Starting phenix.real_space_refine on Wed Sep 17 04:12:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ly6_4118/09_2025/5ly6_4118.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ly6_4118/09_2025/5ly6_4118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ly6_4118/09_2025/5ly6_4118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ly6_4118/09_2025/5ly6_4118.map" model { file = "/net/cci-nas-00/data/ceres_data/5ly6_4118/09_2025/5ly6_4118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ly6_4118/09_2025/5ly6_4118.cif" } resolution = 4.5 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 139 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 2350 2.51 5 N 633 2.21 5 O 735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3725 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3725 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 452} Time building chain proxies: 1.31, per 1000 atoms: 0.35 Number of scatterers: 3725 At special positions: 0 Unit cell: (85.4, 78.4, 127.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 735 8.00 N 633 7.00 C 2350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 110.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 892 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 12.5% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 122 through 137 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.880A pdb=" N ARG B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 227' Processing helix chain 'B' and resid 297 through 304 removed outlier: 4.669A pdb=" N ARG B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing sheet with id=A, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.614A pdb=" N ARG B 31 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 44 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 43 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 357 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 45 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 355 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B 353 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=C, first strand: chain 'B' and resid 147 through 149 removed outlier: 3.577A pdb=" N GLU B 258 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN B 191 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 250 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 197 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 152 through 165 Processing sheet with id=E, first strand: chain 'B' and resid 235 through 237 removed outlier: 4.147A pdb=" N TYR B 331 " --> pdb=" O GLN B 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 345 " --> pdb=" O TYR B 331 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 261 through 264 Processing sheet with id=G, first strand: chain 'B' and resid 408 through 413 removed outlier: 4.183A pdb=" N ARG B 451 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 364 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 368 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 457 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.910A pdb=" N VAL B 372 " --> pdb=" O CYS B 428 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'B' and resid 382 through 384 Processing sheet with id=J, first strand: chain 'B' and resid 440 through 442 removed outlier: 4.087A pdb=" N TYR B 440 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 425 " --> pdb=" O TYR B 440 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS B 442 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 423 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 419 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 380 " --> pdb=" O ARG B 419 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU B 421 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR B 378 " --> pdb=" O LEU B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=J 101 hydrogen bonds defined for protein. 282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.67 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1239 1.34 - 1.46: 424 1.46 - 1.57: 2121 1.57 - 1.69: 1 1.69 - 1.81: 13 Bond restraints: 3798 Sorted by residual: bond pdb=" C THR B 57 " pdb=" N SER B 58 " ideal model delta sigma weight residual 1.332 1.597 -0.265 1.29e-02 6.01e+03 4.22e+02 bond pdb=" N PRO B 413 " pdb=" CD PRO B 413 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.82e+01 bond pdb=" C ILE B 412 " pdb=" N PRO B 413 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.86e+00 bond pdb=" CA ALA B 64 " pdb=" CB ALA B 64 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.55e-02 4.16e+03 3.44e+00 bond pdb=" C HIS B 324 " pdb=" O HIS B 324 " ideal model delta sigma weight residual 1.246 1.231 0.015 9.20e-03 1.18e+04 2.58e+00 ... (remaining 3793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 5147 5.44 - 10.88: 9 10.88 - 16.33: 4 16.33 - 21.77: 0 21.77 - 27.21: 4 Bond angle restraints: 5164 Sorted by residual: angle pdb=" O THR B 57 " pdb=" C THR B 57 " pdb=" N SER B 58 " ideal model delta sigma weight residual 123.24 111.38 11.86 1.23e+00 6.61e-01 9.30e+01 angle pdb=" CA THR B 57 " pdb=" C THR B 57 " pdb=" N SER B 58 " ideal model delta sigma weight residual 115.58 126.98 -11.40 1.48e+00 4.57e-01 5.93e+01 angle pdb=" C LEU B 39 " pdb=" N PRO B 40 " pdb=" CD PRO B 40 " ideal model delta sigma weight residual 125.00 97.79 27.21 4.10e+00 5.95e-02 4.40e+01 angle pdb=" C ASP B 117 " pdb=" N PRO B 118 " pdb=" CD PRO B 118 " ideal model delta sigma weight residual 125.00 99.67 25.33 4.10e+00 5.95e-02 3.82e+01 angle pdb=" C ALA B 273 " pdb=" N PRO B 274 " pdb=" CD PRO B 274 " ideal model delta sigma weight residual 125.00 102.20 22.80 4.10e+00 5.95e-02 3.09e+01 ... (remaining 5159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 1777 17.28 - 34.56: 264 34.56 - 51.85: 163 51.85 - 69.13: 64 69.13 - 86.41: 18 Dihedral angle restraints: 2286 sinusoidal: 905 harmonic: 1381 Sorted by residual: dihedral pdb=" CA ASN B 30 " pdb=" CB ASN B 30 " pdb=" CG ASN B 30 " pdb=" OD1 ASN B 30 " ideal model delta sinusoidal sigma weight residual -90.00 -161.80 71.80 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN B 284 " pdb=" CB ASN B 284 " pdb=" CG ASN B 284 " pdb=" OD1 ASN B 284 " ideal model delta sinusoidal sigma weight residual -90.00 -159.76 69.76 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CG ARG B 147 " pdb=" CD ARG B 147 " pdb=" NE ARG B 147 " pdb=" CZ ARG B 147 " ideal model delta sinusoidal sigma weight residual 180.00 135.95 44.05 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 2283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 498 0.033 - 0.067: 17 0.067 - 0.100: 65 0.100 - 0.133: 4 0.133 - 0.167: 6 Chirality restraints: 590 Sorted by residual: chirality pdb=" CB THR B 63 " pdb=" CA THR B 63 " pdb=" OG1 THR B 63 " pdb=" CG2 THR B 63 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CB THR B 65 " pdb=" CA THR B 65 " pdb=" OG1 THR B 65 " pdb=" CG2 THR B 65 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA ALA B 12 " pdb=" N ALA B 12 " pdb=" C ALA B 12 " pdb=" CB ALA B 12 " both_signs ideal model delta sigma weight residual False 2.48 2.34 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 587 not shown) Planarity restraints: 668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 39 " -0.120 5.00e-02 4.00e+02 1.91e-01 5.81e+01 pdb=" N PRO B 40 " 0.329 5.00e-02 4.00e+02 pdb=" CA PRO B 40 " -0.121 5.00e-02 4.00e+02 pdb=" CD PRO B 40 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 117 " -0.116 5.00e-02 4.00e+02 1.84e-01 5.42e+01 pdb=" N PRO B 118 " 0.318 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " -0.116 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 273 " 0.111 5.00e-02 4.00e+02 1.76e-01 4.93e+01 pdb=" N PRO B 274 " -0.303 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " 0.108 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " 0.084 5.00e-02 4.00e+02 ... (remaining 665 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 20 2.20 - 2.88: 1637 2.88 - 3.55: 4768 3.55 - 4.23: 7738 4.23 - 4.90: 12540 Nonbonded interactions: 26703 Sorted by model distance: nonbonded pdb=" CG1 VAL B 78 " pdb=" CD PRO B 233 " model vdw 1.526 3.860 nonbonded pdb=" OD1 ASP B 295 " pdb=" ND1 HIS B 324 " model vdw 1.808 3.120 nonbonded pdb=" CG2 VAL B 302 " pdb=" CD1 LEU B 313 " model vdw 1.854 3.880 nonbonded pdb=" N LEU B 76 " pdb=" O VAL B 235 " model vdw 1.876 3.120 nonbonded pdb=" CG1 VAL B 78 " pdb=" CG PRO B 233 " model vdw 1.894 3.860 ... (remaining 26698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.180 Find NCS groups from input model: 0.030 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 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 0.265 3798 Z= 0.420 Angle : 1.237 27.209 5164 Z= 0.692 Chirality : 0.034 0.167 590 Planarity : 0.018 0.191 668 Dihedral : 24.278 86.412 1394 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 94.62 Ramachandran Plot: Outliers : 4.90 % Allowed : 20.90 % Favored : 74.20 % Rotamer: Outliers : 36.32 % Allowed : 24.94 % Favored : 38.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.32 (0.32), residues: 469 helix: -1.20 (0.61), residues: 63 sheet: -2.85 (0.35), residues: 189 loop : -4.99 (0.27), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.003 0.000 TYR B 15 PHE 0.001 0.000 PHE B 9 TRP 0.001 0.000 TRP B 436 HIS 0.000 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 3798) covalent geometry : angle 1.23702 ( 5164) hydrogen bonds : bond 0.34678 ( 101) hydrogen bonds : angle 13.77649 ( 282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 64 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8381 (t) REVERT: B 106 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8528 (pt) REVERT: B 151 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.5921 (tp30) REVERT: B 194 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7205 (t0) REVERT: B 236 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8149 (p90) REVERT: B 288 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.5887 (mmtt) REVERT: B 349 ASP cc_start: 0.7404 (p0) cc_final: 0.7117 (p0) REVERT: B 448 VAL cc_start: 0.4786 (OUTLIER) cc_final: 0.4351 (p) outliers start: 150 outliers final: 32 residues processed: 192 average time/residue: 0.0943 time to fit residues: 21.0289 Evaluate side-chains 85 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 46 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 135 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.053166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.045731 restraints weight = 35049.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.046778 restraints weight = 22969.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.047527 restraints weight = 16459.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.048056 restraints weight = 12611.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.048448 restraints weight = 10212.976| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.6762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 3798 Z= 0.194 Angle : 0.815 8.947 5164 Z= 0.426 Chirality : 0.049 0.229 590 Planarity : 0.009 0.107 668 Dihedral : 5.109 26.350 509 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.85 % Allowed : 11.30 % Favored : 87.85 % Rotamer: Outliers : 0.48 % Allowed : 4.36 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.36), residues: 469 helix: -0.22 (0.71), residues: 61 sheet: -2.03 (0.36), residues: 193 loop : -4.09 (0.34), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 337 TYR 0.024 0.002 TYR B 199 PHE 0.023 0.002 PHE B 335 TRP 0.017 0.002 TRP B 456 HIS 0.007 0.002 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 3798) covalent geometry : angle 0.81521 ( 5164) hydrogen bonds : bond 0.04379 ( 101) hydrogen bonds : angle 7.86408 ( 282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.9033 (tp) cc_final: 0.8498 (pt) outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 0.0808 time to fit residues: 4.2970 Evaluate side-chains 22 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 43 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.049749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.042352 restraints weight = 37136.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.043416 restraints weight = 23333.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.044149 restraints weight = 16422.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.044679 restraints weight = 12468.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045068 restraints weight = 10084.647| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.8528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 3798 Z= 0.218 Angle : 0.774 9.435 5164 Z= 0.402 Chirality : 0.046 0.222 590 Planarity : 0.007 0.090 668 Dihedral : 5.312 31.860 509 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.02 % Favored : 89.34 % Rotamer: Outliers : 0.24 % Allowed : 4.84 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.69 (0.36), residues: 469 helix: -0.60 (0.61), residues: 73 sheet: -1.71 (0.36), residues: 216 loop : -4.15 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 69 TYR 0.012 0.002 TYR B 150 PHE 0.010 0.002 PHE B 180 TRP 0.020 0.002 TRP B 278 HIS 0.006 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 3798) covalent geometry : angle 0.77355 ( 5164) hydrogen bonds : bond 0.04930 ( 101) hydrogen bonds : angle 6.06714 ( 282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.9242 (tpp) cc_final: 0.8864 (tpp) REVERT: B 336 LEU cc_start: 0.9328 (tp) cc_final: 0.8736 (pt) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.0855 time to fit residues: 3.3207 Evaluate side-chains 19 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 9 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 44 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.048163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.041161 restraints weight = 38367.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.042145 restraints weight = 24041.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.042854 restraints weight = 16966.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.043316 restraints weight = 12903.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.043668 restraints weight = 10510.835| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.9403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 3798 Z= 0.212 Angle : 0.734 15.028 5164 Z= 0.371 Chirality : 0.045 0.277 590 Planarity : 0.006 0.080 668 Dihedral : 5.114 27.904 509 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.81 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.36), residues: 469 helix: -0.92 (0.60), residues: 72 sheet: -1.64 (0.35), residues: 218 loop : -3.50 (0.36), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 337 TYR 0.017 0.002 TYR B 15 PHE 0.011 0.002 PHE B 43 TRP 0.014 0.002 TRP B 134 HIS 0.004 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 3798) covalent geometry : angle 0.73395 ( 5164) hydrogen bonds : bond 0.04473 ( 101) hydrogen bonds : angle 5.73542 ( 282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.9320 (tp) cc_final: 0.8974 (tt) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0718 time to fit residues: 2.2594 Evaluate side-chains 19 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 30.0000 chunk 13 optimal weight: 0.0970 chunk 41 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.048602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.041605 restraints weight = 39073.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.042605 restraints weight = 24605.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.043270 restraints weight = 17321.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.043708 restraints weight = 13317.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.044077 restraints weight = 10970.129| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.9831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3798 Z= 0.158 Angle : 0.673 10.969 5164 Z= 0.339 Chirality : 0.044 0.186 590 Planarity : 0.005 0.074 668 Dihedral : 4.964 25.690 509 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.17 % Favored : 90.41 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.36), residues: 469 helix: -0.69 (0.63), residues: 71 sheet: -1.34 (0.35), residues: 210 loop : -3.25 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.020 0.002 TYR B 371 PHE 0.008 0.001 PHE B 43 TRP 0.021 0.002 TRP B 134 HIS 0.003 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3798) covalent geometry : angle 0.67311 ( 5164) hydrogen bonds : bond 0.03740 ( 101) hydrogen bonds : angle 5.46179 ( 282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0916 time to fit residues: 2.5754 Evaluate side-chains 16 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.048285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.041396 restraints weight = 39761.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.042372 restraints weight = 24875.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.043048 restraints weight = 17556.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.043528 restraints weight = 13445.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.043829 restraints weight = 10920.196| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 1.0233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3798 Z= 0.167 Angle : 0.663 9.990 5164 Z= 0.333 Chirality : 0.042 0.146 590 Planarity : 0.005 0.068 668 Dihedral : 5.061 22.822 509 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.96 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.85 (0.36), residues: 469 helix: -0.83 (0.61), residues: 71 sheet: -1.18 (0.36), residues: 198 loop : -3.02 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 319 TYR 0.017 0.002 TYR B 331 PHE 0.012 0.001 PHE B 43 TRP 0.015 0.002 TRP B 134 HIS 0.007 0.002 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3798) covalent geometry : angle 0.66290 ( 5164) hydrogen bonds : bond 0.03870 ( 101) hydrogen bonds : angle 5.31187 ( 282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9389 (tptt) cc_final: 0.9159 (tptp) REVERT: B 23 HIS cc_start: 0.7205 (m-70) cc_final: 0.6880 (m90) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0829 time to fit residues: 2.2688 Evaluate side-chains 15 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.040808 restraints weight = 39015.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.041804 restraints weight = 24045.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.042486 restraints weight = 16811.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.042963 restraints weight = 12806.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.043276 restraints weight = 10407.680| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 1.0487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3798 Z= 0.153 Angle : 0.637 8.505 5164 Z= 0.320 Chirality : 0.042 0.145 590 Planarity : 0.005 0.062 668 Dihedral : 5.031 18.904 509 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.32 % Favored : 91.26 % Rotamer: Outliers : 0.24 % Allowed : 1.45 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.37), residues: 469 helix: -0.74 (0.61), residues: 71 sheet: -1.17 (0.35), residues: 208 loop : -3.05 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.016 0.002 TYR B 150 PHE 0.009 0.001 PHE B 43 TRP 0.012 0.001 TRP B 134 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3798) covalent geometry : angle 0.63657 ( 5164) hydrogen bonds : bond 0.03618 ( 101) hydrogen bonds : angle 5.22917 ( 282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9407 (tptt) cc_final: 0.9173 (tptp) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.0691 time to fit residues: 2.1577 Evaluate side-chains 15 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.046375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.039343 restraints weight = 39593.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.040274 restraints weight = 25307.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.040922 restraints weight = 18088.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.041353 restraints weight = 14041.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.041689 restraints weight = 11626.254| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 1.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3798 Z= 0.202 Angle : 0.682 7.367 5164 Z= 0.347 Chirality : 0.042 0.146 590 Planarity : 0.005 0.058 668 Dihedral : 5.304 18.768 509 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.45 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.36), residues: 469 helix: -1.05 (0.59), residues: 71 sheet: -1.24 (0.35), residues: 208 loop : -2.99 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 244 TYR 0.017 0.002 TYR B 15 PHE 0.015 0.002 PHE B 43 TRP 0.015 0.002 TRP B 134 HIS 0.007 0.002 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 3798) covalent geometry : angle 0.68236 ( 5164) hydrogen bonds : bond 0.04136 ( 101) hydrogen bonds : angle 5.41693 ( 282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9432 (tptt) cc_final: 0.9216 (tptp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0804 time to fit residues: 1.9800 Evaluate side-chains 14 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.045097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.038030 restraints weight = 40055.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.038911 restraints weight = 25829.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.039556 restraints weight = 18736.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.040008 restraints weight = 14578.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.040343 restraints weight = 12004.144| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 1.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 3798 Z= 0.265 Angle : 0.774 8.083 5164 Z= 0.398 Chirality : 0.044 0.189 590 Planarity : 0.005 0.055 668 Dihedral : 5.973 19.326 509 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.30 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.35), residues: 469 helix: -1.51 (0.59), residues: 65 sheet: -1.38 (0.33), residues: 213 loop : -3.02 (0.38), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 69 TYR 0.018 0.002 TYR B 15 PHE 0.019 0.003 PHE B 43 TRP 0.013 0.002 TRP B 134 HIS 0.007 0.002 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 3798) covalent geometry : angle 0.77352 ( 5164) hydrogen bonds : bond 0.05022 ( 101) hydrogen bonds : angle 6.00302 ( 282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: B 313 LEU cc_start: 0.9312 (mt) cc_final: 0.9101 (mm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0673 time to fit residues: 1.8798 Evaluate side-chains 14 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 28 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 0.0470 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.047495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.040506 restraints weight = 39106.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.041444 restraints weight = 24856.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.042108 restraints weight = 17703.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.042575 restraints weight = 13713.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.042902 restraints weight = 11234.943| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 1.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3798 Z= 0.115 Angle : 0.635 8.192 5164 Z= 0.320 Chirality : 0.044 0.181 590 Planarity : 0.004 0.053 668 Dihedral : 5.472 29.727 509 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.96 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.37), residues: 469 helix: -0.52 (0.67), residues: 59 sheet: -1.16 (0.34), residues: 224 loop : -2.79 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 337 TYR 0.014 0.001 TYR B 15 PHE 0.011 0.001 PHE B 43 TRP 0.016 0.001 TRP B 134 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3798) covalent geometry : angle 0.63494 ( 5164) hydrogen bonds : bond 0.03423 ( 101) hydrogen bonds : angle 5.27545 ( 282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: B 148 MET cc_start: 0.5119 (pmm) cc_final: 0.4856 (pmm) REVERT: B 313 LEU cc_start: 0.9409 (mt) cc_final: 0.9174 (mm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0669 time to fit residues: 1.9691 Evaluate side-chains 16 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 43 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.046949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.040048 restraints weight = 38315.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.040954 restraints weight = 24645.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.041584 restraints weight = 17710.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.042045 restraints weight = 13806.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.042380 restraints weight = 11367.741| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 1.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3798 Z= 0.160 Angle : 0.631 6.458 5164 Z= 0.322 Chirality : 0.044 0.172 590 Planarity : 0.005 0.067 668 Dihedral : 5.495 26.336 509 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.66 % Favored : 88.91 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.37), residues: 469 helix: -0.92 (0.63), residues: 65 sheet: -1.27 (0.34), residues: 225 loop : -2.86 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 337 TYR 0.012 0.001 TYR B 150 PHE 0.013 0.001 PHE B 43 TRP 0.012 0.001 TRP B 134 HIS 0.004 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3798) covalent geometry : angle 0.63077 ( 5164) hydrogen bonds : bond 0.03674 ( 101) hydrogen bonds : angle 5.29329 ( 282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 837.78 seconds wall clock time: 15 minutes 12.44 seconds (912.44 seconds total)