Starting phenix.real_space_refine on Wed Jul 1 22:52:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfj_44498/07_2026/9bfj_44498.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfj_44498/07_2026/9bfj_44498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bfj_44498/07_2026/9bfj_44498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfj_44498/07_2026/9bfj_44498.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bfj_44498/07_2026/9bfj_44498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfj_44498/07_2026/9bfj_44498.map" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.100 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: 6 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2564 2.51 5 N 578 2.21 5 O 669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3833 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3824 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Chain breaks: 2 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Ad-hoc single atom residues: {' CL': 1, ' NA': 1} Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 0.91, per 1000 atoms: 0.24 Number of scatterers: 3833 At special positions: 0 Unit cell: (73.062, 82.656, 74.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 20 16.00 Na 1 11.00 O 669 8.00 N 578 7.00 C 2564 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: 0.31 Conformation dependent library (CDL) restraints added in 138.4 milliseconds 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 78.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.805A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 85 through 102 removed outlier: 4.701A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 95 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 123 through 157 removed outlier: 3.701A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 160 through 182 removed outlier: 3.582A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 208 Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.043A pdb=" N VAL A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.027A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 297 Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 329 through 363 removed outlier: 4.010A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 399 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.981A pdb=" N LEU A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 426 removed outlier: 4.327A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 449 Processing helix chain 'A' and resid 478 through 505 Processing helix chain 'A' and resid 508 through 512 Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 277 hydrogen bonds defined for protein. 819 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: 0.59 Time building geometry restraints manager: 0.42 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: 1110 1.34 - 1.46: 920 1.46 - 1.58: 1875 1.58 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 3940 Sorted by residual: bond pdb=" C5 CHT A 801 " pdb=" N1 CHT A 801 " ideal model delta sigma weight residual 1.509 1.455 0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C8 CHT A 801 " pdb=" N1 CHT A 801 " ideal model delta sigma weight residual 1.492 1.440 0.052 2.00e-02 2.50e+03 6.82e+00 bond pdb=" C7 CHT A 801 " pdb=" N1 CHT A 801 " ideal model delta sigma weight residual 1.492 1.458 0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C6 CHT A 801 " pdb=" N1 CHT A 801 " ideal model delta sigma weight residual 1.487 1.460 0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C ILE A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.37e+00 ... (remaining 3935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 5258 1.77 - 3.54: 100 3.54 - 5.30: 12 5.30 - 7.07: 10 7.07 - 8.84: 2 Bond angle restraints: 5382 Sorted by residual: angle pdb=" CA LEU A 273 " pdb=" CB LEU A 273 " pdb=" CG LEU A 273 " ideal model delta sigma weight residual 116.30 125.14 -8.84 3.50e+00 8.16e-02 6.38e+00 angle pdb=" CA ILE A 383 " pdb=" CB ILE A 383 " pdb=" CG1 ILE A 383 " ideal model delta sigma weight residual 110.40 114.60 -4.20 1.70e+00 3.46e-01 6.11e+00 angle pdb=" OG1 THR A 313 " pdb=" CB THR A 313 " pdb=" CG2 THR A 313 " ideal model delta sigma weight residual 109.30 104.91 4.39 2.00e+00 2.50e-01 4.82e+00 angle pdb=" C ASP A 309 " pdb=" CA ASP A 309 " pdb=" CB ASP A 309 " ideal model delta sigma weight residual 109.51 113.53 -4.02 1.85e+00 2.92e-01 4.73e+00 angle pdb=" C ILE A 252 " pdb=" N PRO A 253 " pdb=" CD PRO A 253 " ideal model delta sigma weight residual 125.00 133.23 -8.23 4.10e+00 5.95e-02 4.03e+00 ... (remaining 5377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 1985 17.11 - 34.21: 190 34.21 - 51.32: 42 51.32 - 68.42: 9 68.42 - 85.53: 6 Dihedral angle restraints: 2232 sinusoidal: 804 harmonic: 1428 Sorted by residual: dihedral pdb=" CG LYS A 226 " pdb=" CD LYS A 226 " pdb=" CE LYS A 226 " pdb=" NZ LYS A 226 " ideal model delta sinusoidal sigma weight residual -60.00 -117.13 57.13 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N LEU A 51 " pdb=" CA LEU A 51 " pdb=" CB LEU A 51 " pdb=" CG LEU A 51 " ideal model delta sinusoidal sigma weight residual -60.00 -114.52 54.52 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" CA MET A 395 " pdb=" CB MET A 395 " pdb=" CG MET A 395 " pdb=" SD MET A 395 " ideal model delta sinusoidal sigma weight residual 180.00 126.17 53.83 3 1.50e+01 4.44e-03 9.24e+00 ... (remaining 2229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 330 0.028 - 0.057: 189 0.057 - 0.085: 69 0.085 - 0.113: 23 0.113 - 0.141: 13 Chirality restraints: 624 Sorted by residual: chirality pdb=" CB VAL A 424 " pdb=" CA VAL A 424 " pdb=" CG1 VAL A 424 " pdb=" CG2 VAL A 424 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CB VAL A 380 " pdb=" CA VAL A 380 " pdb=" CG1 VAL A 380 " pdb=" CG2 VAL A 380 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA PRO A 310 " pdb=" N PRO A 310 " pdb=" C PRO A 310 " pdb=" CB PRO A 310 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 621 not shown) Planarity restraints: 651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 242 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C ASP A 242 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP A 242 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 243 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 67 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.69e+00 pdb=" C TYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR A 67 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 68 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 240 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C TRP A 240 " 0.031 2.00e-02 2.50e+03 pdb=" O TRP A 240 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 241 " -0.010 2.00e-02 2.50e+03 ... (remaining 648 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 238 2.74 - 3.28: 3920 3.28 - 3.82: 6814 3.82 - 4.36: 7880 4.36 - 4.90: 13608 Nonbonded interactions: 32460 Sorted by model distance: nonbonded pdb=" O VAL A 63 " pdb="NA NA A 803 " model vdw 2.196 3.210 nonbonded pdb=" O GLY A 389 " pdb=" OG1 THR A 393 " model vdw 2.218 3.040 nonbonded pdb=" O ALA A 60 " pdb="NA NA A 803 " model vdw 2.226 3.210 nonbonded pdb=" O ALA A 169 " pdb=" OG1 THR A 173 " model vdw 2.248 3.040 nonbonded pdb=" O ASN A 491 " pdb=" OG SER A 495 " model vdw 2.262 3.040 ... (remaining 32455 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: 1.180 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.320 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:8.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3940 Z= 0.203 Angle : 0.654 8.840 5382 Z= 0.342 Chirality : 0.043 0.141 624 Planarity : 0.006 0.037 651 Dihedral : 15.095 85.531 1328 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.36), residues: 490 helix: 0.87 (0.25), residues: 374 sheet: None (None), residues: 0 loop : -0.38 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 260 TYR 0.020 0.002 TYR A 269 PHE 0.013 0.002 PHE A 3 TRP 0.008 0.002 TRP A 379 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 3940) covalent geometry : angle 0.65352 / 0.34 ( 5382) hydrogen bonds : bond 0.13012 / 8.34 ( 277) hydrogen bonds : angle 5.83275 / 4.36 ( 819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.181 Fit side-chains REVERT: A 382 ARG cc_start: 0.7089 (mtt180) cc_final: 0.6784 (mtm-85) REVERT: A 386 PHE cc_start: 0.7753 (m-80) cc_final: 0.6674 (t80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.4523 time to fit residues: 23.1489 Evaluate side-chains 46 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105846 restraints weight = 4044.077| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.11 r_work: 0.3057 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3940 Z= 0.113 Angle : 0.475 6.638 5382 Z= 0.247 Chirality : 0.037 0.123 624 Planarity : 0.004 0.032 651 Dihedral : 4.510 56.553 535 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.00 % Allowed : 11.97 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.85 (0.38), residues: 490 helix: 1.66 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.11 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 446 TYR 0.012 0.001 TYR A 269 PHE 0.008 0.001 PHE A 244 TRP 0.007 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 3940) covalent geometry : angle 0.47464 / 0.25 ( 5382) hydrogen bonds : bond 0.04180 / 2.55 ( 277) hydrogen bonds : angle 4.42053 / 3.35 ( 819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.099 Fit side-chains REVERT: A 386 PHE cc_start: 0.7775 (m-80) cc_final: 0.6506 (t80) REVERT: A 400 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7966 (tptp) outliers start: 8 outliers final: 0 residues processed: 51 average time/residue: 0.3200 time to fit residues: 17.1098 Evaluate side-chains 49 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106111 restraints weight = 4084.295| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.26 r_work: 0.3093 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3940 Z= 0.114 Angle : 0.481 10.609 5382 Z= 0.243 Chirality : 0.037 0.124 624 Planarity : 0.004 0.030 651 Dihedral : 4.522 59.103 535 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.25 % Allowed : 12.72 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.91 (0.38), residues: 490 helix: 1.74 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.26 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.010 0.001 TYR A 269 PHE 0.006 0.001 PHE A 244 TRP 0.007 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 3940) covalent geometry : angle 0.48135 / 0.24 ( 5382) hydrogen bonds : bond 0.04074 / 2.48 ( 277) hydrogen bonds : angle 4.27713 / 3.24 ( 819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.143 Fit side-chains REVERT: A 386 PHE cc_start: 0.7825 (m-80) cc_final: 0.6597 (t80) REVERT: A 400 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7942 (tptp) outliers start: 5 outliers final: 0 residues processed: 53 average time/residue: 0.2927 time to fit residues: 16.3164 Evaluate side-chains 50 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.0470 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.149150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102507 restraints weight = 4022.780| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.26 r_work: 0.3034 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3940 Z= 0.186 Angle : 0.549 7.983 5382 Z= 0.282 Chirality : 0.041 0.133 624 Planarity : 0.004 0.029 651 Dihedral : 4.613 52.715 535 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.24 % Allowed : 13.47 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.68 (0.38), residues: 490 helix: 1.55 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.24 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 446 TYR 0.012 0.002 TYR A 331 PHE 0.012 0.001 PHE A 258 TRP 0.009 0.002 TRP A 228 HIS 0.001 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 3940) covalent geometry : angle 0.54915 / 0.28 ( 5382) hydrogen bonds : bond 0.04975 / 3.01 ( 277) hydrogen bonds : angle 4.54445 / 3.43 ( 819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.143 Fit side-chains REVERT: A 386 PHE cc_start: 0.7905 (m-80) cc_final: 0.6622 (t80) REVERT: A 395 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: A 400 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8000 (tptp) outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 0.3729 time to fit residues: 20.8081 Evaluate side-chains 53 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105334 restraints weight = 4080.708| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.17 r_work: 0.3087 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 3940 Z= 0.112 Angle : 0.472 6.529 5382 Z= 0.241 Chirality : 0.037 0.127 624 Planarity : 0.004 0.029 651 Dihedral : 4.238 45.665 535 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.25 % Allowed : 14.71 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.81 (0.38), residues: 490 helix: 1.64 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.31 (0.59), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 446 TYR 0.008 0.001 TYR A 269 PHE 0.007 0.001 PHE A 196 TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 3940) covalent geometry : angle 0.47164 / 0.24 ( 5382) hydrogen bonds : bond 0.03977 / 2.43 ( 277) hydrogen bonds : angle 4.28699 / 3.24 ( 819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.094 Fit side-chains REVERT: A 386 PHE cc_start: 0.7848 (m-80) cc_final: 0.6601 (t80) REVERT: A 400 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7946 (tptp) outliers start: 5 outliers final: 1 residues processed: 54 average time/residue: 0.3236 time to fit residues: 18.3989 Evaluate side-chains 49 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.151630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105111 restraints weight = 4132.056| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.23 r_work: 0.3069 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3940 Z= 0.121 Angle : 0.480 6.261 5382 Z= 0.246 Chirality : 0.037 0.128 624 Planarity : 0.004 0.027 651 Dihedral : 4.208 43.807 535 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.00 % Allowed : 15.46 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.79 (0.38), residues: 490 helix: 1.63 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.35 (0.58), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 260 TYR 0.009 0.001 TYR A 331 PHE 0.007 0.001 PHE A 258 TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 3940) covalent geometry : angle 0.47956 / 0.25 ( 5382) hydrogen bonds : bond 0.04122 / 2.51 ( 277) hydrogen bonds : angle 4.30831 / 3.25 ( 819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.151 Fit side-chains REVERT: A 386 PHE cc_start: 0.7847 (m-80) cc_final: 0.6580 (t80) REVERT: A 400 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7900 (tptp) outliers start: 4 outliers final: 1 residues processed: 51 average time/residue: 0.3914 time to fit residues: 20.9655 Evaluate side-chains 49 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105889 restraints weight = 4152.957| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.26 r_work: 0.3078 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 3940 Z= 0.115 Angle : 0.474 6.180 5382 Z= 0.244 Chirality : 0.037 0.126 624 Planarity : 0.004 0.027 651 Dihedral : 4.150 43.127 535 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.00 % Allowed : 14.46 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.91 (0.38), residues: 490 helix: 1.70 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.25 (0.58), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 446 TYR 0.008 0.001 TYR A 331 PHE 0.007 0.001 PHE A 196 TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 3940) covalent geometry : angle 0.47365 / 0.24 ( 5382) hydrogen bonds : bond 0.03960 / 2.42 ( 277) hydrogen bonds : angle 4.24477 / 3.21 ( 819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.170 Fit side-chains REVERT: A 386 PHE cc_start: 0.7841 (m-80) cc_final: 0.6569 (t80) REVERT: A 400 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7858 (tptp) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.3907 time to fit residues: 21.3466 Evaluate side-chains 51 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 48 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107351 restraints weight = 4163.267| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.31 r_work: 0.3098 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3940 Z= 0.107 Angle : 0.475 9.720 5382 Z= 0.238 Chirality : 0.037 0.124 624 Planarity : 0.003 0.027 651 Dihedral : 4.107 43.657 535 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.75 % Allowed : 15.71 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.99 (0.38), residues: 490 helix: 1.76 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.22 (0.58), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 446 TYR 0.008 0.001 TYR A 331 PHE 0.006 0.001 PHE A 196 TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 3940) covalent geometry : angle 0.47468 / 0.24 ( 5382) hydrogen bonds : bond 0.03749 / 2.30 ( 277) hydrogen bonds : angle 4.15524 / 3.14 ( 819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.156 Fit side-chains REVERT: A 386 PHE cc_start: 0.7818 (m-80) cc_final: 0.6569 (t80) REVERT: A 400 LYS cc_start: 0.8449 (mmtm) cc_final: 0.7782 (tptp) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.3412 time to fit residues: 19.3193 Evaluate side-chains 51 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 67 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.152790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106336 restraints weight = 4116.538| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.25 r_work: 0.3086 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3940 Z= 0.116 Angle : 0.488 9.371 5382 Z= 0.247 Chirality : 0.037 0.126 624 Planarity : 0.003 0.027 651 Dihedral : 4.130 42.959 535 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.25 % Allowed : 15.46 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.98 (0.38), residues: 490 helix: 1.75 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.21 (0.58), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 382 TYR 0.009 0.001 TYR A 331 PHE 0.006 0.001 PHE A 196 TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 3940) covalent geometry : angle 0.48821 / 0.25 ( 5382) hydrogen bonds : bond 0.03916 / 2.39 ( 277) hydrogen bonds : angle 4.20800 / 3.18 ( 819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.114 Fit side-chains REVERT: A 386 PHE cc_start: 0.7820 (m-80) cc_final: 0.6565 (t80) REVERT: A 400 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7819 (tptp) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.3438 time to fit residues: 19.1705 Evaluate side-chains 52 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.0570 chunk 21 optimal weight: 0.0670 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.154923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109038 restraints weight = 4178.912| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.33 r_work: 0.3128 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3940 Z= 0.101 Angle : 0.468 9.308 5382 Z= 0.236 Chirality : 0.036 0.123 624 Planarity : 0.003 0.027 651 Dihedral : 4.052 43.908 535 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.75 % Allowed : 15.71 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.38), residues: 490 helix: 1.84 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.20 (0.58), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 446 TYR 0.008 0.001 TYR A 465 PHE 0.006 0.001 PHE A 196 TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 ( 3940) covalent geometry : angle 0.46842 / 0.24 ( 5382) hydrogen bonds : bond 0.03513 / 2.17 ( 277) hydrogen bonds : angle 4.08609 / 3.08 ( 819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.142 Fit side-chains REVERT: A 386 PHE cc_start: 0.7792 (m-80) cc_final: 0.6544 (t80) REVERT: A 400 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7724 (tptp) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.3602 time to fit residues: 19.3496 Evaluate side-chains 51 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 48 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108379 restraints weight = 4154.604| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.30 r_work: 0.3122 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 3940 Z= 0.105 Angle : 0.475 9.224 5382 Z= 0.240 Chirality : 0.037 0.123 624 Planarity : 0.003 0.027 651 Dihedral : 4.049 43.504 535 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.00 % Allowed : 15.21 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.38), residues: 490 helix: 1.85 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.20 (0.58), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 382 TYR 0.008 0.001 TYR A 465 PHE 0.007 0.001 PHE A 196 TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 3940) covalent geometry : angle 0.47531 / 0.24 ( 5382) hydrogen bonds : bond 0.03634 / 2.23 ( 277) hydrogen bonds : angle 4.09086 / 3.09 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1590.52 seconds wall clock time: 27 minutes 49.53 seconds (1669.53 seconds total)