Starting phenix.real_space_refine on Tue Mar 3 12:35:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nu8_49798/03_2026/9nu8_49798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nu8_49798/03_2026/9nu8_49798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nu8_49798/03_2026/9nu8_49798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nu8_49798/03_2026/9nu8_49798.map" model { file = "/net/cci-nas-00/data/ceres_data/9nu8_49798/03_2026/9nu8_49798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nu8_49798/03_2026/9nu8_49798.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 22 5.16 5 C 2828 2.51 5 N 680 2.21 5 O 695 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4225 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3890 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 24, 'TRANS': 485} Chain: "B" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Time building chain proxies: 1.07, per 1000 atoms: 0.25 Number of scatterers: 4225 At special positions: 0 Unit cell: (74.75, 78.65, 79.95, 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 22 16.00 O 695 8.00 N 680 7.00 C 2828 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: 0.32 Conformation dependent library (CDL) restraints added in 118.9 milliseconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1026 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid -9 through 32 removed outlier: 3.979A pdb=" N ALA A -3 " --> pdb=" O THR A -7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A -2 " --> pdb=" O THR A -6 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 5 " --> pdb=" O LYS A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 Proline residue: A 48 - end of helix Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 58 through 75 removed outlier: 3.633A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 77 through 105 Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.631A pdb=" N LEU A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 164 through 178 removed outlier: 3.824A pdb=" N ASN A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 removed outlier: 3.611A pdb=" N PHE A 182 " --> pdb=" O ALA A 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 186 through 203 removed outlier: 4.071A pdb=" N ALA A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.604A pdb=" N LEU A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 255 removed outlier: 3.671A pdb=" N MET A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 260 through 297 Proline residue: A 275 - end of helix removed outlier: 4.366A pdb=" N ALA A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.565A pdb=" N SER A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 328 removed outlier: 3.703A pdb=" N LEU A 316 " --> pdb=" O ARG A 312 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.501A pdb=" N GLN A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 377 removed outlier: 3.758A pdb=" N ALA A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLY A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Proline residue: A 372 - end of helix removed outlier: 3.963A pdb=" N ARG A 377 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 406 removed outlier: 3.744A pdb=" N VAL A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLY A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 406 through 432 removed outlier: 3.756A pdb=" N LEU A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 466 Processing helix chain 'A' and resid 473 through 499 Processing helix chain 'B' and resid 65 through 90 removed outlier: 3.588A pdb=" N ARG B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 90 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 100 removed outlier: 3.890A pdb=" N ILE B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 1032 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: 0.67 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1261 1.34 - 1.46: 733 1.46 - 1.57: 2291 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 4327 Sorted by residual: bond pdb=" CA THR A 394 " pdb=" C THR A 394 " ideal model delta sigma weight residual 1.524 1.510 0.013 1.27e-02 6.20e+03 1.12e+00 bond pdb=" CG LEU A 68 " pdb=" CD1 LEU A 68 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.03e+00 bond pdb=" CG LEU A 95 " pdb=" CD1 LEU A 95 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CA GLY A 234 " pdb=" C GLY A 234 " ideal model delta sigma weight residual 1.515 1.529 -0.014 1.43e-02 4.89e+03 9.98e-01 bond pdb=" CB VAL A 84 " pdb=" CG2 VAL A 84 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.23e-01 ... (remaining 4322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 5634 1.50 - 3.00: 218 3.00 - 4.50: 27 4.50 - 6.00: 18 6.00 - 7.51: 1 Bond angle restraints: 5898 Sorted by residual: angle pdb=" C GLY A 280 " pdb=" N VAL A 281 " pdb=" CA VAL A 281 " ideal model delta sigma weight residual 120.30 114.89 5.41 1.64e+00 3.72e-01 1.09e+01 angle pdb=" C SER A 73 " pdb=" N LYS A 74 " pdb=" CA LYS A 74 " ideal model delta sigma weight residual 121.63 116.46 5.17 1.91e+00 2.74e-01 7.34e+00 angle pdb=" CA TYR A 339 " pdb=" CB TYR A 339 " pdb=" CG TYR A 339 " ideal model delta sigma weight residual 113.90 109.54 4.36 1.80e+00 3.09e-01 5.87e+00 angle pdb=" CA LEU A 95 " pdb=" CB LEU A 95 " pdb=" CG LEU A 95 " ideal model delta sigma weight residual 116.30 108.79 7.51 3.50e+00 8.16e-02 4.60e+00 angle pdb=" C LEU A 429 " pdb=" N ARG A 430 " pdb=" CA ARG A 430 " ideal model delta sigma weight residual 122.54 119.20 3.34 1.65e+00 3.67e-01 4.10e+00 ... (remaining 5893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 2300 17.65 - 35.30: 199 35.30 - 52.96: 29 52.96 - 70.61: 7 70.61 - 88.26: 1 Dihedral angle restraints: 2536 sinusoidal: 944 harmonic: 1592 Sorted by residual: dihedral pdb=" CA ASN A 183 " pdb=" C ASN A 183 " pdb=" N PRO A 184 " pdb=" CA PRO A 184 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA PRO A 180 " pdb=" C PRO A 180 " pdb=" N TYR A 181 " pdb=" CA TYR A 181 " ideal model delta harmonic sigma weight residual -180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLN A 338 " pdb=" C GLN A 338 " pdb=" N TYR A 339 " pdb=" CA TYR A 339 " ideal model delta harmonic sigma weight residual -180.00 -163.94 -16.06 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 445 0.038 - 0.076: 203 0.076 - 0.114: 58 0.114 - 0.151: 13 0.151 - 0.189: 2 Chirality restraints: 721 Sorted by residual: chirality pdb=" CB VAL A 281 " pdb=" CA VAL A 281 " pdb=" CG1 VAL A 281 " pdb=" CG2 VAL A 281 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CB VAL A 112 " pdb=" CA VAL A 112 " pdb=" CG1 VAL A 112 " pdb=" CG2 VAL A 112 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA PRO A 331 " pdb=" N PRO A 331 " pdb=" C PRO A 331 " pdb=" CB PRO A 331 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 718 not shown) Planarity restraints: 710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 277 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C GLY A 277 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY A 277 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 278 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 234 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO A 235 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 330 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 331 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.026 5.00e-02 4.00e+02 ... (remaining 707 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 16 2.65 - 3.21: 4311 3.21 - 3.77: 6762 3.77 - 4.34: 8948 4.34 - 4.90: 14587 Nonbonded interactions: 34624 Sorted by model distance: nonbonded pdb=" O VAL A 109 " pdb=" OG1 THR A 113 " model vdw 2.087 3.040 nonbonded pdb=" O LEU A 391 " pdb=" OG1 THR A 394 " model vdw 2.295 3.040 nonbonded pdb=" NH2 ARG A 270 " pdb=" O ASN B 100 " model vdw 2.319 3.120 nonbonded pdb=" O SER A 470 " pdb=" NH2 ARG A 477 " model vdw 2.320 3.120 nonbonded pdb=" NZ LYS A 368 " pdb=" O LEU B 103 " model vdw 2.332 3.120 ... (remaining 34619 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.390 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.150 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 0.036 4327 Z= 0.274 Angle : 0.730 7.506 5898 Z= 0.384 Chirality : 0.046 0.189 721 Planarity : 0.006 0.051 710 Dihedral : 13.199 88.259 1510 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.31), residues: 546 helix: -1.18 (0.19), residues: 452 sheet: None (None), residues: 0 loop : 1.36 (0.73), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 81 TYR 0.020 0.002 TYR A 71 PHE 0.014 0.002 PHE A 32 TRP 0.025 0.002 TRP A 441 HIS 0.004 0.002 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00623 ( 4327) covalent geometry : angle 0.73026 ( 5898) hydrogen bonds : bond 0.13710 ( 347) hydrogen bonds : angle 5.88077 ( 1032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.162 Fit side-chains REVERT: A -8 LYS cc_start: 0.8068 (tttt) cc_final: 0.7845 (tttm) REVERT: A 1 LYS cc_start: 0.7900 (pptt) cc_final: 0.7238 (tttt) REVERT: A 482 MET cc_start: 0.8445 (tmm) cc_final: 0.6677 (mmt) REVERT: A 486 LEU cc_start: 0.8465 (mm) cc_final: 0.8190 (mm) REVERT: B 96 GLU cc_start: 0.8577 (tp30) cc_final: 0.8232 (tp30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0736 time to fit residues: 10.3600 Evaluate side-chains 74 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 53 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: A 155 ASN A 398 ASN A 464 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117010 restraints weight = 6760.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120138 restraints weight = 3185.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122220 restraints weight = 1921.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123633 restraints weight = 1366.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124585 restraints weight = 1071.888| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4327 Z= 0.162 Angle : 0.628 9.110 5898 Z= 0.310 Chirality : 0.040 0.137 721 Planarity : 0.005 0.043 710 Dihedral : 4.082 19.894 587 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.70 % Allowed : 13.96 % Favored : 83.33 % 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: 1.73 (0.35), residues: 546 helix: 1.23 (0.23), residues: 458 sheet: None (None), residues: 0 loop : 1.22 (0.80), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 270 TYR 0.012 0.002 TYR A 339 PHE 0.017 0.001 PHE B 86 TRP 0.006 0.001 TRP A 154 HIS 0.004 0.002 HIS A 464 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4327) covalent geometry : angle 0.62773 ( 5898) hydrogen bonds : bond 0.05330 ( 347) hydrogen bonds : angle 4.37475 ( 1032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.151 Fit side-chains REVERT: A -8 LYS cc_start: 0.7587 (tttt) cc_final: 0.7356 (tttm) REVERT: A 1 LYS cc_start: 0.7551 (pptt) cc_final: 0.7173 (tttt) REVERT: A 152 ASN cc_start: 0.8988 (m-40) cc_final: 0.8712 (m-40) REVERT: A 375 TYR cc_start: 0.9164 (m-10) cc_final: 0.8914 (m-10) REVERT: A 406 LYS cc_start: 0.8522 (mtmm) cc_final: 0.7826 (mmtp) REVERT: A 482 MET cc_start: 0.8295 (tmm) cc_final: 0.7770 (tmm) REVERT: A 486 LEU cc_start: 0.8234 (mm) cc_final: 0.7802 (mm) outliers start: 12 outliers final: 8 residues processed: 98 average time/residue: 0.0442 time to fit residues: 5.9658 Evaluate side-chains 79 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 88 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 168 ASN A 300 HIS A 398 ASN A 464 HIS B 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118972 restraints weight = 6751.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122201 restraints weight = 3177.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124332 restraints weight = 1912.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125773 restraints weight = 1357.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126588 restraints weight = 1066.165| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4327 Z= 0.138 Angle : 0.555 6.011 5898 Z= 0.274 Chirality : 0.038 0.121 721 Planarity : 0.004 0.040 710 Dihedral : 3.829 18.490 587 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.48 % Allowed : 18.69 % Favored : 78.83 % 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: 2.66 (0.36), residues: 546 helix: 1.94 (0.24), residues: 460 sheet: None (None), residues: 0 loop : 1.03 (0.79), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 270 TYR 0.010 0.001 TYR A 339 PHE 0.007 0.001 PHE B 93 TRP 0.007 0.001 TRP A 154 HIS 0.012 0.002 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4327) covalent geometry : angle 0.55540 ( 5898) hydrogen bonds : bond 0.04741 ( 347) hydrogen bonds : angle 4.09445 ( 1032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.153 Fit side-chains REVERT: A 1 LYS cc_start: 0.7561 (pptt) cc_final: 0.7121 (tttt) REVERT: A 108 TRP cc_start: 0.7399 (m-90) cc_final: 0.7128 (m-10) REVERT: A 375 TYR cc_start: 0.9160 (m-10) cc_final: 0.8899 (m-10) REVERT: A 406 LYS cc_start: 0.8430 (mtmm) cc_final: 0.7680 (mmtp) REVERT: A 482 MET cc_start: 0.8260 (tmm) cc_final: 0.7788 (tmm) REVERT: A 486 LEU cc_start: 0.8249 (mm) cc_final: 0.7962 (mm) outliers start: 11 outliers final: 6 residues processed: 87 average time/residue: 0.0552 time to fit residues: 6.5158 Evaluate side-chains 75 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.0050 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119318 restraints weight = 6649.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122444 restraints weight = 3126.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124646 restraints weight = 1898.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126057 restraints weight = 1331.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127039 restraints weight = 1042.461| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4327 Z= 0.142 Angle : 0.576 8.902 5898 Z= 0.280 Chirality : 0.038 0.121 721 Planarity : 0.004 0.039 710 Dihedral : 3.779 17.861 587 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.25 % Allowed : 20.05 % Favored : 77.70 % 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: 3.02 (0.37), residues: 546 helix: 2.24 (0.24), residues: 461 sheet: None (None), residues: 0 loop : 0.75 (0.77), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 377 TYR 0.009 0.001 TYR A 339 PHE 0.017 0.001 PHE B 86 TRP 0.005 0.001 TRP A 154 HIS 0.012 0.002 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4327) covalent geometry : angle 0.57554 ( 5898) hydrogen bonds : bond 0.04534 ( 347) hydrogen bonds : angle 3.98476 ( 1032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.169 Fit side-chains REVERT: A 1 LYS cc_start: 0.7547 (pptt) cc_final: 0.7043 (tttt) REVERT: A 375 TYR cc_start: 0.9162 (m-10) cc_final: 0.8863 (m-10) REVERT: A 406 LYS cc_start: 0.8454 (mtmm) cc_final: 0.7847 (mmtt) REVERT: A 431 LYS cc_start: 0.8333 (ttmm) cc_final: 0.7836 (tttm) REVERT: A 482 MET cc_start: 0.8213 (tmm) cc_final: 0.7737 (tmm) REVERT: A 486 LEU cc_start: 0.8265 (mm) cc_final: 0.7950 (mm) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.0485 time to fit residues: 5.2154 Evaluate side-chains 78 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.0370 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120807 restraints weight = 6650.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123926 restraints weight = 3134.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.126118 restraints weight = 1896.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.127536 restraints weight = 1331.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128392 restraints weight = 1039.345| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4327 Z= 0.132 Angle : 0.539 5.389 5898 Z= 0.264 Chirality : 0.037 0.125 721 Planarity : 0.004 0.040 710 Dihedral : 3.676 16.993 587 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.70 % Allowed : 20.50 % Favored : 76.80 % 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: 3.29 (0.37), residues: 546 helix: 2.42 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.84 (0.80), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 377 TYR 0.008 0.001 TYR A 339 PHE 0.011 0.001 PHE B 86 TRP 0.004 0.001 TRP A 154 HIS 0.008 0.002 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4327) covalent geometry : angle 0.53858 ( 5898) hydrogen bonds : bond 0.04322 ( 347) hydrogen bonds : angle 3.85783 ( 1032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.137 Fit side-chains REVERT: A 108 TRP cc_start: 0.7364 (m-90) cc_final: 0.7055 (m-10) REVERT: A 375 TYR cc_start: 0.9163 (m-10) cc_final: 0.8892 (m-10) REVERT: A 406 LYS cc_start: 0.8421 (mtmm) cc_final: 0.7830 (mmtt) REVERT: A 431 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7816 (tttm) REVERT: A 482 MET cc_start: 0.8203 (tmm) cc_final: 0.7737 (tmm) REVERT: A 486 LEU cc_start: 0.8241 (mm) cc_final: 0.7905 (mm) outliers start: 12 outliers final: 10 residues processed: 84 average time/residue: 0.0450 time to fit residues: 5.2782 Evaluate side-chains 83 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119151 restraints weight = 6823.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122294 restraints weight = 3219.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124461 restraints weight = 1951.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125484 restraints weight = 1381.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126715 restraints weight = 1132.048| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4327 Z= 0.154 Angle : 0.572 8.793 5898 Z= 0.276 Chirality : 0.037 0.123 721 Planarity : 0.004 0.040 710 Dihedral : 3.673 16.580 587 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.15 % Allowed : 21.62 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.37), residues: 546 helix: 2.47 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.92 (0.82), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.011 0.001 TYR A 2 PHE 0.008 0.001 PHE B 86 TRP 0.003 0.000 TRP A 154 HIS 0.007 0.001 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4327) covalent geometry : angle 0.57156 ( 5898) hydrogen bonds : bond 0.04399 ( 347) hydrogen bonds : angle 3.89895 ( 1032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.150 Fit side-chains REVERT: A 375 TYR cc_start: 0.9172 (m-10) cc_final: 0.8894 (m-10) REVERT: A 406 LYS cc_start: 0.8455 (mtmm) cc_final: 0.7875 (mmtt) REVERT: A 431 LYS cc_start: 0.8292 (ttmm) cc_final: 0.7824 (tttm) REVERT: A 482 MET cc_start: 0.8245 (tmm) cc_final: 0.7772 (tmm) REVERT: A 486 LEU cc_start: 0.8289 (mm) cc_final: 0.7968 (mm) outliers start: 14 outliers final: 13 residues processed: 85 average time/residue: 0.0462 time to fit residues: 5.5437 Evaluate side-chains 87 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118733 restraints weight = 6860.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121916 restraints weight = 3224.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124082 restraints weight = 1931.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125467 restraints weight = 1352.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126437 restraints weight = 1063.636| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4327 Z= 0.156 Angle : 0.562 6.384 5898 Z= 0.275 Chirality : 0.038 0.168 721 Planarity : 0.004 0.040 710 Dihedral : 3.669 16.404 587 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.70 % Allowed : 22.07 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.37), residues: 546 helix: 2.48 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.87 (0.80), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.009 0.001 TYR A 2 PHE 0.008 0.001 PHE A 41 TRP 0.004 0.001 TRP A 108 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4327) covalent geometry : angle 0.56220 ( 5898) hydrogen bonds : bond 0.04426 ( 347) hydrogen bonds : angle 3.89883 ( 1032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.181 Fit side-chains REVERT: A 375 TYR cc_start: 0.9170 (m-10) cc_final: 0.8896 (m-10) REVERT: A 406 LYS cc_start: 0.8438 (mtmm) cc_final: 0.7885 (mmtt) REVERT: A 431 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7837 (tttm) REVERT: A 482 MET cc_start: 0.8249 (tmm) cc_final: 0.7754 (tmm) REVERT: A 486 LEU cc_start: 0.8281 (mm) cc_final: 0.7946 (mm) outliers start: 12 outliers final: 12 residues processed: 85 average time/residue: 0.0442 time to fit residues: 5.2662 Evaluate side-chains 86 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119079 restraints weight = 6645.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122178 restraints weight = 3170.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124339 restraints weight = 1931.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125745 restraints weight = 1365.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126612 restraints weight = 1070.222| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4327 Z= 0.156 Angle : 0.581 10.847 5898 Z= 0.279 Chirality : 0.038 0.165 721 Planarity : 0.004 0.041 710 Dihedral : 3.672 16.328 587 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.60 % Allowed : 21.85 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.37), residues: 546 helix: 2.48 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.89 (0.81), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.009 0.001 TYR A 2 PHE 0.008 0.001 PHE A 41 TRP 0.003 0.000 TRP A 154 HIS 0.005 0.001 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4327) covalent geometry : angle 0.58055 ( 5898) hydrogen bonds : bond 0.04417 ( 347) hydrogen bonds : angle 3.91480 ( 1032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.139 Fit side-chains REVERT: A 375 TYR cc_start: 0.9170 (m-10) cc_final: 0.8899 (m-10) REVERT: A 406 LYS cc_start: 0.8433 (mtmm) cc_final: 0.7905 (mmtt) REVERT: A 431 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7841 (tttm) REVERT: A 482 MET cc_start: 0.8244 (tmm) cc_final: 0.7749 (tmm) REVERT: A 486 LEU cc_start: 0.8280 (mm) cc_final: 0.7948 (mm) outliers start: 16 outliers final: 16 residues processed: 85 average time/residue: 0.0429 time to fit residues: 5.1741 Evaluate side-chains 90 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.0010 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128704 restraints weight = 6605.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132096 restraints weight = 3122.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134401 restraints weight = 1888.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135902 restraints weight = 1331.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.136775 restraints weight = 1044.319| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4327 Z= 0.124 Angle : 0.537 7.016 5898 Z= 0.261 Chirality : 0.037 0.172 721 Planarity : 0.004 0.041 710 Dihedral : 3.608 15.965 587 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.15 % Allowed : 21.85 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.37), residues: 546 helix: 2.64 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.81 (0.81), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.007 0.001 TYR A 2 PHE 0.008 0.001 PHE B 93 TRP 0.002 0.000 TRP A 441 HIS 0.005 0.001 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4327) covalent geometry : angle 0.53732 ( 5898) hydrogen bonds : bond 0.04151 ( 347) hydrogen bonds : angle 3.78886 ( 1032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.142 Fit side-chains REVERT: A 171 MET cc_start: 0.8356 (ttm) cc_final: 0.8146 (ttm) REVERT: A 375 TYR cc_start: 0.9154 (m-10) cc_final: 0.8897 (m-10) REVERT: A 393 LEU cc_start: 0.8660 (mm) cc_final: 0.8290 (mt) REVERT: A 402 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7930 (tt) REVERT: A 406 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7821 (mmtt) REVERT: A 431 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7824 (tttm) REVERT: A 482 MET cc_start: 0.8184 (tmm) cc_final: 0.7759 (tmm) REVERT: A 486 LEU cc_start: 0.8294 (mm) cc_final: 0.7963 (mm) outliers start: 14 outliers final: 11 residues processed: 85 average time/residue: 0.0429 time to fit residues: 5.1484 Evaluate side-chains 86 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121268 restraints weight = 6439.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124674 restraints weight = 3036.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126955 restraints weight = 1826.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128442 restraints weight = 1285.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129331 restraints weight = 1006.154| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4327 Z= 0.165 Angle : 0.590 10.993 5898 Z= 0.284 Chirality : 0.039 0.159 721 Planarity : 0.004 0.042 710 Dihedral : 3.640 15.764 587 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.83 % Allowed : 21.17 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.37), residues: 546 helix: 2.54 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.80 (0.82), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.008 0.001 TYR A 2 PHE 0.009 0.001 PHE A 135 TRP 0.003 0.001 TRP A 154 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 4327) covalent geometry : angle 0.58999 ( 5898) hydrogen bonds : bond 0.04362 ( 347) hydrogen bonds : angle 3.89813 ( 1032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.093 Fit side-chains REVERT: A 375 TYR cc_start: 0.9166 (m-10) cc_final: 0.8898 (m-10) REVERT: A 393 LEU cc_start: 0.8664 (mm) cc_final: 0.8304 (mt) REVERT: A 406 LYS cc_start: 0.8462 (mtmm) cc_final: 0.7866 (mmtt) REVERT: A 431 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7846 (tttm) REVERT: A 482 MET cc_start: 0.8202 (tmm) cc_final: 0.7742 (tmm) REVERT: A 486 LEU cc_start: 0.8307 (mm) cc_final: 0.7987 (mm) outliers start: 17 outliers final: 15 residues processed: 85 average time/residue: 0.0476 time to fit residues: 5.4124 Evaluate side-chains 91 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.0570 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116501 restraints weight = 6770.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119694 restraints weight = 3220.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.121782 restraints weight = 1934.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123158 restraints weight = 1364.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124103 restraints weight = 1070.060| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4327 Z= 0.137 Angle : 0.549 7.017 5898 Z= 0.267 Chirality : 0.038 0.162 721 Planarity : 0.004 0.041 710 Dihedral : 3.615 15.691 587 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.15 % Allowed : 21.85 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.52 (0.37), residues: 546 helix: 2.60 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.74 (0.81), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.008 0.001 TYR A 2 PHE 0.009 0.001 PHE B 86 TRP 0.003 0.000 TRP A 469 HIS 0.005 0.001 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4327) covalent geometry : angle 0.54932 ( 5898) hydrogen bonds : bond 0.04241 ( 347) hydrogen bonds : angle 3.84625 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 932.70 seconds wall clock time: 16 minutes 39.05 seconds (999.05 seconds total)