Starting phenix.real_space_refine on Wed Jul 1 20:45:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8acb_15345/07_2026/8acb_15345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8acb_15345/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8acb_15345/07_2026/8acb_15345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8acb_15345/07_2026/8acb_15345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8acb_15345/07_2026/8acb_15345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8acb_15345/07_2026/8acb_15345.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8acb_15345/07_2026/8acb_15345.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8acb_15345/07_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-dev-6108/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: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Time building chain proxies: 0.74, per 1000 atoms: 0.41 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: 0.16 Conformation dependent library (CDL) restraints added in 70.7 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: 0.22 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: 0.21 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=" O5' U B 2 " pdb=" C5' U B 2 " ideal model delta sigma weight residual 1.420 1.450 -0.030 1.50e-02 4.44e+03 4.06e+00 bond pdb=" O5' U B 5 " pdb=" C5' U B 5 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.77e+00 bond pdb=" P U B 4 " pdb=" O5' U B 4 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.50e-02 4.44e+03 3.57e+00 bond pdb=" O5' U B 1 " pdb=" C5' U B 1 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.25e+00 bond pdb=" O5' U B 3 " pdb=" C5' U B 3 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.14e+00 ... (remaining 1855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 2487 2.05 - 4.11: 38 4.11 - 6.16: 15 6.16 - 8.21: 3 8.21 - 10.27: 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 120.20 109.93 10.27 1.50e+00 4.44e-01 4.68e+01 angle pdb=" O4' U B 4 " pdb=" C4' U B 4 " pdb=" C3' U B 4 " ideal model delta sigma weight residual 106.10 101.15 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" C4' U B 4 " pdb=" C3' U B 4 " pdb=" C2' U B 4 " ideal model delta sigma weight residual 102.60 98.80 3.80 1.00e+00 1.00e+00 1.45e+01 angle pdb=" C3' U B 2 " pdb=" O3' U B 2 " pdb=" P U B 3 " ideal model delta sigma weight residual 120.20 114.83 5.37 1.50e+00 4.44e-01 1.28e+01 angle pdb=" O3' U B 4 " pdb=" P U B 5 " pdb=" O5' U B 5 " ideal model delta sigma weight residual 104.00 108.21 -4.21 1.50e+00 4.44e-01 7.89e+00 ... (remaining 2539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.02: 1083 33.02 - 66.03: 20 66.03 - 99.05: 1 99.05 - 132.06: 0 132.06 - 165.08: 1 Dihedral angle restraints: 1105 sinusoidal: 465 harmonic: 640 Sorted by residual: dihedral pdb=" O4' U B 5 " pdb=" C1' U B 5 " pdb=" N1 U B 5 " pdb=" C2 U B 5 " ideal model delta sinusoidal sigma weight residual 200.00 34.92 165.08 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" C5' U B 4 " pdb=" C4' U B 4 " pdb=" C3' U B 4 " pdb=" O3' U B 4 " ideal model delta sinusoidal sigma weight residual 147.00 179.12 -32.12 1 8.00e+00 1.56e-02 2.30e+01 dihedral pdb=" C3' U B 4 " pdb=" C4' U B 4 " pdb=" O4' U B 4 " pdb=" C1' U B 4 " ideal model delta sinusoidal sigma weight residual -2.00 -34.08 32.08 1 8.00e+00 1.56e-02 2.29e+01 ... (remaining 1102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 273 0.112 - 0.223: 6 0.223 - 0.335: 1 0.335 - 0.446: 1 0.446 - 0.558: 4 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 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.78e+00 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 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.60e+00 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 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.44e+00 ... (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: 0.550 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.340 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.330 ------------------------------------------------------------------------------- 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= 0.196 Angle : 0.711 10.266 2544 Z= 0.384 Chirality : 0.079 0.558 285 Planarity : 0.003 0.025 321 Dihedral : 13.941 165.075 693 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 0.00363 / 0.20 ( 1860) covalent geometry : angle 0.71054 / 0.38 ( 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 : 0.071 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: 0.7376 time to fit residues: 42.7282 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 : 0.114 ------------------------------------------------------------------------------- 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: 0.8980 overall best weight: 2.5994 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.146223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125436 restraints weight = 2362.208| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.77 r_work: 0.3332 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1860 Z= 0.137 Angle : 0.563 5.469 2544 Z= 0.283 Chirality : 0.040 0.143 285 Planarity : 0.004 0.036 321 Dihedral : 12.695 172.295 298 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.14 % Allowed : 11.93 % Favored : 86.93 % 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: -0.85 (0.57), residues: 218 helix: 0.42 (0.53), residues: 96 sheet: 1.40 (1.08), residues: 10 loop : -1.68 (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 245 PHE 0.010 0.002 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 0.00316 / 0.14 ( 1860) covalent geometry : angle 0.56319 / 0.28 ( 2544) hydrogen bonds : bond 0.04482 / 3.11 ( 61) hydrogen bonds : angle 4.14288 / 2.86 ( 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 55 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.074 Fit side-chains REVERT: A 138 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8114 (tm-30) outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 0.7481 time to fit residues: 40.1582 Evaluate side-chains 50 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.065 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 20 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.145433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124585 restraints weight = 2403.202| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.84 r_work: 0.3313 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2320 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= 0.104 Angle : 0.495 4.928 2544 Z= 0.248 Chirality : 0.038 0.131 285 Planarity : 0.003 0.033 321 Dihedral : 12.550 171.180 298 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.27 % Allowed : 12.50 % Favored : 85.23 % 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: -0.75 (0.57), residues: 218 helix: 0.58 (0.53), residues: 96 sheet: 1.45 (1.26), residues: 10 loop : -1.71 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 244 TYR 0.010 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 0.00238 / 0.10 ( 1860) covalent geometry : angle 0.49525 / 0.25 ( 2544) hydrogen bonds : bond 0.03796 / 2.63 ( 61) hydrogen bonds : angle 3.74199 / 2.56 ( 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 54 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.099 Fit side-chains REVERT: A 294 GLU cc_start: 0.7975 (pm20) cc_final: 0.7746 (pm20) outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 0.7128 time to fit residues: 36.0933 Evaluate side-chains 50 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 0.0020 chunk 6 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.149716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129190 restraints weight = 2470.545| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.87 r_work: 0.3375 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2465 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= 0.081 Angle : 0.447 5.005 2544 Z= 0.223 Chirality : 0.035 0.109 285 Planarity : 0.003 0.029 321 Dihedral : 12.379 166.828 298 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.84 % Allowed : 13.07 % 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: -0.51 (0.58), residues: 218 helix: 0.81 (0.54), residues: 96 sheet: 1.75 (1.37), residues: 10 loop : -1.64 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 204 TYR 0.010 0.001 TYR A 190 PHE 0.007 0.001 PHE A 249 TRP 0.006 0.001 TRP A 179 HIS 0.000 0.000 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.08 ( 1860) covalent geometry : angle 0.44744 / 0.22 ( 2544) hydrogen bonds : bond 0.03001 / 2.06 ( 61) hydrogen bonds : angle 3.48262 / 2.35 ( 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: 5 poor density : 51 time to evaluate : 0.070 Fit side-chains REVERT: A 93 ARG cc_start: 0.4753 (OUTLIER) cc_final: 0.3648 (mtt180) REVERT: A 126 GLU cc_start: 0.8651 (mt-10) cc_final: 0.7345 (tm-30) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.6583 time to fit residues: 36.0175 Evaluate side-chains 52 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.052 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 282 LEU 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: 0.9980 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117667 restraints weight = 2429.872| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.80 r_work: 0.3211 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1860 Z= 0.180 Angle : 0.599 6.422 2544 Z= 0.298 Chirality : 0.042 0.154 285 Planarity : 0.005 0.038 321 Dihedral : 12.965 177.371 298 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 2.27 % Allowed : 15.34 % Favored : 82.39 % 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: -0.62 (0.58), residues: 218 helix: 0.83 (0.54), residues: 97 sheet: 1.67 (1.38), residues: 10 loop : -1.84 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 259 TYR 0.009 0.002 TYR A 190 PHE 0.012 0.002 PHE A 249 TRP 0.005 0.001 TRP A 179 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 1860) covalent geometry : angle 0.59910 / 0.30 ( 2544) hydrogen bonds : bond 0.04353 / 3.02 ( 61) hydrogen bonds : angle 3.76752 / 2.55 ( 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 53 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.070 Fit side-chains REVERT: A 93 ARG cc_start: 0.4691 (OUTLIER) cc_final: 0.3673 (mtt180) REVERT: A 126 GLU cc_start: 0.8694 (mt-10) cc_final: 0.7429 (tm-30) REVERT: A 181 MET cc_start: 0.9019 (ttp) cc_final: 0.8706 (ttt) REVERT: A 219 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7949 (pp20) REVERT: A 276 ARG cc_start: 0.7552 (ttp-170) cc_final: 0.7236 (ttp-170) outliers start: 4 outliers final: 1 residues processed: 51 average time/residue: 0.6963 time to fit residues: 35.9388 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 : 0.040 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.139407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118781 restraints weight = 2409.198| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.84 r_work: 0.3238 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2987 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= 0.138 Angle : 0.565 6.232 2544 Z= 0.278 Chirality : 0.040 0.143 285 Planarity : 0.004 0.037 321 Dihedral : 12.581 175.236 298 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.84 % Allowed : 14.77 % Favored : 82.39 % 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: 0.85 (0.54), residues: 96 sheet: 1.73 (1.38), residues: 10 loop : -1.82 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 244 TYR 0.012 0.002 TYR A 190 PHE 0.011 0.002 PHE A 249 TRP 0.006 0.001 TRP A 179 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 1860) covalent geometry : angle 0.56471 / 0.28 ( 2544) hydrogen bonds : bond 0.03847 / 2.67 ( 61) hydrogen bonds : angle 3.63120 / 2.47 ( 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 56 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.071 Fit side-chains REVERT: A 93 ARG cc_start: 0.4768 (OUTLIER) cc_final: 0.3853 (mtt180) REVERT: A 126 GLU cc_start: 0.8671 (mt-10) cc_final: 0.7365 (tm-30) REVERT: A 138 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: A 181 MET cc_start: 0.9018 (ttp) cc_final: 0.8683 (ttt) REVERT: A 219 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8010 (pp20) REVERT: A 276 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.7249 (ttp-170) REVERT: A 294 GLU cc_start: 0.8010 (pm20) cc_final: 0.7765 (pm20) outliers start: 5 outliers final: 1 residues processed: 53 average time/residue: 0.7496 time to fit residues: 40.2162 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 : 0.065 ------------------------------------------------------------------------------- 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: 4.9990 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.139817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119023 restraints weight = 2406.291| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.80 r_work: 0.3246 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3162 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= 0.116 Angle : 0.536 6.221 2544 Z= 0.265 Chirality : 0.039 0.129 285 Planarity : 0.004 0.035 321 Dihedral : 12.052 168.416 298 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.41 % Allowed : 14.20 % Favored : 82.39 % 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: -0.52 (0.58), residues: 218 helix: 0.86 (0.54), residues: 96 sheet: 1.82 (1.44), residues: 10 loop : -1.71 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 244 TYR 0.013 0.001 TYR A 190 PHE 0.011 0.001 PHE A 249 TRP 0.008 0.001 TRP A 179 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 1860) covalent geometry : angle 0.53571 / 0.26 ( 2544) hydrogen bonds : bond 0.03696 / 2.56 ( 61) hydrogen bonds : angle 3.53412 / 2.40 ( 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: 6 poor density : 50 time to evaluate : 0.077 Fit side-chains REVERT: A 93 ARG cc_start: 0.4841 (OUTLIER) cc_final: 0.3870 (mtt180) REVERT: A 126 GLU cc_start: 0.8693 (mt-10) cc_final: 0.7369 (tm-30) REVERT: A 138 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: A 181 MET cc_start: 0.9003 (ttp) cc_final: 0.8716 (ttt) REVERT: A 219 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7973 (pp20) REVERT: A 276 ARG cc_start: 0.7547 (ttp-170) cc_final: 0.7204 (ttp-170) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.4703 time to fit residues: 25.2609 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 : 0.036 ------------------------------------------------------------------------------- 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 188 VAL 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: 0.0970 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 overall best weight: 2.9782 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.138326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117645 restraints weight = 2393.763| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.80 r_work: 0.3230 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 0.031 1860 Z= 0.139 Angle : 0.576 6.285 2544 Z= 0.283 Chirality : 0.040 0.141 285 Planarity : 0.004 0.036 321 Dihedral : 12.176 170.047 298 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % 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: -0.58 (0.57), residues: 218 helix: 0.85 (0.54), residues: 96 sheet: 1.76 (1.43), 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 0.015 0.002 TYR A 190 PHE 0.011 0.001 PHE A 249 TRP 0.007 0.001 TRP A 179 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 1860) covalent geometry : angle 0.57639 / 0.28 ( 2544) hydrogen bonds : bond 0.03929 / 2.72 ( 61) hydrogen bonds : angle 3.59139 / 2.43 ( 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 56 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.046 Fit side-chains REVERT: A 93 ARG cc_start: 0.4763 (OUTLIER) cc_final: 0.3863 (mtt180) REVERT: A 126 GLU cc_start: 0.8691 (mt-10) cc_final: 0.7369 (tm-30) REVERT: A 138 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: A 181 MET cc_start: 0.8986 (ttp) cc_final: 0.8661 (ttt) REVERT: A 219 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8022 (pp20) REVERT: A 276 ARG cc_start: 0.7549 (ttp-170) cc_final: 0.7204 (ttp-170) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.4947 time to fit residues: 26.5318 Evaluate side-chains 55 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.044 ------------------------------------------------------------------------------- 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 188 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.138475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117942 restraints weight = 2417.787| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.81 r_work: 0.3225 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3290 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= 0.128 Angle : 0.555 6.212 2544 Z= 0.275 Chirality : 0.040 0.140 285 Planarity : 0.004 0.036 321 Dihedral : 12.145 169.263 298 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 : 15.91 % Favored : 81.25 % 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: 0.82 (0.54), residues: 96 sheet: 1.89 (1.49), residues: 10 loop : -1.74 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 259 TYR 0.017 0.001 TYR A 190 PHE 0.011 0.001 PHE A 249 TRP 0.007 0.001 TRP A 179 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 1860) covalent geometry : angle 0.55478 / 0.28 ( 2544) hydrogen bonds : bond 0.03811 / 2.64 ( 61) hydrogen bonds : angle 3.53136 / 2.40 ( 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 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: 0.4853 (OUTLIER) cc_final: 0.3846 (mtt180) REVERT: A 126 GLU cc_start: 0.8689 (mt-10) cc_final: 0.7371 (tm-30) REVERT: A 138 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: A 181 MET cc_start: 0.8997 (ttp) cc_final: 0.8693 (ttt) REVERT: A 219 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7996 (pp20) REVERT: A 276 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.7205 (ttp-170) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 0.5312 time to fit residues: 27.4199 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 ------------------------------------------------------------------------------- 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 188 VAL 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: 7.9990 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 0.0060 chunk 21 optimal weight: 0.0370 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.9476 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.143437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122892 restraints weight = 2421.793| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.82 r_work: 0.3295 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3140 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= 0.091 Angle : 0.492 6.030 2544 Z= 0.243 Chirality : 0.037 0.112 285 Planarity : 0.003 0.032 321 Dihedral : 11.909 165.276 298 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.70 % Allowed : 17.05 % Favored : 81.25 % 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: -0.47 (0.58), residues: 218 helix: 0.89 (0.54), residues: 96 sheet: 1.98 (1.51), residues: 10 loop : -1.68 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 244 TYR 0.015 0.001 TYR A 190 PHE 0.009 0.001 PHE A 249 TRP 0.009 0.001 TRP A 179 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 1860) covalent geometry : angle 0.49229 / 0.24 ( 2544) hydrogen bonds : bond 0.03274 / 2.25 ( 61) hydrogen bonds : angle 3.38057 / 2.30 ( 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 54 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.046 Fit side-chains REVERT: A 93 ARG cc_start: 0.4622 (OUTLIER) cc_final: 0.3574 (mtt180) REVERT: A 126 GLU cc_start: 0.8659 (mt-10) cc_final: 0.7327 (tm-30) REVERT: A 181 MET cc_start: 0.8930 (ttp) cc_final: 0.8672 (ttt) REVERT: A 219 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7920 (pp20) REVERT: A 276 ARG cc_start: 0.7467 (ttp-170) cc_final: 0.7091 (ttp-170) outliers start: 3 outliers final: 1 residues processed: 52 average time/residue: 0.4751 time to fit residues: 25.0152 Evaluate side-chains 53 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.044 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.0270 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.139922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119559 restraints weight = 2470.921| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.79 r_work: 0.3262 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3156 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= 0.111 Angle : 0.525 6.231 2544 Z= 0.258 Chirality : 0.038 0.118 285 Planarity : 0.004 0.033 321 Dihedral : 11.909 166.133 298 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 1.70 % Allowed : 17.05 % Favored : 81.25 % 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: -0.41 (0.58), residues: 218 helix: 0.97 (0.54), residues: 96 sheet: 1.90 (1.50), residues: 10 loop : -1.67 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 259 TYR 0.017 0.002 TYR A 190 PHE 0.011 0.001 PHE A 249 TRP 0.008 0.001 TRP A 179 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 1860) covalent geometry : angle 0.52506 / 0.26 ( 2544) hydrogen bonds : bond 0.03538 / 2.45 ( 61) hydrogen bonds : angle 3.43389 / 2.34 ( 177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1216.20 seconds wall clock time: 21 minutes 36.76 seconds (1296.76 seconds total)