Starting phenix.real_space_refine on Wed Sep 17 04:16:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh6_14725/09_2025/7zh6_14725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh6_14725/09_2025/7zh6_14725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zh6_14725/09_2025/7zh6_14725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh6_14725/09_2025/7zh6_14725_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zh6_14725/09_2025/7zh6_14725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh6_14725/09_2025/7zh6_14725.map" } resolution = 3.67 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= 0.001 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 2501 2.51 5 N 621 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3771 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3746 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain breaks: 4 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'C0R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.30, per 1000 atoms: 0.34 Number of scatterers: 3771 At special positions: 0 Unit cell: (101.64, 63.36, 79.2, 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 627 8.00 N 621 7.00 C 2501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 144.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 870 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 2 sheets defined 79.9% alpha, 0.8% 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 3 through 11 removed outlier: 3.691A pdb=" N LEU A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 43 removed outlier: 4.419A pdb=" N VAL A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.789A pdb=" N ARG A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.941A pdb=" N GLU A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 150 through 179 removed outlier: 3.677A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.722A pdb=" N ILE A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 234 removed outlier: 3.531A pdb=" N PHE A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 263 Proline residue: A 258 - end of helix removed outlier: 3.506A pdb=" N TYR A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 Proline residue: A 277 - end of helix removed outlier: 3.644A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 344 through 372 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.749A pdb=" N GLU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 401 removed outlier: 3.557A pdb=" N ALA A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 426 removed outlier: 3.921A pdb=" N PHE A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 461 removed outlier: 4.363A pdb=" N ARG A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 466 through 495 removed outlier: 3.561A pdb=" N VAL A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.946A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.982A pdb=" N MET A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.659A pdb=" N ASP A 531 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 532 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.715A pdb=" N TRP A 50 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 257 hydrogen bonds defined for protein. 759 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: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 621 1.33 - 1.45: 1028 1.45 - 1.57: 2188 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3867 Sorted by residual: bond pdb=" N THR A 297 " pdb=" CA THR A 297 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.00e-02 1.00e+04 9.98e+00 bond pdb=" N ASN A 335 " pdb=" CA ASN A 335 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.62e+00 bond pdb=" N ILE A 311 " pdb=" CA ILE A 311 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.10e+00 bond pdb=" N ILE A 264 " pdb=" CA ILE A 264 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 8.97e+00 bond pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.18e-02 7.18e+03 8.83e+00 ... (remaining 3862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 4985 1.95 - 3.89: 251 3.89 - 5.84: 23 5.84 - 7.78: 7 7.78 - 9.73: 3 Bond angle restraints: 5269 Sorted by residual: angle pdb=" N ARG A 128 " pdb=" CA ARG A 128 " pdb=" C ARG A 128 " ideal model delta sigma weight residual 114.62 108.91 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N PRO A 76 " pdb=" CA PRO A 76 " pdb=" C PRO A 76 " ideal model delta sigma weight residual 114.92 108.98 5.94 1.19e+00 7.06e-01 2.50e+01 angle pdb=" O GLU A 533 " pdb=" C GLU A 533 " pdb=" N LYS A 534 " ideal model delta sigma weight residual 122.03 126.35 -4.32 1.08e+00 8.57e-01 1.60e+01 angle pdb=" C GLU A 533 " pdb=" N LYS A 534 " pdb=" CA LYS A 534 " ideal model delta sigma weight residual 121.70 128.65 -6.95 1.80e+00 3.09e-01 1.49e+01 angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.71 107.31 4.40 1.15e+00 7.56e-01 1.46e+01 ... (remaining 5264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 2011 18.07 - 36.14: 212 36.14 - 54.21: 47 54.21 - 72.28: 9 72.28 - 90.35: 7 Dihedral angle restraints: 2286 sinusoidal: 929 harmonic: 1357 Sorted by residual: dihedral pdb=" CB CYS A 90 " pdb=" SG CYS A 90 " pdb=" SG CYS A 148 " pdb=" CB CYS A 148 " ideal model delta sinusoidal sigma weight residual -86.00 -155.72 69.72 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" C ARG A 298 " pdb=" N ARG A 298 " pdb=" CA ARG A 298 " pdb=" CB ARG A 298 " ideal model delta harmonic sigma weight residual -122.60 -131.28 8.68 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CB GLU A 519 " pdb=" CG GLU A 519 " pdb=" CD GLU A 519 " pdb=" OE1 GLU A 519 " ideal model delta sinusoidal sigma weight residual 0.00 -90.35 90.35 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 2283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 429 0.046 - 0.092: 108 0.092 - 0.138: 57 0.138 - 0.184: 17 0.184 - 0.230: 6 Chirality restraints: 617 Sorted by residual: chirality pdb=" CA ARG A 298 " pdb=" N ARG A 298 " pdb=" C ARG A 298 " pdb=" CB ARG A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA VAL A 333 " pdb=" N VAL A 333 " pdb=" C VAL A 333 " pdb=" CB VAL A 333 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU A 186 " pdb=" N LEU A 186 " pdb=" C LEU A 186 " pdb=" CB LEU A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 614 not shown) Planarity restraints: 647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 C0R A 601 " -0.017 2.00e-02 2.50e+03 8.14e-02 8.29e+01 pdb=" C3 C0R A 601 " 0.100 2.00e-02 2.50e+03 pdb=" C4 C0R A 601 " -0.129 2.00e-02 2.50e+03 pdb=" C5 C0R A 601 " -0.027 2.00e-02 2.50e+03 pdb=" C6 C0R A 601 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 183 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C VAL A 183 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL A 183 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 184 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 262 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C TYR A 262 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR A 262 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE A 263 " 0.014 2.00e-02 2.50e+03 ... (remaining 644 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 8 2.27 - 2.92: 1669 2.92 - 3.58: 6083 3.58 - 4.24: 8096 4.24 - 4.90: 13806 Nonbonded interactions: 29662 Sorted by model distance: nonbonded pdb=" CD1 ILE A 523 " pdb=" OE1 GLU A 533 " model vdw 1.607 3.460 nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.143 3.040 nonbonded pdb=" CE2 PHE A 4 " pdb=" NE ARG A 293 " model vdw 2.154 3.420 nonbonded pdb=" O PHE A 468 " pdb=" OG SER A 471 " model vdw 2.230 3.040 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 466 " model vdw 2.235 3.120 ... (remaining 29657 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 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.800 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 0.062 3869 Z= 0.412 Angle : 0.900 9.731 5273 Z= 0.586 Chirality : 0.057 0.230 617 Planarity : 0.005 0.081 647 Dihedral : 15.908 90.348 1410 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.26 % Allowed : 28.46 % Favored : 70.28 % 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 aren not related in a simple way. whole: 0.99 (0.40), residues: 468 helix: 1.81 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -3.22 (0.46), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 89 TYR 0.008 0.001 TYR A 174 PHE 0.016 0.001 PHE A 41 TRP 0.012 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 3867) covalent geometry : angle 0.89954 ( 5269) SS BOND : bond 0.00451 ( 2) SS BOND : angle 1.23957 ( 4) hydrogen bonds : bond 0.13600 ( 257) hydrogen bonds : angle 5.45187 ( 759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.144 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 105 average time/residue: 0.0592 time to fit residues: 7.9927 Evaluate side-chains 89 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 150 ASN A 414 ASN A 457 ASN A 467 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.170053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.148585 restraints weight = 6993.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.153231 restraints weight = 3680.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.156496 restraints weight = 2304.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158586 restraints weight = 1594.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160268 restraints weight = 1208.419| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3869 Z= 0.157 Angle : 0.680 9.065 5273 Z= 0.336 Chirality : 0.042 0.155 617 Planarity : 0.005 0.045 647 Dihedral : 4.457 32.901 579 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.29 % Allowed : 25.44 % Favored : 69.27 % 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 aren not related in a simple way. whole: 1.15 (0.39), residues: 468 helix: 1.89 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -3.20 (0.47), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 407 TYR 0.010 0.002 TYR A 174 PHE 0.014 0.002 PHE A 213 TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3867) covalent geometry : angle 0.67954 ( 5269) SS BOND : bond 0.00215 ( 2) SS BOND : angle 1.07414 ( 4) hydrogen bonds : bond 0.05144 ( 257) hydrogen bonds : angle 4.48010 ( 759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.135 Fit side-chains REVERT: A 14 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: A 124 LEU cc_start: 0.8258 (tt) cc_final: 0.7909 (mp) REVERT: A 290 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6116 (mt-10) outliers start: 21 outliers final: 12 residues processed: 109 average time/residue: 0.0479 time to fit residues: 7.0303 Evaluate side-chains 100 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 494 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.166767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145493 restraints weight = 6731.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.150029 restraints weight = 3556.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.153167 restraints weight = 2216.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.155506 restraints weight = 1539.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.156956 restraints weight = 1134.012| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3869 Z= 0.153 Angle : 0.661 9.040 5273 Z= 0.326 Chirality : 0.041 0.155 617 Planarity : 0.004 0.040 647 Dihedral : 4.360 31.359 579 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.79 % Allowed : 25.44 % Favored : 68.77 % 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 aren not related in a simple way. whole: 1.31 (0.39), residues: 468 helix: 1.96 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -3.01 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.011 0.002 TYR A 93 PHE 0.015 0.002 PHE A 213 TRP 0.008 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3867) covalent geometry : angle 0.66161 ( 5269) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.44750 ( 4) hydrogen bonds : bond 0.04965 ( 257) hydrogen bonds : angle 4.39802 ( 759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.125 Fit side-chains REVERT: A 14 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: A 124 LEU cc_start: 0.8328 (tt) cc_final: 0.7964 (mp) REVERT: A 290 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6286 (mt-10) outliers start: 23 outliers final: 18 residues processed: 113 average time/residue: 0.0453 time to fit residues: 6.9377 Evaluate side-chains 111 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.165645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.144154 restraints weight = 6836.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.148676 restraints weight = 3653.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.151773 restraints weight = 2294.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154140 restraints weight = 1608.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.155610 restraints weight = 1195.115| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3869 Z= 0.150 Angle : 0.624 9.210 5273 Z= 0.312 Chirality : 0.040 0.157 617 Planarity : 0.004 0.036 647 Dihedral : 4.419 33.749 579 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.30 % Allowed : 26.95 % Favored : 66.75 % 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 aren not related in a simple way. whole: 1.34 (0.39), residues: 468 helix: 1.96 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -2.94 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.011 0.001 TYR A 461 PHE 0.015 0.002 PHE A 213 TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3867) covalent geometry : angle 0.62396 ( 5269) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.40725 ( 4) hydrogen bonds : bond 0.04855 ( 257) hydrogen bonds : angle 4.34861 ( 759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.148 Fit side-chains REVERT: A 14 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: A 93 TYR cc_start: 0.6178 (m-80) cc_final: 0.5422 (m-80) REVERT: A 124 LEU cc_start: 0.8397 (tt) cc_final: 0.7895 (mp) REVERT: A 290 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6307 (mt-10) REVERT: A 347 MET cc_start: 0.8290 (ttt) cc_final: 0.8031 (ttt) outliers start: 25 outliers final: 23 residues processed: 115 average time/residue: 0.0514 time to fit residues: 7.9682 Evaluate side-chains 116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 335 ASN A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.165423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144177 restraints weight = 6880.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.148702 restraints weight = 3649.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.151854 restraints weight = 2274.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.154038 restraints weight = 1558.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.155510 restraints weight = 1154.698| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3869 Z= 0.143 Angle : 0.645 9.184 5273 Z= 0.314 Chirality : 0.040 0.157 617 Planarity : 0.004 0.038 647 Dihedral : 4.416 34.067 579 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 7.05 % Allowed : 27.20 % Favored : 65.74 % 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 aren not related in a simple way. whole: 1.32 (0.39), residues: 468 helix: 1.95 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -2.98 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 343 TYR 0.022 0.002 TYR A 284 PHE 0.014 0.001 PHE A 213 TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3867) covalent geometry : angle 0.64503 ( 5269) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.31569 ( 4) hydrogen bonds : bond 0.04684 ( 257) hydrogen bonds : angle 4.28088 ( 759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.153 Fit side-chains REVERT: A 14 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6700 (m-80) REVERT: A 93 TYR cc_start: 0.6086 (m-80) cc_final: 0.5434 (m-80) REVERT: A 124 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7794 (mp) REVERT: A 238 GLN cc_start: 0.8042 (mp10) cc_final: 0.7158 (mp10) REVERT: A 290 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6338 (mt-10) REVERT: A 347 MET cc_start: 0.8242 (ttt) cc_final: 0.7983 (ttt) outliers start: 28 outliers final: 20 residues processed: 113 average time/residue: 0.0520 time to fit residues: 7.8215 Evaluate side-chains 112 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.164854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.143973 restraints weight = 6866.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148560 restraints weight = 3631.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.151642 restraints weight = 2245.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.153717 restraints weight = 1536.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.155260 restraints weight = 1143.844| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3869 Z= 0.147 Angle : 0.636 9.147 5273 Z= 0.315 Chirality : 0.040 0.158 617 Planarity : 0.004 0.039 647 Dihedral : 4.327 32.727 579 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 7.05 % Allowed : 29.72 % Favored : 63.22 % 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 aren not related in a simple way. whole: 1.28 (0.39), residues: 468 helix: 1.93 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -3.02 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 343 TYR 0.010 0.001 TYR A 461 PHE 0.014 0.001 PHE A 213 TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3867) covalent geometry : angle 0.63583 ( 5269) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.35404 ( 4) hydrogen bonds : bond 0.04723 ( 257) hydrogen bonds : angle 4.30210 ( 759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.112 Fit side-chains REVERT: A 14 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: A 34 PHE cc_start: 0.6988 (m-80) cc_final: 0.6711 (m-80) REVERT: A 93 TYR cc_start: 0.6114 (m-80) cc_final: 0.5580 (m-80) REVERT: A 124 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7602 (mp) REVERT: A 238 GLN cc_start: 0.8001 (mp10) cc_final: 0.7429 (mp10) REVERT: A 281 PHE cc_start: 0.8149 (m-80) cc_final: 0.7947 (m-80) REVERT: A 347 MET cc_start: 0.8121 (ttt) cc_final: 0.7873 (ttt) outliers start: 28 outliers final: 23 residues processed: 120 average time/residue: 0.0499 time to fit residues: 7.9043 Evaluate side-chains 118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN A 162 ASN A 271 GLN A 414 ASN A 457 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.163470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.142102 restraints weight = 7169.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146716 restraints weight = 3800.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149873 restraints weight = 2361.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.152003 restraints weight = 1622.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.153568 restraints weight = 1212.226| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3869 Z= 0.148 Angle : 0.656 9.401 5273 Z= 0.321 Chirality : 0.041 0.170 617 Planarity : 0.005 0.040 647 Dihedral : 4.343 33.174 579 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.55 % Allowed : 29.97 % Favored : 63.48 % 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 aren not related in a simple way. whole: 1.27 (0.39), residues: 468 helix: 1.91 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -2.97 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 343 TYR 0.009 0.001 TYR A 93 PHE 0.015 0.001 PHE A 41 TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3867) covalent geometry : angle 0.65666 ( 5269) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.31707 ( 4) hydrogen bonds : bond 0.04686 ( 257) hydrogen bonds : angle 4.31937 ( 759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.152 Fit side-chains REVERT: A 14 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: A 124 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7544 (mp) REVERT: A 238 GLN cc_start: 0.8035 (mp10) cc_final: 0.7570 (mp10) REVERT: A 281 PHE cc_start: 0.8123 (m-80) cc_final: 0.7895 (m-80) REVERT: A 347 MET cc_start: 0.8258 (ttt) cc_final: 0.8012 (ttt) REVERT: A 527 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7068 (tp30) outliers start: 26 outliers final: 23 residues processed: 114 average time/residue: 0.0539 time to fit residues: 8.0585 Evaluate side-chains 116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 46 optimal weight: 0.0770 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 414 ASN A 457 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.165701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.144368 restraints weight = 6955.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.149051 restraints weight = 3680.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.152203 restraints weight = 2280.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.154365 restraints weight = 1573.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.156031 restraints weight = 1170.676| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3869 Z= 0.142 Angle : 0.665 9.501 5273 Z= 0.322 Chirality : 0.040 0.160 617 Planarity : 0.004 0.042 647 Dihedral : 4.278 33.375 579 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.55 % Allowed : 30.73 % Favored : 62.72 % 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 aren not related in a simple way. whole: 1.25 (0.39), residues: 468 helix: 1.90 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -2.94 (0.52), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 343 TYR 0.008 0.001 TYR A 49 PHE 0.014 0.001 PHE A 41 TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3867) covalent geometry : angle 0.66559 ( 5269) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.34908 ( 4) hydrogen bonds : bond 0.04564 ( 257) hydrogen bonds : angle 4.27727 ( 759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.146 Fit side-chains REVERT: A 14 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6750 (m-80) REVERT: A 34 PHE cc_start: 0.6808 (m-80) cc_final: 0.6500 (m-80) REVERT: A 124 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7443 (mp) REVERT: A 347 MET cc_start: 0.8205 (ttt) cc_final: 0.7941 (ttt) REVERT: A 527 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7048 (tp30) REVERT: A 530 ASP cc_start: 0.7706 (t0) cc_final: 0.7284 (t0) outliers start: 26 outliers final: 22 residues processed: 114 average time/residue: 0.0466 time to fit residues: 7.2940 Evaluate side-chains 115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.163215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142243 restraints weight = 6961.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.146796 restraints weight = 3718.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.149921 restraints weight = 2318.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.152120 restraints weight = 1598.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.153654 restraints weight = 1180.297| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3869 Z= 0.152 Angle : 0.670 9.774 5273 Z= 0.332 Chirality : 0.041 0.164 617 Planarity : 0.005 0.044 647 Dihedral : 4.269 33.136 579 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.79 % Allowed : 30.73 % Favored : 63.48 % 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 aren not related in a simple way. whole: 1.26 (0.39), residues: 468 helix: 1.90 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -2.96 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 343 TYR 0.008 0.001 TYR A 49 PHE 0.015 0.001 PHE A 41 TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3867) covalent geometry : angle 0.67056 ( 5269) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.36606 ( 4) hydrogen bonds : bond 0.04644 ( 257) hydrogen bonds : angle 4.30037 ( 759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.152 Fit side-chains REVERT: A 34 PHE cc_start: 0.6843 (m-80) cc_final: 0.6523 (m-80) REVERT: A 124 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7434 (mp) REVERT: A 343 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7647 (ttp-110) REVERT: A 347 MET cc_start: 0.8300 (ttt) cc_final: 0.8028 (ttt) REVERT: A 527 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7076 (tp30) REVERT: A 530 ASP cc_start: 0.7684 (t0) cc_final: 0.7257 (t0) outliers start: 23 outliers final: 21 residues processed: 110 average time/residue: 0.0455 time to fit residues: 6.6815 Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.162791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141627 restraints weight = 7138.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.146240 restraints weight = 3785.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149359 restraints weight = 2352.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.151439 restraints weight = 1617.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.153018 restraints weight = 1210.357| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3869 Z= 0.160 Angle : 0.708 10.326 5273 Z= 0.350 Chirality : 0.042 0.161 617 Planarity : 0.005 0.044 647 Dihedral : 4.329 33.035 579 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.54 % Allowed : 30.73 % Favored : 63.73 % 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 aren not related in a simple way. whole: 1.16 (0.39), residues: 468 helix: 1.83 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -2.99 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 343 TYR 0.008 0.001 TYR A 49 PHE 0.016 0.002 PHE A 41 TRP 0.008 0.001 TRP A 358 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 3867) covalent geometry : angle 0.70845 ( 5269) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.40578 ( 4) hydrogen bonds : bond 0.04817 ( 257) hydrogen bonds : angle 4.34972 ( 759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.147 Fit side-chains REVERT: A 34 PHE cc_start: 0.6952 (m-80) cc_final: 0.6633 (m-80) REVERT: A 124 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7379 (mp) REVERT: A 347 MET cc_start: 0.8276 (ttt) cc_final: 0.8007 (ttt) REVERT: A 527 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7093 (tp30) REVERT: A 530 ASP cc_start: 0.7720 (t0) cc_final: 0.7286 (t0) outliers start: 22 outliers final: 21 residues processed: 107 average time/residue: 0.0451 time to fit residues: 6.6198 Evaluate side-chains 110 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.159001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137729 restraints weight = 7080.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142121 restraints weight = 3860.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145165 restraints weight = 2465.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.147333 restraints weight = 1733.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148784 restraints weight = 1302.834| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 3869 Z= 0.174 Angle : 0.707 9.738 5273 Z= 0.356 Chirality : 0.042 0.164 617 Planarity : 0.005 0.044 647 Dihedral : 4.454 32.696 579 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 5.79 % Allowed : 30.23 % Favored : 63.98 % 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 aren not related in a simple way. whole: 1.11 (0.39), residues: 468 helix: 1.77 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -3.01 (0.53), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 343 TYR 0.010 0.001 TYR A 49 PHE 0.017 0.002 PHE A 41 TRP 0.007 0.001 TRP A 358 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 3867) covalent geometry : angle 0.70728 ( 5269) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.49798 ( 4) hydrogen bonds : bond 0.05035 ( 257) hydrogen bonds : angle 4.48248 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 860.23 seconds wall clock time: 15 minutes 32.82 seconds (932.82 seconds total)