Starting phenix.real_space_refine on Tue Feb 3 12:31:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bs9_44865/02_2026/9bs9_44865.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bs9_44865/02_2026/9bs9_44865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bs9_44865/02_2026/9bs9_44865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bs9_44865/02_2026/9bs9_44865.map" model { file = "/net/cci-nas-00/data/ceres_data/9bs9_44865/02_2026/9bs9_44865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bs9_44865/02_2026/9bs9_44865.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1343 2.51 5 N 311 2.21 5 O 340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2008 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1984 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 128 Planarities with less than four sites: {'TYR:plan': 5, 'ARG:plan': 7, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 97 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'7LD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.65, per 1000 atoms: 0.32 Number of scatterers: 2008 At special positions: 0 Unit cell: (66.88, 68.64, 66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 340 8.00 N 311 7.00 C 1343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 130.7 milliseconds 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 92.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'R' and resid 35 through 62 removed outlier: 4.117A pdb=" N THR R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU R 40 " --> pdb=" O TYR R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 86 Processing helix chain 'R' and resid 86 through 98 removed outlier: 4.565A pdb=" N TRP R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 138 Processing helix chain 'R' and resid 138 through 144 Processing helix chain 'R' and resid 144 through 168 removed outlier: 3.535A pdb=" N ARG R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 173 Processing helix chain 'R' and resid 186 through 198 Processing helix chain 'R' and resid 198 through 223 Processing helix chain 'R' and resid 365 through 398 removed outlier: 3.654A pdb=" N LYS R 369 " --> pdb=" O GLN R 365 " (cutoff:3.500A) Proline residue: R 388 - end of helix Processing helix chain 'R' and resid 404 through 428 removed outlier: 3.817A pdb=" N TYR R 408 " --> pdb=" O PRO R 404 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix removed outlier: 3.530A pdb=" N THR R 427 " --> pdb=" O PRO R 423 " (cutoff:3.500A) Processing helix chain 'R' and resid 430 through 439 180 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.20 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 589 1.34 - 1.46: 487 1.46 - 1.58: 956 1.58 - 1.70: 1 1.70 - 1.82: 21 Bond restraints: 2054 Sorted by residual: bond pdb=" C16 7LD R 501 " pdb=" N3 7LD R 501 " ideal model delta sigma weight residual 1.348 1.405 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" N LYS R 149 " pdb=" CA LYS R 149 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.77e+00 bond pdb=" N GLN R 373 " pdb=" CA GLN R 373 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.68e+00 bond pdb=" CB ILE R 383 " pdb=" CG2 ILE R 383 " ideal model delta sigma weight residual 1.521 1.588 -0.067 3.30e-02 9.18e+02 4.12e+00 bond pdb=" C11 7LD R 501 " pdb=" N2 7LD R 501 " ideal model delta sigma weight residual 1.455 1.493 -0.038 2.00e-02 2.50e+03 3.70e+00 ... (remaining 2049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 2627 1.63 - 3.26: 159 3.26 - 4.89: 26 4.89 - 6.52: 10 6.52 - 8.15: 5 Bond angle restraints: 2827 Sorted by residual: angle pdb=" C VAL R 87 " pdb=" N MET R 88 " pdb=" CA MET R 88 " ideal model delta sigma weight residual 120.09 124.49 -4.40 1.25e+00 6.40e-01 1.24e+01 angle pdb=" CA THR R 153 " pdb=" CB THR R 153 " pdb=" OG1 THR R 153 " ideal model delta sigma weight residual 109.60 104.64 4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" CA VAL R 200 " pdb=" C VAL R 200 " pdb=" N PRO R 201 " ideal model delta sigma weight residual 118.88 122.84 -3.96 1.54e+00 4.22e-01 6.63e+00 angle pdb=" CA TYR R 408 " pdb=" CB TYR R 408 " pdb=" CG TYR R 408 " ideal model delta sigma weight residual 113.90 118.33 -4.43 1.80e+00 3.09e-01 6.05e+00 angle pdb=" CA THR R 153 " pdb=" C THR R 153 " pdb=" O THR R 153 " ideal model delta sigma weight residual 120.42 117.82 2.60 1.06e+00 8.90e-01 6.00e+00 ... (remaining 2822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 1167 35.74 - 71.49: 39 71.49 - 107.23: 1 107.23 - 142.97: 0 142.97 - 178.72: 1 Dihedral angle restraints: 1208 sinusoidal: 422 harmonic: 786 Sorted by residual: dihedral pdb=" C16 7LD R 501 " pdb=" C17 7LD R 501 " pdb=" N3 7LD R 501 " pdb=" C18 7LD R 501 " ideal model delta sinusoidal sigma weight residual 91.75 -86.97 178.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA PHE R 198 " pdb=" C PHE R 198 " pdb=" N TYR R 199 " pdb=" CA TYR R 199 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE R 397 " pdb=" C ILE R 397 " pdb=" N HIS R 398 " pdb=" CA HIS R 398 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 1205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 306 0.061 - 0.123: 57 0.123 - 0.184: 4 0.184 - 0.245: 1 0.245 - 0.307: 1 Chirality restraints: 369 Sorted by residual: chirality pdb=" C11 7LD R 501 " pdb=" C15 7LD R 501 " pdb=" C9 7LD R 501 " pdb=" N2 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE R 210 " pdb=" CA ILE R 210 " pdb=" CG1 ILE R 210 " pdb=" CG2 ILE R 210 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA ILE R 403 " pdb=" N ILE R 403 " pdb=" C ILE R 403 " pdb=" CB ILE R 403 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 366 not shown) Planarity restraints: 332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 218 " 0.214 9.50e-02 1.11e+02 9.61e-02 6.33e+00 pdb=" NE ARG R 218 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG R 218 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG R 218 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG R 218 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 403 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO R 404 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 404 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 404 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 186 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO R 187 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 187 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 187 " 0.026 5.00e-02 4.00e+02 ... (remaining 329 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 524 2.81 - 3.33: 2165 3.33 - 3.86: 3466 3.86 - 4.38: 3840 4.38 - 4.90: 6496 Nonbonded interactions: 16491 Sorted by model distance: nonbonded pdb=" O ILE R 424 " pdb=" OG1 THR R 428 " model vdw 2.291 3.040 nonbonded pdb=" OD1 ASP R 114 " pdb=" N2 7LD R 501 " model vdw 2.354 3.120 nonbonded pdb=" O PRO R 423 " pdb=" OG1 THR R 427 " model vdw 2.357 3.040 nonbonded pdb=" OG1 THR R 69 " pdb=" OH TYR R 142 " model vdw 2.393 3.040 nonbonded pdb=" O VAL R 190 " pdb=" OG SER R 194 " model vdw 2.408 3.040 ... (remaining 16486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.250 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.410 Find NCS groups from input model: 0.000 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.006 0.067 2055 Z= 0.296 Angle : 0.945 8.145 2829 Z= 0.502 Chirality : 0.048 0.307 369 Planarity : 0.008 0.096 332 Dihedral : 16.776 178.717 689 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.47 % Allowed : 17.92 % Favored : 81.60 % 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: 1.43 (0.49), residues: 257 helix: 1.20 (0.32), residues: 216 sheet: None (None), residues: 0 loop : -0.01 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG R 218 TYR 0.026 0.003 TYR R 408 PHE 0.017 0.002 PHE R 382 TRP 0.007 0.002 TRP R 160 HIS 0.010 0.005 HIS R 398 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 2054) covalent geometry : angle 0.94466 ( 2827) SS BOND : bond 0.00304 ( 1) SS BOND : angle 0.78805 ( 2) hydrogen bonds : bond 0.14364 ( 180) hydrogen bonds : angle 6.07118 ( 534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.088 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.2885 time to fit residues: 11.2807 Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN R 365 GLN ** R 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.182819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.166334 restraints weight = 2328.914| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.05 r_work: 0.3979 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2055 Z= 0.159 Angle : 0.594 6.573 2829 Z= 0.319 Chirality : 0.042 0.142 369 Planarity : 0.005 0.047 332 Dihedral : 11.799 161.949 300 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.89 % Allowed : 14.62 % Favored : 83.49 % 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: 2.57 (0.49), residues: 257 helix: 1.94 (0.32), residues: 218 sheet: None (None), residues: 0 loop : 0.55 (1.13), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 218 TYR 0.013 0.002 TYR R 408 PHE 0.010 0.002 PHE R 411 TRP 0.009 0.002 TRP R 160 HIS 0.004 0.002 HIS R 106 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 2054) covalent geometry : angle 0.59418 ( 2827) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.77461 ( 2) hydrogen bonds : bond 0.05524 ( 180) hydrogen bonds : angle 4.59943 ( 534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.055 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 36 average time/residue: 0.2558 time to fit residues: 9.4637 Evaluate side-chains 34 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN R 398 HIS R 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.183346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.166628 restraints weight = 2300.555| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.05 r_work: 0.3983 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2055 Z= 0.149 Angle : 0.573 6.503 2829 Z= 0.304 Chirality : 0.041 0.141 369 Planarity : 0.005 0.047 332 Dihedral : 11.630 161.136 299 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.30 % Allowed : 13.68 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.50), residues: 257 helix: 2.19 (0.32), residues: 219 sheet: None (None), residues: 0 loop : 0.61 (1.14), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 218 TYR 0.011 0.002 TYR R 408 PHE 0.010 0.002 PHE R 189 TRP 0.008 0.001 TRP R 160 HIS 0.008 0.003 HIS R 398 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2054) covalent geometry : angle 0.57239 ( 2827) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.79677 ( 2) hydrogen bonds : bond 0.05204 ( 180) hydrogen bonds : angle 4.47891 ( 534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.046 Fit side-chains REVERT: R 373 GLN cc_start: 0.7426 (mm-40) cc_final: 0.6969 (pt0) outliers start: 7 outliers final: 2 residues processed: 36 average time/residue: 0.2542 time to fit residues: 9.4105 Evaluate side-chains 34 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN R 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.184440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.167276 restraints weight = 2232.025| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.05 r_work: 0.3993 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2055 Z= 0.140 Angle : 0.554 6.432 2829 Z= 0.292 Chirality : 0.041 0.170 369 Planarity : 0.004 0.046 332 Dihedral : 11.487 160.389 299 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.77 % Allowed : 12.74 % Favored : 83.49 % 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: 3.08 (0.50), residues: 257 helix: 2.27 (0.32), residues: 221 sheet: None (None), residues: 0 loop : 0.69 (1.21), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG R 219 TYR 0.010 0.002 TYR R 408 PHE 0.010 0.001 PHE R 189 TRP 0.007 0.001 TRP R 160 HIS 0.006 0.002 HIS R 398 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2054) covalent geometry : angle 0.55357 ( 2827) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.79233 ( 2) hydrogen bonds : bond 0.04927 ( 180) hydrogen bonds : angle 4.39244 ( 534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.046 Fit side-chains REVERT: R 373 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6964 (pt0) outliers start: 8 outliers final: 3 residues processed: 39 average time/residue: 0.2437 time to fit residues: 9.7804 Evaluate side-chains 35 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN R 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.183230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.166168 restraints weight = 2284.195| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.06 r_work: 0.3978 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2055 Z= 0.148 Angle : 0.536 5.173 2829 Z= 0.288 Chirality : 0.041 0.145 369 Planarity : 0.004 0.046 332 Dihedral : 11.545 160.150 299 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.30 % Allowed : 13.68 % Favored : 83.02 % 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: 3.04 (0.49), residues: 257 helix: 2.26 (0.32), residues: 221 sheet: None (None), residues: 0 loop : 0.54 (1.19), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 219 TYR 0.010 0.002 TYR R 408 PHE 0.010 0.001 PHE R 189 TRP 0.008 0.001 TRP R 160 HIS 0.006 0.003 HIS R 398 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 2054) covalent geometry : angle 0.53604 ( 2827) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.84849 ( 2) hydrogen bonds : bond 0.05204 ( 180) hydrogen bonds : angle 4.36397 ( 534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.046 Fit side-chains REVERT: R 373 GLN cc_start: 0.7343 (mm-40) cc_final: 0.6986 (pt0) outliers start: 7 outliers final: 3 residues processed: 37 average time/residue: 0.2704 time to fit residues: 10.2725 Evaluate side-chains 35 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN R 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.182449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.165618 restraints weight = 2235.228| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.05 r_work: 0.3972 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2055 Z= 0.153 Angle : 0.598 9.583 2829 Z= 0.304 Chirality : 0.041 0.141 369 Planarity : 0.004 0.039 332 Dihedral : 11.552 159.700 299 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.30 % Allowed : 14.62 % Favored : 82.08 % 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: 3.07 (0.50), residues: 257 helix: 2.26 (0.32), residues: 221 sheet: None (None), residues: 0 loop : 0.70 (1.23), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG R 151 TYR 0.011 0.002 TYR R 408 PHE 0.010 0.001 PHE R 189 TRP 0.008 0.002 TRP R 90 HIS 0.005 0.002 HIS R 398 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2054) covalent geometry : angle 0.59740 ( 2827) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.84576 ( 2) hydrogen bonds : bond 0.05267 ( 180) hydrogen bonds : angle 4.37388 ( 534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.046 Fit side-chains REVERT: R 140 MET cc_start: 0.6043 (mmm) cc_final: 0.5829 (mmm) REVERT: R 373 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7048 (pt0) REVERT: R 398 HIS cc_start: 0.4616 (m90) cc_final: 0.4414 (m170) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 0.2733 time to fit residues: 9.8164 Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.182610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166367 restraints weight = 2283.199| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.05 r_work: 0.3982 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2055 Z= 0.143 Angle : 0.567 9.281 2829 Z= 0.291 Chirality : 0.040 0.139 369 Planarity : 0.004 0.038 332 Dihedral : 11.503 160.693 299 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.83 % Allowed : 15.09 % Favored : 82.08 % 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: 3.14 (0.50), residues: 257 helix: 2.33 (0.32), residues: 221 sheet: None (None), residues: 0 loop : 0.54 (1.23), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG R 151 TYR 0.011 0.002 TYR R 408 PHE 0.010 0.001 PHE R 189 TRP 0.008 0.001 TRP R 90 HIS 0.002 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2054) covalent geometry : angle 0.56716 ( 2827) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.78576 ( 2) hydrogen bonds : bond 0.05028 ( 180) hydrogen bonds : angle 4.32216 ( 534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.047 Fit side-chains REVERT: R 373 GLN cc_start: 0.7361 (mm-40) cc_final: 0.6995 (pt0) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.2918 time to fit residues: 10.1989 Evaluate side-chains 35 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN R 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.184693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.168350 restraints weight = 2307.669| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.07 r_work: 0.4001 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2055 Z= 0.130 Angle : 0.571 10.474 2829 Z= 0.285 Chirality : 0.039 0.137 369 Planarity : 0.004 0.036 332 Dihedral : 11.423 162.048 299 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.36 % Allowed : 16.51 % Favored : 81.13 % 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: 3.39 (0.50), residues: 257 helix: 2.51 (0.32), residues: 221 sheet: None (None), residues: 0 loop : 0.51 (1.23), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG R 151 TYR 0.011 0.001 TYR R 408 PHE 0.009 0.001 PHE R 390 TRP 0.009 0.001 TRP R 413 HIS 0.005 0.002 HIS R 398 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 2054) covalent geometry : angle 0.57128 ( 2827) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.65436 ( 2) hydrogen bonds : bond 0.04604 ( 180) hydrogen bonds : angle 4.22300 ( 534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.050 Fit side-chains REVERT: R 373 GLN cc_start: 0.7321 (mm-40) cc_final: 0.6969 (pt0) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.2688 time to fit residues: 9.9447 Evaluate side-chains 34 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 168 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 0.0870 chunk 5 optimal weight: 0.2980 chunk 10 optimal weight: 0.1980 chunk 14 optimal weight: 0.0070 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.188268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.171773 restraints weight = 2312.906| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.07 r_work: 0.4031 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2055 Z= 0.116 Angle : 0.499 8.763 2829 Z= 0.259 Chirality : 0.039 0.144 369 Planarity : 0.004 0.036 332 Dihedral : 11.238 163.144 299 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.36 % Allowed : 17.45 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.71 (0.50), residues: 257 helix: 2.75 (0.32), residues: 221 sheet: None (None), residues: 0 loop : 0.48 (1.21), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 218 TYR 0.011 0.001 TYR R 408 PHE 0.007 0.001 PHE R 189 TRP 0.012 0.001 TRP R 413 HIS 0.001 0.000 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 2054) covalent geometry : angle 0.49859 ( 2827) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.39753 ( 2) hydrogen bonds : bond 0.04101 ( 180) hydrogen bonds : angle 4.08689 ( 534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.047 Fit side-chains REVERT: R 373 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6934 (pt0) outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.2664 time to fit residues: 9.3023 Evaluate side-chains 34 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.183473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.166788 restraints weight = 2310.551| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.08 r_work: 0.3980 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2055 Z= 0.144 Angle : 0.606 11.860 2829 Z= 0.304 Chirality : 0.040 0.140 369 Planarity : 0.004 0.037 332 Dihedral : 11.476 160.663 299 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.83 % Allowed : 16.98 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.50), residues: 257 helix: 2.52 (0.32), residues: 221 sheet: None (None), residues: 0 loop : 0.37 (1.22), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG R 151 TYR 0.009 0.002 TYR R 408 PHE 0.009 0.001 PHE R 390 TRP 0.009 0.002 TRP R 160 HIS 0.002 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2054) covalent geometry : angle 0.60562 ( 2827) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.81165 ( 2) hydrogen bonds : bond 0.05053 ( 180) hydrogen bonds : angle 4.26097 ( 534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.046 Fit side-chains REVERT: R 203 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7226 (mp) REVERT: R 373 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6986 (pt0) outliers start: 6 outliers final: 5 residues processed: 34 average time/residue: 0.2753 time to fit residues: 9.6335 Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 180 ASN Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.181628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164748 restraints weight = 2346.346| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.11 r_work: 0.3965 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2055 Z= 0.153 Angle : 0.588 8.976 2829 Z= 0.305 Chirality : 0.041 0.140 369 Planarity : 0.004 0.037 332 Dihedral : 11.545 159.712 299 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.25 % Allowed : 15.09 % Favored : 80.66 % 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: 3.08 (0.50), residues: 257 helix: 2.32 (0.32), residues: 221 sheet: None (None), residues: 0 loop : 0.30 (1.21), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 151 TYR 0.010 0.002 TYR R 408 PHE 0.010 0.001 PHE R 390 TRP 0.010 0.002 TRP R 90 HIS 0.002 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 2054) covalent geometry : angle 0.58809 ( 2827) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.90350 ( 2) hydrogen bonds : bond 0.05277 ( 180) hydrogen bonds : angle 4.30410 ( 534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 822.75 seconds wall clock time: 14 minutes 42.32 seconds (882.32 seconds total)