Starting phenix.real_space_refine on Sat May 2 12:05:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1b_62740/05_2026/9l1b_62740_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1b_62740/05_2026/9l1b_62740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l1b_62740/05_2026/9l1b_62740_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1b_62740/05_2026/9l1b_62740_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l1b_62740/05_2026/9l1b_62740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1b_62740/05_2026/9l1b_62740.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3043 2.51 5 N 681 2.21 5 O 764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4524 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4415 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 28, 'TRANS': 524} Chain breaks: 1 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 109 Unusual residues: {' CL': 1, ' NA': 2, 'CLR': 1, 'TAU': 1, 'Y01': 2} Classifications: {'undetermined': 7, 'water': 1} Link IDs: {None: 7} Time building chain proxies: 0.83, per 1000 atoms: 0.18 Number of scatterers: 4524 At special positions: 0 Unit cell: (79.92, 71.28, 84.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 2 11.00 O 764 8.00 N 681 7.00 C 3043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.04 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: 0.27 Conformation dependent library (CDL) restraints added in 99.3 milliseconds 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 77.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.502A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.795A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 removed outlier: 3.519A pdb=" N VAL A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 117 removed outlier: 3.674A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.151A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 4.262A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.735A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 removed outlier: 4.603A pdb=" N LYS A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 267 removed outlier: 3.768A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.989A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.479A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.808A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.126A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.627A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 416 removed outlier: 3.573A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 removed outlier: 3.828A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.278A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.353A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.153A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 586 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 281 hydrogen bonds defined for protein. 834 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: 0.44 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 661 1.31 - 1.44: 1404 1.44 - 1.57: 2561 1.57 - 1.71: 0 1.71 - 1.84: 47 Bond restraints: 4673 Sorted by residual: bond pdb=" C PRO A 213 " pdb=" O PRO A 213 " ideal model delta sigma weight residual 1.237 1.179 0.059 1.20e-02 6.94e+03 2.39e+01 bond pdb=" N THR A 242 " pdb=" CA THR A 242 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.16e-02 7.43e+03 1.23e+01 bond pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N ARG A 592 " pdb=" CA ARG A 592 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.29e-02 6.01e+03 8.98e+00 bond pdb=" N VAL A 245 " pdb=" CA VAL A 245 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.00e+00 ... (remaining 4668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 6190 2.67 - 5.33: 183 5.33 - 8.00: 11 8.00 - 10.67: 2 10.67 - 13.34: 1 Bond angle restraints: 6387 Sorted by residual: angle pdb=" N PRO A 213 " pdb=" CA PRO A 213 " pdb=" C PRO A 213 " ideal model delta sigma weight residual 113.40 106.78 6.62 1.34e+00 5.57e-01 2.44e+01 angle pdb=" N PRO A 68 " pdb=" CA PRO A 68 " pdb=" C PRO A 68 " ideal model delta sigma weight residual 113.47 120.41 -6.94 1.43e+00 4.89e-01 2.35e+01 angle pdb=" C ARG A 177 " pdb=" N LYS A 178 " pdb=" CA LYS A 178 " ideal model delta sigma weight residual 123.05 116.61 6.44 1.40e+00 5.10e-01 2.11e+01 angle pdb=" O2 TAU A 704 " pdb=" S TAU A 704 " pdb=" O3 TAU A 704 " ideal model delta sigma weight residual 113.11 99.77 13.34 3.00e+00 1.11e-01 1.98e+01 angle pdb=" CA GLY A 214 " pdb=" C GLY A 214 " pdb=" O GLY A 214 " ideal model delta sigma weight residual 122.78 117.94 4.84 1.20e+00 6.94e-01 1.62e+01 ... (remaining 6382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 2552 23.45 - 46.89: 196 46.89 - 70.34: 36 70.34 - 93.79: 7 93.79 - 117.23: 1 Dihedral angle restraints: 2792 sinusoidal: 1199 harmonic: 1593 Sorted by residual: dihedral pdb=" CBC Y01 A 707 " pdb=" CAR Y01 A 707 " pdb=" CAT Y01 A 707 " pdb=" CBH Y01 A 707 " ideal model delta sinusoidal sigma weight residual -57.13 60.10 -117.23 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" N CYS A 171 " pdb=" C CYS A 171 " pdb=" CA CYS A 171 " pdb=" CB CYS A 171 " ideal model delta harmonic sigma weight residual 122.80 113.83 8.97 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" CAT Y01 A 707 " pdb=" CAR Y01 A 707 " pdb=" CBC Y01 A 707 " pdb=" OAW Y01 A 707 " ideal model delta sinusoidal sigma weight residual 178.96 90.61 88.35 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 2789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 601 0.071 - 0.141: 84 0.141 - 0.212: 12 0.212 - 0.283: 5 0.283 - 0.354: 1 Chirality restraints: 703 Sorted by residual: chirality pdb=" CA CYS A 171 " pdb=" N CYS A 171 " pdb=" C CYS A 171 " pdb=" CB CYS A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA PRO A 68 " pdb=" N PRO A 68 " pdb=" C PRO A 68 " pdb=" CB PRO A 68 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CG LEU A 306 " pdb=" CB LEU A 306 " pdb=" CD1 LEU A 306 " pdb=" CD2 LEU A 306 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 700 not shown) Planarity restraints: 765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 240 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG A 240 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG A 240 " -0.024 2.00e-02 2.50e+03 pdb=" N SER A 241 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 177 " -0.256 9.50e-02 1.11e+02 1.15e-01 8.09e+00 pdb=" NE ARG A 177 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 177 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 177 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 177 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 167 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C ASN A 167 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 167 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 168 " -0.012 2.00e-02 2.50e+03 ... (remaining 762 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 957 2.77 - 3.30: 4561 3.30 - 3.84: 7899 3.84 - 4.37: 9603 4.37 - 4.90: 16265 Nonbonded interactions: 39285 Sorted by model distance: nonbonded pdb=" O SER A 311 " pdb=" OG SER A 314 " model vdw 2.240 3.040 nonbonded pdb=" O LEU A 398 " pdb=" OD1 ASP A 401 " model vdw 2.254 3.040 nonbonded pdb=" O VAL A 59 " pdb="NA NA A 702 " model vdw 2.275 2.470 nonbonded pdb="NA NA A 701 " pdb=" O1 TAU A 704 " model vdw 2.305 2.470 nonbonded pdb=" OD1 ASN A 63 " pdb="NA NA A 701 " model vdw 2.315 2.470 ... (remaining 39280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.240 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 0.059 4674 Z= 0.408 Angle : 0.972 13.337 6389 Z= 0.622 Chirality : 0.054 0.354 703 Planarity : 0.008 0.115 765 Dihedral : 16.580 117.231 1781 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 23.68 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.34), residues: 549 helix: 0.40 (0.25), residues: 387 sheet: None (None), residues: 0 loop : -1.20 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 583 TYR 0.029 0.001 TYR A 69 PHE 0.013 0.002 PHE A 58 TRP 0.018 0.002 TRP A 218 HIS 0.005 0.002 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 4673) covalent geometry : angle 0.97080 ( 6387) SS BOND : bond 0.00492 ( 1) SS BOND : angle 2.57291 ( 2) hydrogen bonds : bond 0.16566 ( 281) hydrogen bonds : angle 7.30185 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.094 Fit side-chains REVERT: A 190 ASN cc_start: 0.5855 (m-40) cc_final: 0.5621 (t0) REVERT: A 428 ARG cc_start: 0.7506 (ttt-90) cc_final: 0.6891 (ptp-170) REVERT: A 506 TYR cc_start: 0.7849 (m-10) cc_final: 0.7539 (m-10) REVERT: A 563 ILE cc_start: 0.8776 (mt) cc_final: 0.8556 (mm) REVERT: A 599 ASN cc_start: 0.6677 (p0) cc_final: 0.6397 (p0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2701 time to fit residues: 36.0919 Evaluate side-chains 84 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 179 ASN A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109027 restraints weight = 6403.408| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.76 r_work: 0.3170 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4674 Z= 0.132 Angle : 0.596 6.389 6389 Z= 0.299 Chirality : 0.040 0.194 703 Planarity : 0.004 0.032 765 Dihedral : 8.145 59.216 812 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.17 % Allowed : 22.41 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.36), residues: 549 helix: 1.27 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.87 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 427 TYR 0.017 0.001 TYR A 69 PHE 0.023 0.002 PHE A 572 TRP 0.019 0.001 TRP A 218 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4673) covalent geometry : angle 0.59557 ( 6387) SS BOND : bond 0.00006 ( 1) SS BOND : angle 1.17186 ( 2) hydrogen bonds : bond 0.04672 ( 281) hydrogen bonds : angle 5.01725 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: A 53 SER cc_start: 0.8714 (m) cc_final: 0.8348 (p) REVERT: A 190 ASN cc_start: 0.5951 (m-40) cc_final: 0.5622 (t0) REVERT: A 286 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7889 (mt-10) REVERT: A 293 ASP cc_start: 0.8284 (m-30) cc_final: 0.8023 (m-30) REVERT: A 428 ARG cc_start: 0.7686 (ttt-90) cc_final: 0.6583 (ptp-110) REVERT: A 563 ILE cc_start: 0.8540 (mt) cc_final: 0.8178 (mm) REVERT: A 599 ASN cc_start: 0.7043 (p0) cc_final: 0.6713 (p0) outliers start: 15 outliers final: 7 residues processed: 105 average time/residue: 0.2112 time to fit residues: 23.5033 Evaluate side-chains 92 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 567 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107756 restraints weight = 6433.634| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.01 r_work: 0.3153 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4674 Z= 0.130 Angle : 0.554 6.542 6389 Z= 0.277 Chirality : 0.040 0.194 703 Planarity : 0.004 0.044 765 Dihedral : 7.380 54.101 812 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.38 % Allowed : 22.83 % Favored : 73.78 % 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: 1.32 (0.36), residues: 549 helix: 1.57 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.68 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 575 TYR 0.022 0.001 TYR A 426 PHE 0.013 0.001 PHE A 58 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4673) covalent geometry : angle 0.55432 ( 6387) SS BOND : bond 0.00109 ( 1) SS BOND : angle 0.70002 ( 2) hydrogen bonds : bond 0.04193 ( 281) hydrogen bonds : angle 4.77007 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: A 53 SER cc_start: 0.8023 (m) cc_final: 0.7512 (p) REVERT: A 190 ASN cc_start: 0.5453 (m-40) cc_final: 0.4982 (t0) REVERT: A 256 MET cc_start: 0.7857 (tpt) cc_final: 0.7518 (tpp) REVERT: A 286 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7560 (mt-10) REVERT: A 428 ARG cc_start: 0.7351 (ttt-90) cc_final: 0.6124 (ptp-110) REVERT: A 599 ASN cc_start: 0.7313 (p0) cc_final: 0.6862 (p0) outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 0.2017 time to fit residues: 20.1051 Evaluate side-chains 91 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 51 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107294 restraints weight = 6358.519| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.98 r_work: 0.3141 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4674 Z= 0.127 Angle : 0.547 7.057 6389 Z= 0.271 Chirality : 0.040 0.189 703 Planarity : 0.004 0.034 765 Dihedral : 7.088 52.749 812 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.44 % Allowed : 22.62 % Favored : 72.94 % 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: 1.48 (0.37), residues: 549 helix: 1.69 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.66 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.017 0.001 TYR A 69 PHE 0.013 0.001 PHE A 458 TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4673) covalent geometry : angle 0.54707 ( 6387) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.67292 ( 2) hydrogen bonds : bond 0.03984 ( 281) hydrogen bonds : angle 4.65219 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8036 (m) cc_final: 0.7573 (p) REVERT: A 190 ASN cc_start: 0.5483 (m-40) cc_final: 0.5021 (t0) REVERT: A 286 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7618 (mt-10) REVERT: A 428 ARG cc_start: 0.7387 (ttt-90) cc_final: 0.6172 (ptp-110) REVERT: A 599 ASN cc_start: 0.7374 (p0) cc_final: 0.6949 (p0) outliers start: 21 outliers final: 14 residues processed: 92 average time/residue: 0.2102 time to fit residues: 20.4776 Evaluate side-chains 88 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107020 restraints weight = 6393.053| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.98 r_work: 0.3149 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4674 Z= 0.128 Angle : 0.538 7.454 6389 Z= 0.266 Chirality : 0.040 0.188 703 Planarity : 0.004 0.034 765 Dihedral : 6.980 51.686 812 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.02 % Allowed : 23.26 % Favored : 72.73 % 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 are not related in a simple way. whole: 1.48 (0.36), residues: 549 helix: 1.70 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.70 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.020 0.001 TYR A 426 PHE 0.014 0.001 PHE A 458 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4673) covalent geometry : angle 0.53843 ( 6387) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.63035 ( 2) hydrogen bonds : bond 0.03963 ( 281) hydrogen bonds : angle 4.64593 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8067 (m) cc_final: 0.7564 (p) REVERT: A 190 ASN cc_start: 0.5424 (m-40) cc_final: 0.5126 (t0) REVERT: A 381 MET cc_start: 0.8153 (mtp) cc_final: 0.7930 (mtt) REVERT: A 428 ARG cc_start: 0.7387 (ttt-90) cc_final: 0.6174 (ptp-110) REVERT: A 599 ASN cc_start: 0.7400 (p0) cc_final: 0.6993 (p0) outliers start: 19 outliers final: 13 residues processed: 86 average time/residue: 0.2069 time to fit residues: 18.8805 Evaluate side-chains 86 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 567 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105892 restraints weight = 6500.066| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.98 r_work: 0.3124 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4674 Z= 0.134 Angle : 0.544 7.879 6389 Z= 0.268 Chirality : 0.040 0.188 703 Planarity : 0.004 0.034 765 Dihedral : 6.903 49.341 812 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.44 % Allowed : 22.41 % Favored : 73.15 % 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 (0.36), residues: 549 helix: 1.79 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.92 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.017 0.001 TYR A 69 PHE 0.016 0.001 PHE A 458 TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4673) covalent geometry : angle 0.54440 ( 6387) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.65508 ( 2) hydrogen bonds : bond 0.03935 ( 281) hydrogen bonds : angle 4.58408 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8142 (m) cc_final: 0.7612 (p) REVERT: A 190 ASN cc_start: 0.5349 (m-40) cc_final: 0.5092 (t0) REVERT: A 428 ARG cc_start: 0.7363 (ttt-90) cc_final: 0.6161 (ptp-110) REVERT: A 599 ASN cc_start: 0.7406 (p0) cc_final: 0.7013 (p0) outliers start: 21 outliers final: 15 residues processed: 86 average time/residue: 0.2051 time to fit residues: 18.7030 Evaluate side-chains 86 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 567 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105898 restraints weight = 6456.317| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.97 r_work: 0.3140 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4674 Z= 0.134 Angle : 0.550 8.725 6389 Z= 0.270 Chirality : 0.040 0.188 703 Planarity : 0.004 0.035 765 Dihedral : 6.855 48.421 812 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.02 % Allowed : 23.26 % Favored : 72.73 % 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 are not related in a simple way. whole: 1.49 (0.36), residues: 549 helix: 1.77 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -0.85 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.019 0.001 TYR A 426 PHE 0.015 0.001 PHE A 458 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4673) covalent geometry : angle 0.54997 ( 6387) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.57425 ( 2) hydrogen bonds : bond 0.03945 ( 281) hydrogen bonds : angle 4.56343 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8101 (m) cc_final: 0.7566 (p) REVERT: A 190 ASN cc_start: 0.5280 (m-40) cc_final: 0.5008 (t0) REVERT: A 428 ARG cc_start: 0.7360 (ttt-90) cc_final: 0.6135 (ptp-110) REVERT: A 460 TYR cc_start: 0.8530 (t80) cc_final: 0.8155 (t80) REVERT: A 599 ASN cc_start: 0.7458 (p0) cc_final: 0.7075 (p0) outliers start: 19 outliers final: 14 residues processed: 87 average time/residue: 0.2012 time to fit residues: 18.5761 Evaluate side-chains 86 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 0.0010 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.107830 restraints weight = 6497.509| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.99 r_work: 0.3158 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4674 Z= 0.112 Angle : 0.537 9.223 6389 Z= 0.262 Chirality : 0.040 0.190 703 Planarity : 0.004 0.034 765 Dihedral : 6.700 48.178 812 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.17 % Allowed : 25.16 % Favored : 71.67 % 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: 1.59 (0.36), residues: 549 helix: 1.85 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.83 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.015 0.001 TYR A 138 PHE 0.018 0.001 PHE A 458 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4673) covalent geometry : angle 0.53680 ( 6387) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.45902 ( 2) hydrogen bonds : bond 0.03704 ( 281) hydrogen bonds : angle 4.49719 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8120 (m) cc_final: 0.7661 (p) REVERT: A 256 MET cc_start: 0.7790 (tpt) cc_final: 0.7488 (tpp) REVERT: A 286 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7198 (mm-30) REVERT: A 428 ARG cc_start: 0.7398 (ttt-90) cc_final: 0.6157 (ptp-110) REVERT: A 460 TYR cc_start: 0.8547 (t80) cc_final: 0.8066 (t80) REVERT: A 599 ASN cc_start: 0.7407 (p0) cc_final: 0.7014 (p0) outliers start: 15 outliers final: 11 residues processed: 84 average time/residue: 0.1964 time to fit residues: 17.5561 Evaluate side-chains 85 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108065 restraints weight = 6354.424| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.96 r_work: 0.3166 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4674 Z= 0.115 Angle : 0.545 9.607 6389 Z= 0.265 Chirality : 0.040 0.189 703 Planarity : 0.004 0.034 765 Dihedral : 6.623 48.447 812 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.38 % Allowed : 25.37 % Favored : 71.25 % 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: 1.58 (0.36), residues: 549 helix: 1.85 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.86 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.015 0.001 TYR A 138 PHE 0.020 0.001 PHE A 458 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4673) covalent geometry : angle 0.54540 ( 6387) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.45551 ( 2) hydrogen bonds : bond 0.03716 ( 281) hydrogen bonds : angle 4.49725 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8181 (m) cc_final: 0.7893 (p) REVERT: A 256 MET cc_start: 0.7804 (tpt) cc_final: 0.7532 (tpp) REVERT: A 286 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7191 (mm-30) REVERT: A 428 ARG cc_start: 0.7399 (ttt-90) cc_final: 0.6159 (ptp-110) REVERT: A 599 ASN cc_start: 0.7418 (p0) cc_final: 0.7023 (p0) outliers start: 16 outliers final: 13 residues processed: 82 average time/residue: 0.2029 time to fit residues: 17.6470 Evaluate side-chains 85 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107616 restraints weight = 6414.382| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.94 r_work: 0.3146 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4674 Z= 0.120 Angle : 0.536 5.976 6389 Z= 0.264 Chirality : 0.040 0.189 703 Planarity : 0.004 0.035 765 Dihedral : 6.601 48.447 812 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.96 % Allowed : 26.43 % Favored : 70.61 % 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: 1.53 (0.36), residues: 549 helix: 1.82 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.90 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.019 0.001 TYR A 426 PHE 0.021 0.001 PHE A 458 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4673) covalent geometry : angle 0.53622 ( 6387) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.51393 ( 2) hydrogen bonds : bond 0.03765 ( 281) hydrogen bonds : angle 4.52203 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8159 (m) cc_final: 0.7857 (p) REVERT: A 256 MET cc_start: 0.7784 (tpt) cc_final: 0.7512 (tpp) REVERT: A 428 ARG cc_start: 0.7373 (ttt-90) cc_final: 0.6134 (ptp-110) REVERT: A 460 TYR cc_start: 0.8522 (t80) cc_final: 0.8080 (t80) REVERT: A 599 ASN cc_start: 0.7425 (p0) cc_final: 0.7034 (p0) outliers start: 14 outliers final: 13 residues processed: 82 average time/residue: 0.1945 time to fit residues: 16.9657 Evaluate side-chains 87 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.122251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105494 restraints weight = 6462.846| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.98 r_work: 0.3133 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4674 Z= 0.141 Angle : 0.566 8.804 6389 Z= 0.276 Chirality : 0.041 0.187 703 Planarity : 0.004 0.035 765 Dihedral : 6.627 48.626 812 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.96 % Allowed : 26.43 % Favored : 70.61 % 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: 1.45 (0.36), residues: 549 helix: 1.75 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.92 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.018 0.001 TYR A 69 PHE 0.022 0.002 PHE A 458 TRP 0.010 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4673) covalent geometry : angle 0.56639 ( 6387) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.63559 ( 2) hydrogen bonds : bond 0.03956 ( 281) hydrogen bonds : angle 4.55769 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 897.52 seconds wall clock time: 17 minutes 6.13 seconds (1026.13 seconds total)