Starting phenix.real_space_refine on Thu Sep 10 19:50:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8acb_15345/09_2026/8acb_15345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8acb_15345/09_2026/8acb_15345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8acb_15345/09_2026/8acb_15345.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8acb_15345/09_2026/8acb_15345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8acb_15345/09_2026/8acb_15345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8acb_15345/09_2026/8acb_15345.map" model { file = "/net/cci-nas-00/data/ceres_data/8acb_15345/09_2026/8acb_15345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8acb_15345/09_2026/8acb_15345.cif" } resolution = 2.6 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= 0.002 sd= 0.019 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 5 5.49 5 S 11 5.16 5 C 1116 2.51 5 N 314 2.21 5 O 369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1815 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1715 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNAv2': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Time building chain proxies: 0.63, per 1000 atoms: 0.35 Number of scatterers: 1815 At special positions: 0 Unit cell: (79.875, 75.615, 123.54, 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 11 16.00 P 5 15.00 O 369 8.00 N 314 7.00 C 1116 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: 0.21 Conformation dependent library (CDL) restraints added in 58.7 milliseconds 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 412 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 47.3% alpha, 4.5% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.856A pdb=" N THR A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.581A pdb=" N VAL A 127 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 128 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 149 Processing helix chain 'A' and resid 151 through 169 removed outlier: 3.629A pdb=" N ILE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 removed outlier: 4.197A pdb=" N HIS A 198 " --> pdb=" O PRO A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 209 removed outlier: 3.571A pdb=" N ILE A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.550A pdb=" N GLU A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 240 through 244 removed outlier: 4.417A pdb=" N ARG A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 3.581A pdb=" N ALA A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.607A pdb=" N GLU A 186 " --> pdb=" O ASP A 183 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.14 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 594 1.34 - 1.46: 308 1.46 - 1.57: 928 1.57 - 1.69: 9 1.69 - 1.81: 21 Bond restraints: 1860 Sorted by residual: bond pdb=" P U B 4 " pdb=" OP2 U B 4 " ideal model delta sigma weight residual 1.485 1.520 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" P U B 2 " pdb=" OP2 U B 2 " ideal model delta sigma weight residual 1.485 1.519 -0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" P U B 3 " pdb=" OP2 U B 3 " ideal model delta sigma weight residual 1.485 1.519 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" P U B 1 " pdb=" OP2 U B 1 " ideal model delta sigma weight residual 1.485 1.514 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" P U B 5 " pdb=" OP1 U B 5 " ideal model delta sigma weight residual 1.485 1.514 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 1855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 2478 1.95 - 3.91: 41 3.91 - 5.86: 19 5.86 - 7.81: 5 7.81 - 9.77: 1 Bond angle restraints: 2544 Sorted by residual: angle pdb=" C3' U B 1 " pdb=" O3' U B 1 " pdb=" P U B 2 " ideal model delta sigma weight residual 119.70 109.93 9.77 1.20e+00 6.94e-01 6.62e+01 angle pdb=" C3' U B 2 " pdb=" O3' U B 2 " pdb=" P U B 3 " ideal model delta sigma weight residual 119.70 114.83 4.87 1.20e+00 6.94e-01 1.65e+01 angle pdb=" C3' U B 3 " pdb=" O3' U B 3 " pdb=" P U B 4 " ideal model delta sigma weight residual 119.70 116.09 3.61 1.20e+00 6.94e-01 9.04e+00 angle pdb=" O3' U B 4 " pdb=" C3' U B 4 " pdb=" C2' U B 4 " ideal model delta sigma weight residual 113.80 107.02 6.78 3.00e+00 1.11e-01 5.10e+00 angle pdb=" OP1 U B 1 " pdb=" P U B 1 " pdb=" OP2 U B 1 " ideal model delta sigma weight residual 119.60 112.90 6.70 3.00e+00 1.11e-01 4.99e+00 ... (remaining 2539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 1005 16.65 - 33.29: 72 33.29 - 49.93: 20 49.93 - 66.58: 5 66.58 - 83.22: 3 Dihedral angle restraints: 1105 sinusoidal: 465 harmonic: 640 Sorted by residual: dihedral pdb=" C4' U B 4 " pdb=" C3' U B 4 " pdb=" C2' U B 4 " pdb=" C1' U B 4 " ideal model delta sinusoidal sigma weight residual 36.34 -43.58 79.92 1 3.10e+00 1.04e-01 8.24e+02 dihedral pdb=" O4' U B 4 " pdb=" C4' U B 4 " pdb=" C3' U B 4 " pdb=" C2' U B 4 " ideal model delta sinusoidal sigma weight residual -35.15 48.07 -83.22 1 4.00e+00 6.25e-02 5.29e+02 dihedral pdb=" O4' U B 4 " pdb=" C2' U B 4 " pdb=" C1' U B 4 " pdb=" C3' U B 4 " ideal model delta sinusoidal sigma weight residual 25.59 -24.75 50.34 3 3.80e+00 6.93e-02 1.38e+02 ... (remaining 1102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 276 0.159 - 0.318: 4 0.318 - 0.477: 0 0.477 - 0.636: 0 0.636 - 0.795: 5 Chirality restraints: 285 Sorted by residual: chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.97 -0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" P U B 4 " pdb=" OP1 U B 4 " pdb=" OP2 U B 4 " pdb=" O5' U B 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.92 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" P U B 2 " pdb=" OP1 U B 2 " pdb=" OP2 U B 2 " pdb=" O5' U B 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.92 -0.74 2.00e-01 2.50e+01 1.39e+01 ... (remaining 282 not shown) Planarity restraints: 321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 103 " 0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO A 104 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 282 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C LEU A 282 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 282 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP A 283 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 121 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.02e-01 pdb=" N PRO A 122 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " 0.012 5.00e-02 4.00e+02 ... (remaining 318 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 420 2.79 - 3.31: 1676 3.31 - 3.84: 2816 3.84 - 4.37: 3266 4.37 - 4.90: 5307 Nonbonded interactions: 13485 Sorted by model distance: nonbonded pdb=" OD1 ASP A 239 " pdb=" OG SER A 241 " model vdw 2.257 3.040 nonbonded pdb=" O GLY A 156 " pdb=" ND2 ASN A 160 " model vdw 2.286 3.120 nonbonded pdb=" O PRO A 257 " pdb=" NZ LYS A 261 " model vdw 2.291 3.120 nonbonded pdb=" OE2 GLU A 168 " pdb=" OH TYR A 227 " model vdw 2.319 3.040 nonbonded pdb=" NE2 GLN A 205 " pdb=" OP1 U B 2 " model vdw 2.485 3.120 ... (remaining 13480 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.480 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 0.035 1860 Z= 0.170 Angle : 0.749 9.766 2544 Z= 0.348 Chirality : 0.108 0.795 285 Planarity : 0.003 0.025 321 Dihedral : 13.676 83.220 693 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.58), residues: 218 helix: 0.34 (0.55), residues: 89 sheet: 1.47 (1.02), residues: 10 loop : -1.44 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.009 0.001 TYR A 245 PHE 0.008 0.001 PHE A 249 TRP 0.004 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 ( 1860) covalent geometry : angle 0.74871 / 0.35 ( 2544) hydrogen bonds : bond 0.23270 / 15.92 ( 61) hydrogen bonds : angle 6.03122 / 4.06 ( 177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.068 Fit side-chains REVERT: A 93 ARG cc_start: 0.5590 (mtt180) cc_final: 0.4671 (mtt180) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.7189 time to fit residues: 41.5414 Evaluate side-chains 52 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.0040 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 0.0970 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 0.0670 overall best weight: 2.4332 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.148746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128218 restraints weight = 2361.460| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.76 r_work: 0.3353 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1860 Z= 0.142 Angle : 0.656 8.314 2544 Z= 0.293 Chirality : 0.053 0.297 285 Planarity : 0.004 0.034 321 Dihedral : 11.696 145.327 298 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.14 % Allowed : 11.36 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.57), residues: 218 helix: 0.46 (0.54), residues: 96 sheet: 1.38 (1.05), residues: 10 loop : -1.64 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 259 TYR 0.008 0.001 TYR A 245 PHE 0.010 0.001 PHE A 249 TRP 0.007 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 1860) covalent geometry : angle 0.65586 / 0.29 ( 2544) hydrogen bonds : bond 0.05122 / 3.57 ( 61) hydrogen bonds : angle 4.21360 / 2.89 ( 177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.072 Fit side-chains REVERT: A 93 ARG cc_start: 0.5871 (mtt180) cc_final: 0.4692 (mtt180) REVERT: A 138 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8137 (tm-30) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.7499 time to fit residues: 41.0019 Evaluate side-chains 51 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125258 restraints weight = 2349.994| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.80 r_work: 0.3320 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1860 Z= 0.130 Angle : 0.645 9.279 2544 Z= 0.286 Chirality : 0.052 0.324 285 Planarity : 0.004 0.036 321 Dihedral : 11.023 138.902 298 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.14 % Allowed : 12.50 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.57), residues: 218 helix: 0.54 (0.53), residues: 96 sheet: 1.39 (1.25), residues: 10 loop : -1.72 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.008 0.001 TYR A 190 PHE 0.011 0.001 PHE A 249 TRP 0.007 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 1860) covalent geometry : angle 0.64534 / 0.29 ( 2544) hydrogen bonds : bond 0.03958 / 2.75 ( 61) hydrogen bonds : angle 3.82097 / 2.62 ( 177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.073 Fit side-chains REVERT: A 168 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8490 (mm-30) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.7520 time to fit residues: 37.3491 Evaluate side-chains 48 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127473 restraints weight = 2370.615| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.80 r_work: 0.3348 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 1860 Z= 0.099 Angle : 0.589 8.883 2544 Z= 0.260 Chirality : 0.049 0.308 285 Planarity : 0.003 0.031 321 Dihedral : 10.868 138.115 298 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.70 % Allowed : 14.20 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.58), residues: 218 helix: 0.71 (0.53), residues: 96 sheet: 2.17 (1.43), residues: 10 loop : -1.66 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 259 TYR 0.012 0.001 TYR A 190 PHE 0.009 0.001 PHE A 249 TRP 0.006 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 1860) covalent geometry : angle 0.58857 / 0.26 ( 2544) hydrogen bonds : bond 0.03509 / 2.42 ( 61) hydrogen bonds : angle 3.62864 / 2.48 ( 177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.066 Fit side-chains REVERT: A 126 GLU cc_start: 0.8637 (mt-10) cc_final: 0.7374 (tm-30) REVERT: A 168 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8479 (mm-30) outliers start: 3 outliers final: 1 residues processed: 55 average time/residue: 0.7067 time to fit residues: 39.4106 Evaluate side-chains 51 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 11 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 18 optimal weight: 0.0020 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 0.0970 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 overall best weight: 3.2192 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.141833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121628 restraints weight = 2385.037| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.82 r_work: 0.3253 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1860 Z= 0.151 Angle : 0.661 9.058 2544 Z= 0.297 Chirality : 0.053 0.337 285 Planarity : 0.004 0.037 321 Dihedral : 11.032 137.974 298 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.41 % Allowed : 14.77 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.58), residues: 218 helix: 0.82 (0.54), residues: 96 sheet: 1.92 (1.46), residues: 10 loop : -1.82 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.009 0.001 TYR A 190 PHE 0.011 0.001 PHE A 249 TRP 0.006 0.001 TRP A 179 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 1860) covalent geometry : angle 0.66113 / 0.30 ( 2544) hydrogen bonds : bond 0.04179 / 2.94 ( 61) hydrogen bonds : angle 3.69175 / 2.53 ( 177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.041 Fit side-chains REVERT: A 93 ARG cc_start: 0.4577 (OUTLIER) cc_final: 0.3766 (mtt180) REVERT: A 126 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7360 (tm-30) REVERT: A 168 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8433 (mm-30) REVERT: A 181 MET cc_start: 0.8956 (ttp) cc_final: 0.8660 (ttt) REVERT: A 219 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7918 (pp20) outliers start: 6 outliers final: 1 residues processed: 53 average time/residue: 0.6646 time to fit residues: 35.6648 Evaluate side-chains 52 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 9 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.143031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122855 restraints weight = 2353.332| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.80 r_work: 0.3288 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1860 Z= 0.124 Angle : 0.630 8.935 2544 Z= 0.281 Chirality : 0.052 0.330 285 Planarity : 0.004 0.035 321 Dihedral : 10.971 137.723 298 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.84 % Allowed : 15.34 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.57), residues: 218 helix: 0.80 (0.53), residues: 96 sheet: 1.85 (1.45), residues: 10 loop : -1.78 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.012 0.001 TYR A 190 PHE 0.010 0.001 PHE A 249 TRP 0.007 0.001 TRP A 179 HIS 0.001 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 1860) covalent geometry : angle 0.62983 / 0.28 ( 2544) hydrogen bonds : bond 0.03796 / 2.66 ( 61) hydrogen bonds : angle 3.57679 / 2.46 ( 177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.040 Fit side-chains REVERT: A 93 ARG cc_start: 0.4668 (OUTLIER) cc_final: 0.3622 (mtt180) REVERT: A 126 GLU cc_start: 0.8642 (mt-10) cc_final: 0.7358 (tm-30) REVERT: A 138 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: A 181 MET cc_start: 0.8909 (ttp) cc_final: 0.8591 (ttt) REVERT: A 219 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7969 (pp20) outliers start: 5 outliers final: 1 residues processed: 51 average time/residue: 0.7057 time to fit residues: 36.3945 Evaluate side-chains 53 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 0.0050 chunk 20 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 overall best weight: 2.7600 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.141282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121205 restraints weight = 2359.154| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.79 r_work: 0.3259 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1860 Z= 0.137 Angle : 0.649 8.664 2544 Z= 0.291 Chirality : 0.052 0.323 285 Planarity : 0.004 0.036 321 Dihedral : 11.018 137.875 298 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 2.84 % Allowed : 15.34 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.57), residues: 218 helix: 0.82 (0.54), residues: 96 sheet: 1.93 (1.46), residues: 10 loop : -1.81 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.013 0.001 TYR A 190 PHE 0.011 0.001 PHE A 249 TRP 0.007 0.001 TRP A 179 HIS 0.001 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 1860) covalent geometry : angle 0.64883 / 0.29 ( 2544) hydrogen bonds : bond 0.03866 / 2.69 ( 61) hydrogen bonds : angle 3.56938 / 2.43 ( 177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.067 Fit side-chains REVERT: A 93 ARG cc_start: 0.4819 (OUTLIER) cc_final: 0.3859 (mtt180) REVERT: A 126 GLU cc_start: 0.8666 (mt-10) cc_final: 0.7376 (tm-30) REVERT: A 138 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: A 181 MET cc_start: 0.8907 (ttp) cc_final: 0.8577 (ttt) REVERT: A 219 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8035 (pp20) outliers start: 5 outliers final: 1 residues processed: 53 average time/residue: 0.6400 time to fit residues: 34.3552 Evaluate side-chains 54 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.137236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117459 restraints weight = 2354.323| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.73 r_work: 0.3219 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1860 Z= 0.201 Angle : 0.754 9.258 2544 Z= 0.340 Chirality : 0.057 0.361 285 Planarity : 0.005 0.040 321 Dihedral : 11.381 139.734 298 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.84 % Allowed : 17.05 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.57), residues: 218 helix: 0.57 (0.53), residues: 98 sheet: 1.91 (1.44), residues: 10 loop : -1.92 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 109 TYR 0.015 0.002 TYR A 190 PHE 0.012 0.002 PHE A 249 TRP 0.007 0.001 TRP A 179 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 ( 1860) covalent geometry : angle 0.75439 / 0.34 ( 2544) hydrogen bonds : bond 0.04492 / 3.12 ( 61) hydrogen bonds : angle 3.68819 / 2.52 ( 177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.049 Fit side-chains REVERT: A 93 ARG cc_start: 0.4643 (OUTLIER) cc_final: 0.3795 (mtt180) REVERT: A 126 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7418 (tm-30) REVERT: A 138 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: A 181 MET cc_start: 0.8913 (ttp) cc_final: 0.8574 (ttt) REVERT: A 219 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8114 (pp20) REVERT: A 282 LEU cc_start: 0.6286 (OUTLIER) cc_final: 0.5864 (tt) outliers start: 5 outliers final: 1 residues processed: 51 average time/residue: 0.6544 time to fit residues: 33.7916 Evaluate side-chains 56 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121478 restraints weight = 2353.967| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.74 r_work: 0.3285 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1860 Z= 0.117 Angle : 0.633 8.833 2544 Z= 0.284 Chirality : 0.051 0.334 285 Planarity : 0.004 0.037 321 Dihedral : 11.090 138.022 298 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.41 % Allowed : 17.05 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.57), residues: 218 helix: 0.70 (0.53), residues: 96 sheet: 1.97 (1.46), residues: 10 loop : -1.85 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 244 TYR 0.015 0.001 TYR A 190 PHE 0.010 0.001 PHE A 249 TRP 0.008 0.001 TRP A 179 HIS 0.001 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 1860) covalent geometry : angle 0.63270 / 0.28 ( 2544) hydrogen bonds : bond 0.03726 / 2.58 ( 61) hydrogen bonds : angle 3.51925 / 2.41 ( 177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.068 Fit side-chains REVERT: A 93 ARG cc_start: 0.4729 (OUTLIER) cc_final: 0.3567 (mtt180) REVERT: A 126 GLU cc_start: 0.8681 (mt-10) cc_final: 0.7426 (tm-30) REVERT: A 138 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: A 181 MET cc_start: 0.8906 (ttp) cc_final: 0.8623 (ttt) REVERT: A 219 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8044 (pp20) outliers start: 6 outliers final: 1 residues processed: 53 average time/residue: 0.6899 time to fit residues: 37.0360 Evaluate side-chains 54 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 0.0060 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119698 restraints weight = 2330.283| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.72 r_work: 0.3257 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1860 Z= 0.142 Angle : 0.673 8.688 2544 Z= 0.301 Chirality : 0.053 0.330 285 Planarity : 0.004 0.037 321 Dihedral : 11.091 137.861 298 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.27 % Allowed : 18.75 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.57), residues: 218 helix: 0.72 (0.54), residues: 96 sheet: 1.94 (1.45), residues: 10 loop : -1.84 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 244 TYR 0.017 0.002 TYR A 190 PHE 0.012 0.002 PHE A 249 TRP 0.008 0.001 TRP A 179 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 1860) covalent geometry : angle 0.67288 / 0.30 ( 2544) hydrogen bonds : bond 0.03953 / 2.74 ( 61) hydrogen bonds : angle 3.55295 / 2.43 ( 177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.070 Fit side-chains REVERT: A 93 ARG cc_start: 0.4823 (OUTLIER) cc_final: 0.3756 (mtt180) REVERT: A 126 GLU cc_start: 0.8676 (mt-10) cc_final: 0.7423 (tm-30) REVERT: A 138 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: A 181 MET cc_start: 0.8909 (ttp) cc_final: 0.8577 (ttt) REVERT: A 219 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8032 (pp20) outliers start: 4 outliers final: 1 residues processed: 53 average time/residue: 0.6967 time to fit residues: 37.3728 Evaluate side-chains 55 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126784 restraints weight = 2388.503| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.78 r_work: 0.3342 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 1860 Z= 0.096 Angle : 0.586 8.124 2544 Z= 0.262 Chirality : 0.050 0.292 285 Planarity : 0.003 0.034 321 Dihedral : 10.842 138.100 298 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.70 % Allowed : 19.32 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.58), residues: 218 helix: 0.83 (0.54), residues: 96 sheet: 1.99 (1.46), residues: 10 loop : -1.77 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 244 TYR 0.018 0.001 TYR A 190 PHE 0.009 0.001 PHE A 249 TRP 0.009 0.001 TRP A 179 HIS 0.001 0.000 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 1860) covalent geometry : angle 0.58615 / 0.26 ( 2544) hydrogen bonds : bond 0.03336 / 2.31 ( 61) hydrogen bonds : angle 3.43388 / 2.36 ( 177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1357.08 seconds wall clock time: 23 minutes 56.30 seconds (1436.30 seconds total)