Starting phenix.real_space_refine on Tue Mar 3 11:19:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7exa_31367/03_2026/7exa_31367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7exa_31367/03_2026/7exa_31367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7exa_31367/03_2026/7exa_31367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7exa_31367/03_2026/7exa_31367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7exa_31367/03_2026/7exa_31367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7exa_31367/03_2026/7exa_31367.map" } resolution = 2.9 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= 0.000 sd= 0.007 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 6 5.49 5 S 19 5.16 5 C 1942 2.51 5 N 530 2.21 5 O 591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3088 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2968 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 0.87, per 1000 atoms: 0.28 Number of scatterers: 3088 At special positions: 0 Unit cell: (91.74, 66.66, 79.86, 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 19 16.00 P 6 15.00 O 591 8.00 N 530 7.00 C 1942 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 121.5 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 69.5% alpha, 3.7% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 Processing helix chain 'A' and resid 44 through 61 Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 83 through 92 removed outlier: 4.289A pdb=" N LEU A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.553A pdb=" N GLY A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 179 removed outlier: 3.582A pdb=" N PHE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 removed outlier: 4.202A pdb=" N ASP A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.639A pdb=" N SER A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 248 through 262 removed outlier: 3.655A pdb=" N MET A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.770A pdb=" N GLY A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 325 through 328 Processing helix chain 'A' and resid 329 through 344 removed outlier: 3.653A pdb=" N VAL A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 358 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.275A pdb=" N VAL A 35 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N CYS A 102 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 37 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL A 39 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLY A 106 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 115 " --> pdb=" O ASP A 105 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 697 1.33 - 1.45: 697 1.45 - 1.57: 1725 1.57 - 1.69: 11 1.69 - 1.81: 31 Bond restraints: 3161 Sorted by residual: bond pdb=" N THR A 145 " pdb=" CA THR A 145 " ideal model delta sigma weight residual 1.453 1.487 -0.033 9.20e-03 1.18e+04 1.32e+01 bond pdb=" N GLN A 187 " pdb=" CA GLN A 187 " ideal model delta sigma weight residual 1.455 1.489 -0.034 9.60e-03 1.09e+04 1.25e+01 bond pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta sigma weight residual 1.462 1.496 -0.035 1.01e-02 9.80e+03 1.18e+01 bond pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.99e+00 bond pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.56e+00 ... (remaining 3156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 3694 1.77 - 3.53: 545 3.53 - 5.30: 56 5.30 - 7.07: 5 7.07 - 8.83: 4 Bond angle restraints: 4304 Sorted by residual: angle pdb=" C4' U B 23 " pdb=" C3' U B 23 " pdb=" O3' U B 23 " ideal model delta sigma weight residual 113.00 121.83 -8.83 1.50e+00 4.44e-01 3.47e+01 angle pdb=" C4' U B 24 " pdb=" C3' U B 24 " pdb=" O3' U B 24 " ideal model delta sigma weight residual 113.00 121.10 -8.10 1.50e+00 4.44e-01 2.91e+01 angle pdb=" C4' U B 20 " pdb=" C3' U B 20 " pdb=" O3' U B 20 " ideal model delta sigma weight residual 113.00 120.61 -7.61 1.50e+00 4.44e-01 2.57e+01 angle pdb=" CA GLY A 244 " pdb=" C GLY A 244 " pdb=" O GLY A 244 " ideal model delta sigma weight residual 122.28 118.38 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" O2' U B 20 " pdb=" C2' U B 20 " pdb=" C1' U B 20 " ideal model delta sigma weight residual 108.40 102.64 5.76 1.50e+00 4.44e-01 1.47e+01 ... (remaining 4299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 1688 17.89 - 35.79: 185 35.79 - 53.68: 40 53.68 - 71.58: 13 71.58 - 89.47: 5 Dihedral angle restraints: 1931 sinusoidal: 839 harmonic: 1092 Sorted by residual: dihedral pdb=" C5' U B 25 " pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" O3' U B 25 " ideal model delta sinusoidal sigma weight residual 147.00 106.23 40.77 1 8.00e+00 1.56e-02 3.64e+01 dihedral pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" C2' U B 25 " pdb=" C1' U B 25 " ideal model delta sinusoidal sigma weight residual -35.00 0.49 -35.49 1 8.00e+00 1.56e-02 2.79e+01 dihedral pdb=" O4' U B 25 " pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" C2' U B 25 " ideal model delta sinusoidal sigma weight residual 24.00 -11.43 35.43 1 8.00e+00 1.56e-02 2.78e+01 ... (remaining 1928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 294 0.052 - 0.105: 120 0.105 - 0.157: 40 0.157 - 0.209: 14 0.209 - 0.261: 12 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA LEU A 90 " pdb=" N LEU A 90 " pdb=" C LEU A 90 " pdb=" CB LEU A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C3' U B 23 " pdb=" C4' U B 23 " pdb=" O3' U B 23 " pdb=" C2' U B 23 " both_signs ideal model delta sigma weight residual False -2.48 -2.23 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 477 not shown) Planarity restraints: 543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 277 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C LEU A 277 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU A 277 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 278 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 24 " -0.020 2.00e-02 2.50e+03 1.21e-02 3.30e+00 pdb=" N1 U B 24 " 0.030 2.00e-02 2.50e+03 pdb=" C2 U B 24 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 24 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U B 24 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 24 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 314 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C ALA A 314 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA A 314 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 315 " -0.010 2.00e-02 2.50e+03 ... (remaining 540 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 16 2.57 - 3.15: 2400 3.15 - 3.73: 4705 3.73 - 4.32: 6964 4.32 - 4.90: 11041 Nonbonded interactions: 25126 Sorted by model distance: nonbonded pdb=" O LYS A 180 " pdb=" O ALA A 184 " model vdw 1.984 3.040 nonbonded pdb=" OG SER A 94 " pdb=" OE1 GLN A 231 " model vdw 2.252 3.040 nonbonded pdb=" O SER A 61 " pdb=" NH2 ARG A 69 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASN A 63 " pdb=" OD2 ASP A 136 " model vdw 2.385 3.040 nonbonded pdb=" O ALA A 64 " pdb=" NH1 ARG A 69 " model vdw 2.394 3.120 ... (remaining 25121 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: 9.930 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.760 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.010 0.042 3161 Z= 0.692 Angle : 1.219 8.833 4304 Z= 0.894 Chirality : 0.074 0.261 480 Planarity : 0.005 0.030 543 Dihedral : 16.181 89.470 1233 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.60 % Allowed : 9.94 % Favored : 88.46 % 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: -0.45 (0.40), residues: 372 helix: -0.46 (0.31), residues: 223 sheet: 0.89 (1.43), residues: 14 loop : 0.20 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 10 TYR 0.022 0.003 TYR A 361 PHE 0.016 0.003 PHE A 289 TRP 0.011 0.002 TRP A 175 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.01040 ( 3161) covalent geometry : angle 1.21858 ( 4304) hydrogen bonds : bond 0.18406 ( 167) hydrogen bonds : angle 6.19003 ( 474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.092 Fit side-chains REVERT: A 6 LYS cc_start: 0.8325 (mttt) cc_final: 0.8024 (mttp) REVERT: A 65 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7552 (mtp180) REVERT: A 88 ILE cc_start: 0.7996 (mm) cc_final: 0.7723 (mm) REVERT: A 214 GLU cc_start: 0.6853 (mp0) cc_final: 0.6228 (mm-30) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.8158 time to fit residues: 50.7052 Evaluate side-chains 43 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 248 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 63 ASN A 68 HIS A 121 ASN A 212 GLN A 238 GLN A 346 GLN A 373 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.130071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.109068 restraints weight = 3058.314| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.03 r_work: 0.2848 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3161 Z= 0.153 Angle : 0.573 5.278 4304 Z= 0.305 Chirality : 0.042 0.198 480 Planarity : 0.004 0.035 543 Dihedral : 9.730 60.423 521 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.88 % Allowed : 12.50 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.44), residues: 372 helix: 1.33 (0.35), residues: 220 sheet: 1.40 (1.46), residues: 14 loop : 1.05 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.017 0.002 TYR A 361 PHE 0.013 0.002 PHE A 289 TRP 0.007 0.002 TRP A 175 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3161) covalent geometry : angle 0.57262 ( 4304) hydrogen bonds : bond 0.05569 ( 167) hydrogen bonds : angle 4.55704 ( 474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.120 Fit side-chains REVERT: A 6 LYS cc_start: 0.8568 (mttt) cc_final: 0.8279 (mttt) REVERT: A 17 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7830 (mm) REVERT: A 208 ARG cc_start: 0.7875 (ttt-90) cc_final: 0.7189 (ttp-170) REVERT: A 214 GLU cc_start: 0.7023 (mp0) cc_final: 0.6484 (tp30) outliers start: 9 outliers final: 4 residues processed: 51 average time/residue: 0.8611 time to fit residues: 44.7445 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 0.0170 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.0670 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.139227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.121861 restraints weight = 3075.758| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.79 r_work: 0.2927 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3161 Z= 0.090 Angle : 0.436 4.666 4304 Z= 0.235 Chirality : 0.038 0.197 480 Planarity : 0.003 0.032 543 Dihedral : 9.139 60.272 517 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.24 % Allowed : 13.46 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.45), residues: 372 helix: 1.98 (0.36), residues: 220 sheet: 1.66 (1.47), residues: 14 loop : 1.38 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.010 0.001 TYR A 361 PHE 0.009 0.001 PHE A 163 TRP 0.003 0.001 TRP A 175 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 3161) covalent geometry : angle 0.43611 ( 4304) hydrogen bonds : bond 0.03620 ( 167) hydrogen bonds : angle 3.99978 ( 474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.112 Fit side-chains REVERT: A 208 ARG cc_start: 0.7939 (ttt-90) cc_final: 0.7315 (ttp-170) REVERT: A 214 GLU cc_start: 0.7050 (mp0) cc_final: 0.6574 (tp30) outliers start: 7 outliers final: 2 residues processed: 52 average time/residue: 0.7669 time to fit residues: 40.6757 Evaluate side-chains 41 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.128964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.109077 restraints weight = 3111.910| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 0.96 r_work: 0.2774 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3161 Z= 0.179 Angle : 0.566 5.041 4304 Z= 0.297 Chirality : 0.042 0.192 480 Planarity : 0.004 0.031 543 Dihedral : 9.223 60.379 516 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.88 % Allowed : 13.46 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.43), residues: 372 helix: 1.75 (0.36), residues: 220 sheet: 2.17 (1.47), residues: 14 loop : 1.02 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.017 0.002 TYR A 361 PHE 0.014 0.002 PHE A 289 TRP 0.009 0.003 TRP A 281 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 3161) covalent geometry : angle 0.56586 ( 4304) hydrogen bonds : bond 0.05686 ( 167) hydrogen bonds : angle 4.28698 ( 474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.094 Fit side-chains REVERT: A 6 LYS cc_start: 0.8548 (mttt) cc_final: 0.8265 (mttt) REVERT: A 208 ARG cc_start: 0.7908 (ttt-90) cc_final: 0.7251 (ttp-170) REVERT: A 214 GLU cc_start: 0.7113 (mp0) cc_final: 0.6632 (tp30) REVERT: A 317 GLU cc_start: 0.7705 (pt0) cc_final: 0.7448 (mt-10) outliers start: 9 outliers final: 5 residues processed: 52 average time/residue: 0.8134 time to fit residues: 43.0511 Evaluate side-chains 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.132096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.111562 restraints weight = 3077.231| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 0.98 r_work: 0.2856 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3161 Z= 0.119 Angle : 0.488 4.818 4304 Z= 0.258 Chirality : 0.039 0.191 480 Planarity : 0.004 0.031 543 Dihedral : 8.935 60.275 516 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 4.17 % Allowed : 13.46 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.43), residues: 372 helix: 1.92 (0.35), residues: 220 sheet: 2.25 (1.53), residues: 14 loop : 1.04 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.014 0.001 TYR A 361 PHE 0.012 0.001 PHE A 270 TRP 0.006 0.002 TRP A 281 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3161) covalent geometry : angle 0.48792 ( 4304) hydrogen bonds : bond 0.04550 ( 167) hydrogen bonds : angle 4.09976 ( 474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.154 Fit side-chains REVERT: A 6 LYS cc_start: 0.8538 (mttt) cc_final: 0.8267 (mttp) REVERT: A 93 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7658 (mtm180) REVERT: A 214 GLU cc_start: 0.7014 (mp0) cc_final: 0.6478 (tp30) REVERT: A 317 GLU cc_start: 0.7733 (pt0) cc_final: 0.7457 (mt-10) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 0.8455 time to fit residues: 49.0752 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 0.0370 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.128906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.107776 restraints weight = 3103.550| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.07 r_work: 0.2827 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3161 Z= 0.165 Angle : 0.546 4.959 4304 Z= 0.288 Chirality : 0.041 0.192 480 Planarity : 0.004 0.030 543 Dihedral : 9.181 60.310 516 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.88 % Allowed : 14.74 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.43), residues: 372 helix: 1.77 (0.35), residues: 220 sheet: 2.38 (1.53), residues: 14 loop : 0.95 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.016 0.002 TYR A 361 PHE 0.014 0.002 PHE A 289 TRP 0.009 0.003 TRP A 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3161) covalent geometry : angle 0.54568 ( 4304) hydrogen bonds : bond 0.05439 ( 167) hydrogen bonds : angle 4.23130 ( 474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.085 Fit side-chains REVERT: A 6 LYS cc_start: 0.8508 (mttt) cc_final: 0.8253 (mttp) REVERT: A 93 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7786 (mtm180) REVERT: A 214 GLU cc_start: 0.7070 (mp0) cc_final: 0.6534 (tp30) REVERT: A 317 GLU cc_start: 0.7790 (pt0) cc_final: 0.7485 (mt-10) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.8751 time to fit residues: 46.3151 Evaluate side-chains 49 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 30.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.133232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.116486 restraints weight = 3099.100| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 0.69 r_work: 0.2898 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3161 Z= 0.104 Angle : 0.460 4.662 4304 Z= 0.245 Chirality : 0.038 0.193 480 Planarity : 0.003 0.031 543 Dihedral : 8.794 60.243 516 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.88 % Allowed : 14.74 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.44), residues: 372 helix: 2.05 (0.35), residues: 220 sheet: 2.30 (1.56), residues: 14 loop : 1.03 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 101 TYR 0.014 0.001 TYR A 361 PHE 0.009 0.001 PHE A 270 TRP 0.005 0.002 TRP A 281 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3161) covalent geometry : angle 0.45989 ( 4304) hydrogen bonds : bond 0.04174 ( 167) hydrogen bonds : angle 3.98448 ( 474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.134 Fit side-chains REVERT: A 214 GLU cc_start: 0.7139 (mp0) cc_final: 0.6610 (tp30) REVERT: A 317 GLU cc_start: 0.7784 (pt0) cc_final: 0.7518 (mt-10) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.8525 time to fit residues: 45.1520 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.133403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.113281 restraints weight = 3118.455| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.28 r_work: 0.2890 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3161 Z= 0.104 Angle : 0.460 4.675 4304 Z= 0.244 Chirality : 0.038 0.191 480 Planarity : 0.003 0.031 543 Dihedral : 8.724 60.212 516 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.44), residues: 372 helix: 2.12 (0.35), residues: 220 sheet: 2.43 (1.56), residues: 14 loop : 1.04 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.014 0.001 TYR A 361 PHE 0.009 0.001 PHE A 270 TRP 0.006 0.002 TRP A 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 3161) covalent geometry : angle 0.45976 ( 4304) hydrogen bonds : bond 0.04177 ( 167) hydrogen bonds : angle 3.90823 ( 474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.114 Fit side-chains REVERT: A 6 LYS cc_start: 0.8509 (mttt) cc_final: 0.8245 (mttp) REVERT: A 41 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7640 (t0) REVERT: A 214 GLU cc_start: 0.7015 (mp0) cc_final: 0.6494 (tp30) REVERT: A 317 GLU cc_start: 0.7731 (pt0) cc_final: 0.7485 (mt-10) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.8323 time to fit residues: 45.8015 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 0.0010 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.134778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.119381 restraints weight = 3140.350| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 0.64 r_work: 0.2923 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3161 Z= 0.099 Angle : 0.451 4.595 4304 Z= 0.240 Chirality : 0.038 0.189 480 Planarity : 0.003 0.033 543 Dihedral : 8.644 60.138 516 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.21 % Allowed : 15.71 % Favored : 81.09 % 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: 2.61 (0.44), residues: 372 helix: 2.18 (0.35), residues: 220 sheet: 2.49 (1.57), residues: 14 loop : 1.06 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.013 0.001 TYR A 361 PHE 0.009 0.001 PHE A 163 TRP 0.004 0.001 TRP A 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 3161) covalent geometry : angle 0.45107 ( 4304) hydrogen bonds : bond 0.03955 ( 167) hydrogen bonds : angle 3.84618 ( 474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.111 Fit side-chains REVERT: A 41 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7695 (t0) REVERT: A 44 ASN cc_start: 0.6474 (m-40) cc_final: 0.5743 (t0) REVERT: A 214 GLU cc_start: 0.7201 (mp0) cc_final: 0.6660 (tp30) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.8220 time to fit residues: 43.6092 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.134792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.117639 restraints weight = 3006.080| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 0.87 r_work: 0.2849 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3161 Z= 0.098 Angle : 0.447 4.596 4304 Z= 0.237 Chirality : 0.038 0.187 480 Planarity : 0.003 0.033 543 Dihedral : 8.629 60.111 516 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.56 % Allowed : 16.67 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.44), residues: 372 helix: 2.22 (0.35), residues: 220 sheet: 2.58 (1.58), residues: 14 loop : 1.15 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.013 0.001 TYR A 361 PHE 0.009 0.001 PHE A 270 TRP 0.005 0.001 TRP A 281 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 3161) covalent geometry : angle 0.44746 ( 4304) hydrogen bonds : bond 0.03930 ( 167) hydrogen bonds : angle 3.79357 ( 474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.120 Fit side-chains REVERT: A 41 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7643 (t0) REVERT: A 44 ASN cc_start: 0.6326 (m-40) cc_final: 0.5695 (t0) REVERT: A 214 GLU cc_start: 0.7082 (mp0) cc_final: 0.6629 (tp30) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.8297 time to fit residues: 43.1266 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 0.0870 chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.136597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.119357 restraints weight = 3068.318| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 0.91 r_work: 0.2897 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3161 Z= 0.091 Angle : 0.436 4.599 4304 Z= 0.231 Chirality : 0.037 0.185 480 Planarity : 0.003 0.034 543 Dihedral : 8.547 60.030 516 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.56 % Allowed : 16.67 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.44), residues: 372 helix: 2.22 (0.35), residues: 221 sheet: 2.58 (1.57), residues: 14 loop : 1.22 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.012 0.001 TYR A 361 PHE 0.008 0.001 PHE A 163 TRP 0.003 0.001 TRP A 281 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 3161) covalent geometry : angle 0.43606 ( 4304) hydrogen bonds : bond 0.03639 ( 167) hydrogen bonds : angle 3.70941 ( 474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1655.20 seconds wall clock time: 28 minutes 54.45 seconds (1734.45 seconds total)