Starting phenix.real_space_refine on Sat May 2 09:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtx_37845/05_2026/8wtx_37845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtx_37845/05_2026/8wtx_37845.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/8wtx_37845/05_2026/8wtx_37845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtx_37845/05_2026/8wtx_37845.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wtx_37845/05_2026/8wtx_37845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtx_37845/05_2026/8wtx_37845.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= -0.001 sd= 0.060 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 2889 2.51 5 N 666 2.21 5 O 724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4300 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4284 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 516} Chain breaks: 1 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'Y60': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.21, per 1000 atoms: 0.28 Number of scatterers: 4300 At special positions: 0 Unit cell: (68.85, 63.75, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 20 16.00 O 724 8.00 N 666 7.00 C 2889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " 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: 0.30 Conformation dependent library (CDL) restraints added in 176.7 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 67.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 80 through 89 removed outlier: 4.460A pdb=" N TYR A 84 " --> pdb=" O TRP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 121 removed outlier: 5.050A pdb=" N MET A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 135 through 166 removed outlier: 3.551A pdb=" N VAL A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.520A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.972A pdb=" N CYS A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.801A pdb=" N VAL A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.044A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 319 removed outlier: 4.140A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.730A pdb=" N ALA A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 373 Processing helix chain 'A' and resid 386 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 402 through 433 Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.947A pdb=" N THR A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 464 through 476 removed outlier: 4.093A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 removed outlier: 3.837A pdb=" N LEU A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'A' and resid 514 through 539 Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 553 through 567 removed outlier: 4.389A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.694A pdb=" N THR A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 removed outlier: 3.908A pdb=" N PHE A 609 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 245 hydrogen bonds defined for protein. 720 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: 0.58 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 635 1.30 - 1.43: 1345 1.43 - 1.56: 2425 1.56 - 1.68: 3 1.68 - 1.81: 32 Bond restraints: 4440 Sorted by residual: bond pdb=" C VAL A 154 " pdb=" O VAL A 154 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.35e-02 5.49e+03 2.49e+01 bond pdb=" C ASN A 153 " pdb=" O ASN A 153 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.32e-02 5.74e+03 1.91e+01 bond pdb=" C GLY A 149 " pdb=" O GLY A 149 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.23e-02 6.61e+03 1.53e+01 bond pdb=" CA GLN A 608 " pdb=" C GLN A 608 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.34e-02 5.57e+03 1.34e+01 bond pdb=" C PHE A 150 " pdb=" O PHE A 150 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.31e-02 5.83e+03 1.23e+01 ... (remaining 4435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 5988 2.96 - 5.91: 61 5.91 - 8.87: 10 8.87 - 11.82: 1 11.82 - 14.78: 1 Bond angle restraints: 6061 Sorted by residual: angle pdb=" N HIS A 613 " pdb=" CA HIS A 613 " pdb=" C HIS A 613 " ideal model delta sigma weight residual 113.12 98.34 14.78 1.25e+00 6.40e-01 1.40e+02 angle pdb=" N TRP A 264 " pdb=" CA TRP A 264 " pdb=" C TRP A 264 " ideal model delta sigma weight residual 114.64 104.57 10.07 1.52e+00 4.33e-01 4.39e+01 angle pdb=" N LEU A 615 " pdb=" CA LEU A 615 " pdb=" C LEU A 615 " ideal model delta sigma weight residual 110.44 104.30 6.14 1.20e+00 6.94e-01 2.62e+01 angle pdb=" N ASN A 153 " pdb=" CA ASN A 153 " pdb=" C ASN A 153 " ideal model delta sigma weight residual 113.28 107.18 6.10 1.22e+00 6.72e-01 2.50e+01 angle pdb=" C ILE A 155 " pdb=" N ILE A 156 " pdb=" CA ILE A 156 " ideal model delta sigma weight residual 120.42 126.30 -5.88 1.42e+00 4.96e-01 1.72e+01 ... (remaining 6056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.73: 2028 13.73 - 27.45: 290 27.45 - 41.18: 118 41.18 - 54.91: 34 54.91 - 68.63: 13 Dihedral angle restraints: 2483 sinusoidal: 934 harmonic: 1549 Sorted by residual: dihedral pdb=" CA VAL A 263 " pdb=" C VAL A 263 " pdb=" N TRP A 264 " pdb=" CA TRP A 264 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" C HIS A 613 " pdb=" N HIS A 613 " pdb=" CA HIS A 613 " pdb=" CB HIS A 613 " ideal model delta harmonic sigma weight residual -122.60 -111.56 -11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" CB CYS A 176 " pdb=" SG CYS A 176 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -53.63 -32.37 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 2480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 618 0.077 - 0.154: 51 0.154 - 0.230: 3 0.230 - 0.307: 2 0.307 - 0.384: 1 Chirality restraints: 675 Sorted by residual: chirality pdb=" CA TYR A 151 " pdb=" N TYR A 151 " pdb=" C TYR A 151 " pdb=" CB TYR A 151 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA TRP A 614 " pdb=" N TRP A 614 " pdb=" C TRP A 614 " pdb=" CB TRP A 614 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLN A 608 " pdb=" N GLN A 608 " pdb=" C GLN A 608 " pdb=" CB GLN A 608 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 672 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 521 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C TRP A 521 " 0.063 2.00e-02 2.50e+03 pdb=" O TRP A 521 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS A 522 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 146 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C LEU A 146 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A 146 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 147 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 82 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 83 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.028 5.00e-02 4.00e+02 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 29 2.61 - 3.18: 3538 3.18 - 3.75: 6271 3.75 - 4.33: 8861 4.33 - 4.90: 15191 Nonbonded interactions: 33890 Sorted by model distance: nonbonded pdb=" O TYR A 332 " pdb=" OD1 ASN A 333 " model vdw 2.035 3.040 nonbonded pdb=" O ALA A 328 " pdb=" OG SER A 331 " model vdw 2.269 3.040 nonbonded pdb=" O ARG A 442 " pdb=" OG1 THR A 446 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR A 84 " pdb=" OD2 ASP A 473 " model vdw 2.365 3.040 nonbonded pdb=" O ALA A 489 " pdb=" OG SER A 493 " model vdw 2.380 3.040 ... (remaining 33885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.150 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 4441 Z= 0.316 Angle : 0.787 14.775 6063 Z= 0.494 Chirality : 0.048 0.384 675 Planarity : 0.005 0.051 737 Dihedral : 16.346 68.634 1494 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.44 % Allowed : 21.29 % Favored : 78.27 % 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 are not related in a simple way. whole: 0.06 (0.38), residues: 532 helix: 1.02 (0.30), residues: 337 sheet: None (None), residues: 0 loop : -1.73 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 216 TYR 0.019 0.002 TYR A 151 PHE 0.018 0.001 PHE A 577 TRP 0.013 0.001 TRP A 614 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 4440) covalent geometry : angle 0.78715 ( 6061) SS BOND : bond 0.00945 ( 1) SS BOND : angle 1.40233 ( 2) hydrogen bonds : bond 0.16693 ( 245) hydrogen bonds : angle 5.78909 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 170 ASN cc_start: 0.7720 (m-40) cc_final: 0.7370 (t0) REVERT: A 215 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7616 (mm-30) REVERT: A 541 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7465 (ttmm) REVERT: A 578 LEU cc_start: 0.7624 (mm) cc_final: 0.7411 (mm) REVERT: A 587 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7252 (mtt180) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.4084 time to fit residues: 28.2721 Evaluate side-chains 54 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.139119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.106787 restraints weight = 4693.279| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.76 r_work: 0.2954 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4441 Z= 0.152 Angle : 0.583 10.356 6063 Z= 0.310 Chirality : 0.042 0.141 675 Planarity : 0.005 0.043 737 Dihedral : 6.253 44.589 590 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.88 % Allowed : 19.51 % Favored : 77.61 % 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: 0.38 (0.38), residues: 532 helix: 1.40 (0.30), residues: 332 sheet: None (None), residues: 0 loop : -1.80 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.018 0.002 TYR A 84 PHE 0.016 0.002 PHE A 94 TRP 0.008 0.001 TRP A 517 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4440) covalent geometry : angle 0.58285 ( 6061) SS BOND : bond 0.00174 ( 1) SS BOND : angle 1.14030 ( 2) hydrogen bonds : bond 0.06526 ( 245) hydrogen bonds : angle 4.63589 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 170 ASN cc_start: 0.7962 (m-40) cc_final: 0.7448 (t0) REVERT: A 206 LYS cc_start: 0.7351 (mttp) cc_final: 0.6595 (pptt) REVERT: A 288 SER cc_start: 0.7956 (m) cc_final: 0.7672 (p) REVERT: A 541 LYS cc_start: 0.7850 (ttpt) cc_final: 0.7397 (ttmm) REVERT: A 612 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7213 (mp10) outliers start: 13 outliers final: 6 residues processed: 69 average time/residue: 0.3929 time to fit residues: 28.4598 Evaluate side-chains 56 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 612 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 25 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.3274 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.144116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113336 restraints weight = 4762.144| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.70 r_work: 0.3043 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4441 Z= 0.105 Angle : 0.493 8.576 6063 Z= 0.261 Chirality : 0.039 0.139 675 Planarity : 0.005 0.038 737 Dihedral : 5.755 40.929 590 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.33 % Allowed : 20.40 % Favored : 76.27 % 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 are not related in a simple way. whole: 0.85 (0.38), residues: 532 helix: 1.64 (0.30), residues: 339 sheet: None (None), residues: 0 loop : -1.43 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 341 TYR 0.014 0.001 TYR A 84 PHE 0.009 0.001 PHE A 94 TRP 0.007 0.001 TRP A 553 HIS 0.003 0.000 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 4440) covalent geometry : angle 0.49297 ( 6061) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.79984 ( 2) hydrogen bonds : bond 0.04410 ( 245) hydrogen bonds : angle 4.29179 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: A 152 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7866 (t80) REVERT: A 170 ASN cc_start: 0.7854 (m-40) cc_final: 0.7374 (t0) REVERT: A 206 LYS cc_start: 0.7164 (mttp) cc_final: 0.6554 (pptt) REVERT: A 541 LYS cc_start: 0.7694 (ttpt) cc_final: 0.7252 (ttmm) REVERT: A 593 THR cc_start: 0.7483 (p) cc_final: 0.6829 (t) REVERT: A 612 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6787 (mp10) outliers start: 15 outliers final: 4 residues processed: 58 average time/residue: 0.3881 time to fit residues: 23.7362 Evaluate side-chains 50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 612 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.0470 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.141352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.110287 restraints weight = 4698.927| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.68 r_work: 0.3000 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4441 Z= 0.115 Angle : 0.503 8.790 6063 Z= 0.265 Chirality : 0.039 0.141 675 Planarity : 0.004 0.038 737 Dihedral : 5.686 39.563 590 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.33 % Allowed : 20.62 % Favored : 76.05 % 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: 1.16 (0.38), residues: 532 helix: 1.93 (0.30), residues: 332 sheet: None (None), residues: 0 loop : -1.31 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 341 TYR 0.016 0.001 TYR A 84 PHE 0.013 0.001 PHE A 94 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4440) covalent geometry : angle 0.50290 ( 6061) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.90818 ( 2) hydrogen bonds : bond 0.05047 ( 245) hydrogen bonds : angle 4.29424 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 152 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7894 (t80) REVERT: A 170 ASN cc_start: 0.7874 (m-40) cc_final: 0.7350 (t0) REVERT: A 206 LYS cc_start: 0.7262 (mttp) cc_final: 0.6565 (pptt) REVERT: A 401 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8188 (m) REVERT: A 541 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7283 (ttmm) REVERT: A 593 THR cc_start: 0.7579 (p) cc_final: 0.6942 (t) REVERT: A 612 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7016 (mm110) outliers start: 15 outliers final: 7 residues processed: 53 average time/residue: 0.3502 time to fit residues: 19.6103 Evaluate side-chains 51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 612 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.144126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113157 restraints weight = 4712.874| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.71 r_work: 0.3035 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4441 Z= 0.103 Angle : 0.474 8.263 6063 Z= 0.249 Chirality : 0.038 0.137 675 Planarity : 0.004 0.037 737 Dihedral : 5.477 37.941 590 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.33 % Allowed : 21.29 % Favored : 75.39 % 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: 1.41 (0.38), residues: 532 helix: 2.07 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.10 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 341 TYR 0.014 0.001 TYR A 84 PHE 0.011 0.001 PHE A 94 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 4440) covalent geometry : angle 0.47386 ( 6061) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.81004 ( 2) hydrogen bonds : bond 0.04381 ( 245) hydrogen bonds : angle 4.20537 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: A 152 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7879 (t80) REVERT: A 170 ASN cc_start: 0.7829 (m-40) cc_final: 0.7309 (t0) REVERT: A 206 LYS cc_start: 0.7209 (mttp) cc_final: 0.6607 (pptt) REVERT: A 300 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.5862 (p90) REVERT: A 401 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8099 (m) REVERT: A 541 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7213 (ttmm) REVERT: A 556 TRP cc_start: 0.7962 (m100) cc_final: 0.7169 (m-10) REVERT: A 593 THR cc_start: 0.7538 (p) cc_final: 0.6926 (t) REVERT: A 612 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6854 (mm110) outliers start: 15 outliers final: 6 residues processed: 54 average time/residue: 0.3301 time to fit residues: 18.9234 Evaluate side-chains 51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 612 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.0010 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.139619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.107946 restraints weight = 4817.160| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.75 r_work: 0.2975 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4441 Z= 0.121 Angle : 0.513 8.973 6063 Z= 0.267 Chirality : 0.040 0.141 675 Planarity : 0.004 0.039 737 Dihedral : 5.653 39.029 590 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.77 % Allowed : 21.06 % Favored : 75.17 % 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: 1.44 (0.38), residues: 532 helix: 2.07 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.02 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.017 0.001 TYR A 84 PHE 0.013 0.001 PHE A 94 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4440) covalent geometry : angle 0.51283 ( 6061) SS BOND : bond 0.00243 ( 1) SS BOND : angle 1.01888 ( 2) hydrogen bonds : bond 0.05305 ( 245) hydrogen bonds : angle 4.31252 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: A 152 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7886 (t80) REVERT: A 170 ASN cc_start: 0.7852 (m-40) cc_final: 0.7322 (t0) REVERT: A 206 LYS cc_start: 0.7322 (mttp) cc_final: 0.6627 (pptt) REVERT: A 401 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8165 (m) REVERT: A 541 LYS cc_start: 0.7675 (ttpt) cc_final: 0.7209 (ttmm) REVERT: A 593 THR cc_start: 0.7539 (p) cc_final: 0.6924 (t) REVERT: A 612 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6849 (mm110) outliers start: 17 outliers final: 9 residues processed: 56 average time/residue: 0.3314 time to fit residues: 19.6751 Evaluate side-chains 53 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 612 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 0.0570 chunk 23 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 0.0980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.143136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.112551 restraints weight = 4812.597| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.66 r_work: 0.3011 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4441 Z= 0.107 Angle : 0.490 8.421 6063 Z= 0.255 Chirality : 0.039 0.137 675 Planarity : 0.004 0.038 737 Dihedral : 5.528 38.825 590 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.10 % Allowed : 21.95 % Favored : 74.94 % 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: 1.67 (0.38), residues: 532 helix: 2.23 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -0.89 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.015 0.001 TYR A 84 PHE 0.011 0.001 PHE A 94 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 4440) covalent geometry : angle 0.49015 ( 6061) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.87897 ( 2) hydrogen bonds : bond 0.04657 ( 245) hydrogen bonds : angle 4.25516 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 152 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7966 (t80) REVERT: A 170 ASN cc_start: 0.7881 (m-40) cc_final: 0.7371 (t0) REVERT: A 206 LYS cc_start: 0.7277 (mttp) cc_final: 0.6695 (pptt) REVERT: A 300 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.5899 (p90) REVERT: A 401 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8161 (m) REVERT: A 541 LYS cc_start: 0.7753 (ttpt) cc_final: 0.7323 (ttmm) REVERT: A 556 TRP cc_start: 0.8066 (m100) cc_final: 0.7318 (m-10) REVERT: A 593 THR cc_start: 0.7714 (p) cc_final: 0.7116 (t) outliers start: 14 outliers final: 8 residues processed: 54 average time/residue: 0.4406 time to fit residues: 25.0150 Evaluate side-chains 53 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 535 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.139350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.108470 restraints weight = 4707.380| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.67 r_work: 0.2980 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4441 Z= 0.132 Angle : 0.540 9.243 6063 Z= 0.280 Chirality : 0.041 0.172 675 Planarity : 0.005 0.059 737 Dihedral : 5.708 39.786 590 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.55 % Allowed : 21.95 % Favored : 74.50 % 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: 1.51 (0.38), residues: 532 helix: 2.08 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -0.89 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 341 TYR 0.018 0.001 TYR A 84 PHE 0.014 0.001 PHE A 94 TRP 0.008 0.001 TRP A 253 HIS 0.002 0.000 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4440) covalent geometry : angle 0.53923 ( 6061) SS BOND : bond 0.00256 ( 1) SS BOND : angle 1.11414 ( 2) hydrogen bonds : bond 0.05681 ( 245) hydrogen bonds : angle 4.39126 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 152 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 170 ASN cc_start: 0.7923 (m-40) cc_final: 0.7398 (t0) REVERT: A 206 LYS cc_start: 0.7313 (mttp) cc_final: 0.6720 (pptt) REVERT: A 401 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8194 (m) REVERT: A 541 LYS cc_start: 0.7834 (ttpt) cc_final: 0.7415 (ttmm) REVERT: A 593 THR cc_start: 0.7714 (p) cc_final: 0.7171 (t) REVERT: A 612 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6909 (mm110) outliers start: 16 outliers final: 9 residues processed: 54 average time/residue: 0.3442 time to fit residues: 19.8596 Evaluate side-chains 52 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 612 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.139685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.108088 restraints weight = 4772.156| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.74 r_work: 0.2987 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4441 Z= 0.120 Angle : 0.527 8.860 6063 Z= 0.270 Chirality : 0.041 0.207 675 Planarity : 0.005 0.052 737 Dihedral : 5.625 39.464 590 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.66 % Allowed : 22.84 % Favored : 74.50 % 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 (0.38), residues: 532 helix: 2.12 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -0.84 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 341 TYR 0.016 0.001 TYR A 84 PHE 0.013 0.001 PHE A 94 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4440) covalent geometry : angle 0.52702 ( 6061) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.97561 ( 2) hydrogen bonds : bond 0.05194 ( 245) hydrogen bonds : angle 4.36012 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 152 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 170 ASN cc_start: 0.7849 (m-40) cc_final: 0.7341 (t0) REVERT: A 206 LYS cc_start: 0.7304 (mttp) cc_final: 0.6661 (pptt) REVERT: A 401 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8172 (m) REVERT: A 541 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7336 (ttmm) REVERT: A 593 THR cc_start: 0.7688 (p) cc_final: 0.7129 (t) outliers start: 12 outliers final: 10 residues processed: 52 average time/residue: 0.4068 time to fit residues: 22.3070 Evaluate side-chains 55 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 547 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.137391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.105948 restraints weight = 4798.484| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.70 r_work: 0.2944 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4441 Z= 0.146 Angle : 0.565 9.465 6063 Z= 0.291 Chirality : 0.042 0.199 675 Planarity : 0.005 0.068 737 Dihedral : 5.819 40.348 590 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.10 % Allowed : 22.62 % Favored : 74.28 % 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 are not related in a simple way. whole: 1.41 (0.38), residues: 532 helix: 1.97 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -0.89 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 341 TYR 0.019 0.002 TYR A 84 PHE 0.014 0.001 PHE A 94 TRP 0.009 0.001 TRP A 253 HIS 0.002 0.000 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4440) covalent geometry : angle 0.56470 ( 6061) SS BOND : bond 0.00267 ( 1) SS BOND : angle 1.18715 ( 2) hydrogen bonds : bond 0.06110 ( 245) hydrogen bonds : angle 4.48205 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 152 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 170 ASN cc_start: 0.7878 (m-40) cc_final: 0.7333 (t0) REVERT: A 206 LYS cc_start: 0.7319 (mttp) cc_final: 0.6745 (pptt) REVERT: A 401 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.8217 (m) REVERT: A 541 LYS cc_start: 0.7801 (ttpt) cc_final: 0.7359 (ttmm) REVERT: A 593 THR cc_start: 0.7678 (p) cc_final: 0.7123 (t) REVERT: A 612 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6922 (mp10) outliers start: 14 outliers final: 10 residues processed: 52 average time/residue: 0.4211 time to fit residues: 23.0442 Evaluate side-chains 55 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 612 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 0.0870 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.138876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.106031 restraints weight = 4743.422| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.83 r_work: 0.2959 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4441 Z= 0.124 Angle : 0.532 8.905 6063 Z= 0.275 Chirality : 0.040 0.183 675 Planarity : 0.005 0.054 737 Dihedral : 5.681 39.734 590 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.55 % Allowed : 21.95 % Favored : 74.50 % 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 (0.38), residues: 532 helix: 2.07 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -0.85 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 341 TYR 0.017 0.001 TYR A 84 PHE 0.013 0.001 PHE A 94 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4440) covalent geometry : angle 0.53184 ( 6061) SS BOND : bond 0.00226 ( 1) SS BOND : angle 1.01337 ( 2) hydrogen bonds : bond 0.05353 ( 245) hydrogen bonds : angle 4.39665 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1412.44 seconds wall clock time: 24 minutes 49.08 seconds (1489.08 seconds total)