 TYR 0.007 0.001 TYR R 109 PHE 0.016 0.001 PHE R 75 TRP 0.016 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2246) covalent geometry : angle 0.55493 ( 3019) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.89107 ( 2) hydrogen bonds : bond 0.03227 ( 166) hydrogen bonds : angle 4.67903 ( 498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.042 Fit side-chains REVERT: R 185 LEU cc_start: 0.7909 (tt) cc_final: 0.7463 (tp) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.0366 time to fit residues: 1.6222 Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.183039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140856 restraints weight = 2119.109| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.86 r_work: 0.3237 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2247 Z= 0.126 Angle : 0.549 10.479 3021 Z= 0.275 Chirality : 0.036 0.159 351 Planarity : 0.005 0.073 350 Dihedral : 9.667 59.237 382 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.86 % Allowed : 16.81 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.57), residues: 262 helix: 2.65 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.17 (0.97), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 262 TYR 0.007 0.001 TYR R 109 PHE 0.018 0.001 PHE R 75 TRP 0.016 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2246) covalent geometry : angle 0.54877 ( 3019) SS BOND : bond 0.00150 ( 1) SS BOND : angle 0.92588 ( 2) hydrogen bonds : bond 0.03175 ( 166) hydrogen bonds : angle 4.65974 ( 498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.049 Fit side-chains REVERT: R 185 LEU cc_start: 0.7907 (tt) cc_final: 0.7441 (tp) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 0.0337 time to fit residues: 1.4816 Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.182501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140257 restraints weight = 2151.008| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.87 r_work: 0.3228 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2247 Z= 0.133 Angle : 0.561 11.074 3021 Z= 0.280 Chirality : 0.037 0.162 351 Planarity : 0.005 0.073 350 Dihedral : 9.739 56.155 382 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.72 % Allowed : 17.24 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.56), residues: 262 helix: 2.57 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -0.75 (1.03), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 262 TYR 0.007 0.001 TYR R 109 PHE 0.019 0.002 PHE R 75 TRP 0.016 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 2246) covalent geometry : angle 0.56111 ( 3019) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.86280 ( 2) hydrogen bonds : bond 0.03225 ( 166) hydrogen bonds : angle 4.68238 ( 498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.046 Fit side-chains REVERT: R 57 HIS cc_start: 0.5022 (OUTLIER) cc_final: 0.3291 (p-80) REVERT: R 185 LEU cc_start: 0.7929 (tt) cc_final: 0.7487 (tp) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.0399 time to fit residues: 1.8338 Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 57 HIS Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.180452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139054 restraints weight = 2165.183| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.83 r_work: 0.3220 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2247 Z= 0.160 Angle : 0.594 11.051 3021 Z= 0.297 Chirality : 0.038 0.174 351 Planarity : 0.005 0.074 350 Dihedral : 10.164 58.372 382 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.86 % Allowed : 17.24 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.56), residues: 262 helix: 2.45 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -0.64 (1.05), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 262 TYR 0.006 0.001 TYR R 109 PHE 0.015 0.002 PHE R 75 TRP 0.017 0.001 TRP R 144 HIS 0.002 0.001 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 2246) covalent geometry : angle 0.59377 ( 3019) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.93340 ( 2) hydrogen bonds : bond 0.03420 ( 166) hydrogen bonds : angle 4.78273 ( 498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.077 Fit side-chains REVERT: R 185 LEU cc_start: 0.7961 (tt) cc_final: 0.7541 (tp) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.0402 time to fit residues: 1.8535 Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.181190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.139624 restraints weight = 2171.752| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.84 r_work: 0.3226 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2247 Z= 0.147 Angle : 0.579 11.023 3021 Z= 0.290 Chirality : 0.038 0.165 351 Planarity : 0.005 0.074 350 Dihedral : 10.048 58.291 382 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.86 % Allowed : 18.10 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.56), residues: 262 helix: 2.54 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -0.90 (1.03), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 262 TYR 0.007 0.001 TYR R 109 PHE 0.017 0.002 PHE R 75 TRP 0.016 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 2246) covalent geometry : angle 0.57846 ( 3019) SS BOND : bond 0.00261 ( 1) SS BOND : angle 0.84942 ( 2) hydrogen bonds : bond 0.03335 ( 166) hydrogen bonds : angle 4.75188 ( 498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.080 Fit side-chains REVERT: R 185 LEU cc_start: 0.7923 (tt) cc_final: 0.7517 (tp) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 0.0432 time to fit residues: 1.9453 Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.0370 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.184079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141574 restraints weight = 2182.262| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.89 r_work: 0.3254 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2247 Z= 0.115 Angle : 0.546 10.942 3021 Z= 0.274 Chirality : 0.036 0.150 351 Planarity : 0.005 0.074 350 Dihedral : 9.583 58.281 382 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.29 % Allowed : 17.67 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.57), residues: 262 helix: 2.76 (0.37), residues: 203 sheet: None (None), residues: 0 loop : -1.36 (0.96), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 262 TYR 0.007 0.001 TYR R 109 PHE 0.019 0.002 PHE R 167 TRP 0.015 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 2246) covalent geometry : angle 0.54553 ( 3019) SS BOND : bond 0.00281 ( 1) SS BOND : angle 0.82141 ( 2) hydrogen bonds : bond 0.03081 ( 166) hydrogen bonds : angle 4.60240 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 681.90 seconds wall clock time: 12 minutes 26.47 seconds (746.47 seconds total)