Starting phenix.real_space_refine on Wed Jul 1 23:21:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uuy_26806/07_2026/7uuy_26806.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uuy_26806/07_2026/7uuy_26806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uuy_26806/07_2026/7uuy_26806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uuy_26806/07_2026/7uuy_26806.map" model { file = "/net/cci-nas-00/data/ceres_data/7uuy_26806/07_2026/7uuy_26806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uuy_26806/07_2026/7uuy_26806.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uuy_26806/07_2026/7uuy_26806.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uuy_26806/07_2026/7uuy_26806.cif" } resolution = 3.3 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= 0.003 sd= 0.062 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 P 1 5.49 5 S 27 5.16 5 C 2512 2.51 5 N 601 2.21 5 O 668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3809 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3767 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 24, 'TRANS': 478} Chain breaks: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 0.96, per 1000 atoms: 0.25 Number of scatterers: 3809 At special positions: 0 Unit cell: (66.216, 85.44, 85.44, 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) S 27 16.00 P 1 15.00 O 668 8.00 N 601 7.00 C 2512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 483 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 144.0 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 79.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 14 through 31 removed outlier: 4.277A pdb=" N GLY A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 69 through 84 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 88 through 101 removed outlier: 4.034A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.624A pdb=" N LEU A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.710A pdb=" N GLU A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 161 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 164 through 180 Processing helix chain 'A' and resid 190 through 213 removed outlier: 4.173A pdb=" N VAL A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.559A pdb=" N LEU A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 268 removed outlier: 4.036A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 307 Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.855A pdb=" N LEU A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 370 removed outlier: 3.643A pdb=" N THR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.145A pdb=" N ARG A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 409 removed outlier: 4.294A pdb=" N LYS A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 423 removed outlier: 3.624A pdb=" N GLY A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 4.118A pdb=" N LEU A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 466 removed outlier: 3.568A pdb=" N THR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.509A pdb=" N GLY A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 543 removed outlier: 4.327A pdb=" N GLY A 527 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.645A pdb=" N LEU A 553 " --> pdb=" O ARG A 550 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 792 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: 0.42 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 615 1.33 - 1.45: 1036 1.45 - 1.57: 2202 1.57 - 1.69: 2 1.69 - 1.82: 42 Bond restraints: 3897 Sorted by residual: bond pdb=" O14 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.527 1.654 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" O11 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.703 1.645 0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.526 1.491 0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" O13 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.522 1.491 0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C1 3PH A 701 " pdb=" O11 3PH A 701 " ideal model delta sigma weight residual 1.385 1.409 -0.024 2.00e-02 2.50e+03 1.47e+00 ... (remaining 3892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 5237 1.85 - 3.69: 59 3.69 - 5.54: 14 5.54 - 7.39: 1 7.39 - 9.23: 2 Bond angle restraints: 5313 Sorted by residual: angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" C VAL A 270 " ideal model delta sigma weight residual 112.29 108.82 3.47 9.40e-01 1.13e+00 1.36e+01 angle pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " pdb=" O14 3PH A 701 " ideal model delta sigma weight residual 113.84 104.61 9.23 3.00e+00 1.11e-01 9.48e+00 angle pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " pdb=" O13 3PH A 701 " ideal model delta sigma weight residual 115.12 123.51 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" CB MET A 23 " pdb=" CG MET A 23 " pdb=" SD MET A 23 " ideal model delta sigma weight residual 112.70 118.57 -5.87 3.00e+00 1.11e-01 3.82e+00 angle pdb=" N GLY A 93 " pdb=" CA GLY A 93 " pdb=" C GLY A 93 " ideal model delta sigma weight residual 112.49 110.13 2.36 1.21e+00 6.83e-01 3.81e+00 ... (remaining 5308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2041 15.79 - 31.58: 156 31.58 - 47.37: 37 47.37 - 63.16: 10 63.16 - 78.96: 5 Dihedral angle restraints: 2249 sinusoidal: 829 harmonic: 1420 Sorted by residual: dihedral pdb=" CA LEU A 558 " pdb=" CB LEU A 558 " pdb=" CG LEU A 558 " pdb=" CD1 LEU A 558 " ideal model delta sinusoidal sigma weight residual 180.00 123.13 56.87 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN A 136 " pdb=" CA GLN A 136 " pdb=" CB GLN A 136 " pdb=" CG GLN A 136 " ideal model delta sinusoidal sigma weight residual -180.00 -123.34 -56.66 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" N ASN A 97 " pdb=" CA ASN A 97 " pdb=" CB ASN A 97 " pdb=" CG ASN A 97 " ideal model delta sinusoidal sigma weight residual 60.00 116.64 -56.64 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 489 0.039 - 0.078: 122 0.078 - 0.117: 24 0.117 - 0.156: 0 0.156 - 0.195: 1 Chirality restraints: 636 Sorted by residual: chirality pdb=" C2 3PH A 701 " pdb=" C1 3PH A 701 " pdb=" C3 3PH A 701 " pdb=" O21 3PH A 701 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" CA PRO A 312 " pdb=" N PRO A 312 " pdb=" C PRO A 312 " pdb=" CB PRO A 312 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA PRO A 337 " pdb=" N PRO A 337 " pdb=" C PRO A 337 " pdb=" CB PRO A 337 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.20e-01 ... (remaining 633 not shown) Planarity restraints: 644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 195 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C VAL A 195 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 195 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 311 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 312 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 247 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C PHE A 247 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE A 247 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 248 " 0.009 2.00e-02 2.50e+03 ... (remaining 641 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 42 2.63 - 3.20: 3759 3.20 - 3.77: 5984 3.77 - 4.33: 8119 4.33 - 4.90: 13789 Nonbonded interactions: 31693 Sorted by model distance: nonbonded pdb=" ND2 ASN A 262 " pdb=" OE1 GLN A 265 " model vdw 2.067 3.120 nonbonded pdb=" O HIS A 273 " pdb=" OG1 THR A 274 " model vdw 2.097 3.040 nonbonded pdb=" ND2 ASN A 441 " pdb=" O GLY A 546 " model vdw 2.211 3.120 nonbonded pdb=" OD1 ASP A 311 " pdb=" OH TYR A 324 " model vdw 2.228 3.040 nonbonded pdb=" O HIS A 226 " pdb=" OG SER A 227 " model vdw 2.332 3.040 ... (remaining 31688 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.010 Find NCS groups from input model: 0.130 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.004 0.127 3898 Z= 0.188 Angle : 0.580 9.235 5315 Z= 0.291 Chirality : 0.035 0.195 636 Planarity : 0.004 0.045 644 Dihedral : 13.239 78.955 1348 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.25 % Allowed : 10.83 % Favored : 88.92 % 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: 0.72 (0.41), residues: 495 helix: 1.24 (0.30), residues: 359 sheet: None (None), residues: 0 loop : -1.54 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 374 TYR 0.023 0.001 TYR A 17 PHE 0.010 0.001 PHE A 304 TRP 0.004 0.001 TRP A 15 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 ( 3897) covalent geometry : angle 0.58049 / 0.29 ( 5313) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.20382 / 0.12 ( 2) hydrogen bonds : bond 0.14916 / 10.12 ( 265) hydrogen bonds : angle 6.88579 / 4.93 ( 792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.6749 (mtm) cc_final: 0.6330 (mtp) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.0525 time to fit residues: 4.0242 Evaluate side-chains 57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109276 restraints weight = 5253.420| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.68 r_work: 0.3155 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3898 Z= 0.154 Angle : 0.580 8.880 5315 Z= 0.291 Chirality : 0.039 0.159 636 Planarity : 0.005 0.046 644 Dihedral : 6.833 59.861 570 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.02 % Allowed : 9.82 % Favored : 88.16 % 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: 1.38 (0.41), residues: 495 helix: 1.67 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.25 (0.62), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.015 0.002 TYR A 17 PHE 0.013 0.002 PHE A 12 TRP 0.006 0.001 TRP A 559 HIS 0.001 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 3897) covalent geometry : angle 0.58023 / 0.29 ( 5313) SS BOND : bond 0.00042 / 0.02 ( 1) SS BOND : angle 0.67381 / 0.38 ( 2) hydrogen bonds : bond 0.03803 / 2.50 ( 265) hydrogen bonds : angle 4.54882 / 3.29 ( 792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.139 Fit side-chains REVERT: A 198 MET cc_start: 0.6757 (mtm) cc_final: 0.6342 (mtm) REVERT: A 516 ASP cc_start: 0.8261 (t0) cc_final: 0.7990 (t0) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.0535 time to fit residues: 4.4640 Evaluate side-chains 55 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 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 = 0.3550 r_free = 0.3550 target = 0.131528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109075 restraints weight = 5228.055| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.61 r_work: 0.3144 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3898 Z= 0.155 Angle : 0.565 6.891 5315 Z= 0.282 Chirality : 0.039 0.171 636 Planarity : 0.004 0.047 644 Dihedral : 6.561 55.746 570 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.02 % Allowed : 12.85 % Favored : 85.14 % 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: 1.57 (0.41), residues: 495 helix: 1.82 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.22 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.014 0.001 TYR A 17 PHE 0.030 0.002 PHE A 12 TRP 0.006 0.001 TRP A 15 HIS 0.001 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 3897) covalent geometry : angle 0.56532 / 0.28 ( 5313) SS BOND : bond 0.00061 / 0.03 ( 1) SS BOND : angle 0.55074 / 0.31 ( 2) hydrogen bonds : bond 0.03512 / 2.33 ( 265) hydrogen bonds : angle 4.37619 / 3.18 ( 792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.138 Fit side-chains REVERT: A 97 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.7711 (t0) REVERT: A 516 ASP cc_start: 0.8271 (t0) cc_final: 0.7941 (t0) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.0559 time to fit residues: 4.1337 Evaluate side-chains 53 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 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 = 0.3544 r_free = 0.3544 target = 0.131015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108037 restraints weight = 5294.316| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.67 r_work: 0.3131 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3898 Z= 0.175 Angle : 0.573 7.986 5315 Z= 0.285 Chirality : 0.040 0.202 636 Planarity : 0.005 0.047 644 Dihedral : 6.497 55.649 570 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.27 % Allowed : 14.11 % Favored : 83.63 % 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: 1.61 (0.40), residues: 495 helix: 1.82 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.12 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.013 0.001 TYR A 17 PHE 0.040 0.002 PHE A 12 TRP 0.006 0.001 TRP A 559 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.17 ( 3897) covalent geometry : angle 0.57330 / 0.29 ( 5313) SS BOND : bond 0.00063 / 0.03 ( 1) SS BOND : angle 0.49954 / 0.28 ( 2) hydrogen bonds : bond 0.03446 / 2.28 ( 265) hydrogen bonds : angle 4.35645 / 3.17 ( 792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.132 Fit side-chains REVERT: A 11 THR cc_start: 0.8378 (m) cc_final: 0.8086 (p) REVERT: A 17 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.6700 (m-80) REVERT: A 97 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.7797 (t0) REVERT: A 198 MET cc_start: 0.7162 (mtm) cc_final: 0.6603 (mtp) REVERT: A 516 ASP cc_start: 0.8300 (t0) cc_final: 0.7937 (t0) outliers start: 9 outliers final: 4 residues processed: 59 average time/residue: 0.0543 time to fit residues: 4.2831 Evaluate side-chains 56 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 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 = 0.3553 r_free = 0.3553 target = 0.131815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108930 restraints weight = 5273.076| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.65 r_work: 0.3147 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3898 Z= 0.157 Angle : 0.565 6.999 5315 Z= 0.280 Chirality : 0.039 0.172 636 Planarity : 0.004 0.047 644 Dihedral : 6.441 57.304 570 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.76 % Allowed : 16.37 % Favored : 81.86 % 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: 1.70 (0.41), residues: 495 helix: 1.91 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.16 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.012 0.001 TYR A 17 PHE 0.025 0.002 PHE A 12 TRP 0.007 0.001 TRP A 559 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 3897) covalent geometry : angle 0.56458 / 0.28 ( 5313) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 0.43877 / 0.25 ( 2) hydrogen bonds : bond 0.03336 / 2.21 ( 265) hydrogen bonds : angle 4.30655 / 3.14 ( 792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.146 Fit side-chains REVERT: A 11 THR cc_start: 0.8282 (m) cc_final: 0.7945 (p) REVERT: A 17 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6635 (m-80) REVERT: A 23 MET cc_start: 0.7871 (tpp) cc_final: 0.7567 (tpp) REVERT: A 516 ASP cc_start: 0.8292 (t0) cc_final: 0.7895 (t0) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 0.0475 time to fit residues: 3.4967 Evaluate side-chains 58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 9 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 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 = 0.3564 r_free = 0.3564 target = 0.132599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109460 restraints weight = 5349.730| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.68 r_work: 0.3153 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3898 Z= 0.143 Angle : 0.542 6.547 5315 Z= 0.270 Chirality : 0.039 0.172 636 Planarity : 0.004 0.045 644 Dihedral : 6.373 59.580 570 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.02 % Allowed : 17.13 % Favored : 80.86 % 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: 1.75 (0.41), residues: 495 helix: 1.97 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.23 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.012 0.001 TYR A 17 PHE 0.022 0.002 PHE A 12 TRP 0.006 0.001 TRP A 15 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 3897) covalent geometry : angle 0.54238 / 0.27 ( 5313) SS BOND : bond 0.00052 / 0.03 ( 1) SS BOND : angle 0.39446 / 0.22 ( 2) hydrogen bonds : bond 0.03228 / 2.14 ( 265) hydrogen bonds : angle 4.22622 / 3.08 ( 792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.136 Fit side-chains REVERT: A 17 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: A 23 MET cc_start: 0.7852 (tpp) cc_final: 0.7637 (tpt) REVERT: A 67 PHE cc_start: 0.8218 (t80) cc_final: 0.7958 (t80) REVERT: A 516 ASP cc_start: 0.8402 (t0) cc_final: 0.7996 (t0) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 0.0569 time to fit residues: 4.3163 Evaluate side-chains 55 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109456 restraints weight = 5357.086| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.70 r_work: 0.3149 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 3898 Z= 0.152 Angle : 0.564 6.925 5315 Z= 0.277 Chirality : 0.039 0.161 636 Planarity : 0.004 0.045 644 Dihedral : 6.295 57.047 570 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.76 % Allowed : 17.38 % Favored : 80.86 % 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: 1.68 (0.40), residues: 495 helix: 2.04 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.46 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.014 0.001 TYR A 17 PHE 0.037 0.002 PHE A 12 TRP 0.009 0.001 TRP A 255 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 ( 3897) covalent geometry : angle 0.56434 / 0.28 ( 5313) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.37174 / 0.21 ( 2) hydrogen bonds : bond 0.03248 / 2.16 ( 265) hydrogen bonds : angle 4.25739 / 3.10 ( 792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.082 Fit side-chains REVERT: A 11 THR cc_start: 0.8431 (m) cc_final: 0.8148 (p) REVERT: A 17 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.6677 (m-80) REVERT: A 23 MET cc_start: 0.7846 (tpp) cc_final: 0.7628 (tpt) REVERT: A 516 ASP cc_start: 0.8416 (t0) cc_final: 0.7995 (t0) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.0527 time to fit residues: 3.6151 Evaluate side-chains 56 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 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 = 0.3586 r_free = 0.3586 target = 0.134463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111568 restraints weight = 5279.466| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.68 r_work: 0.3187 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3898 Z= 0.119 Angle : 0.533 6.123 5315 Z= 0.265 Chirality : 0.038 0.155 636 Planarity : 0.004 0.043 644 Dihedral : 6.169 54.837 570 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.02 % Allowed : 17.38 % Favored : 80.60 % 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: 1.92 (0.40), residues: 495 helix: 2.19 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.34 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.014 0.001 TYR A 17 PHE 0.027 0.002 PHE A 12 TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 3897) covalent geometry : angle 0.53297 / 0.27 ( 5313) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 0.29146 / 0.17 ( 2) hydrogen bonds : bond 0.03005 / 1.98 ( 265) hydrogen bonds : angle 4.10988 / 2.98 ( 792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.131 Fit side-chains REVERT: A 17 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: A 23 MET cc_start: 0.7781 (tpp) cc_final: 0.7563 (tpt) REVERT: A 423 ILE cc_start: 0.8894 (mm) cc_final: 0.8609 (mt) REVERT: A 516 ASP cc_start: 0.8376 (t0) cc_final: 0.7938 (t0) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.0610 time to fit residues: 4.6861 Evaluate side-chains 58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 0.0030 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 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 = 0.3592 r_free = 0.3592 target = 0.134969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112302 restraints weight = 5332.115| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.67 r_work: 0.3192 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3898 Z= 0.114 Angle : 0.580 15.470 5315 Z= 0.273 Chirality : 0.038 0.154 636 Planarity : 0.004 0.042 644 Dihedral : 5.953 51.988 570 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.02 % Allowed : 18.89 % Favored : 79.09 % 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: 1.92 (0.40), residues: 495 helix: 2.14 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.31 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 374 TYR 0.021 0.001 TYR A 242 PHE 0.024 0.002 PHE A 12 TRP 0.008 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 3897) covalent geometry : angle 0.58040 / 0.27 ( 5313) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 0.33171 / 0.19 ( 2) hydrogen bonds : bond 0.02911 / 1.91 ( 265) hydrogen bonds : angle 4.09158 / 2.97 ( 792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.140 Fit side-chains REVERT: A 17 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: A 23 MET cc_start: 0.7744 (tpp) cc_final: 0.7461 (tpt) REVERT: A 178 TYR cc_start: 0.7960 (m-80) cc_final: 0.7501 (m-10) REVERT: A 423 ILE cc_start: 0.8897 (mm) cc_final: 0.8613 (mt) REVERT: A 516 ASP cc_start: 0.8339 (t0) cc_final: 0.7934 (t0) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.0485 time to fit residues: 3.8571 Evaluate side-chains 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 0.0270 chunk 4 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 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 = 0.3598 r_free = 0.3598 target = 0.135151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112444 restraints weight = 5286.188| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.66 r_work: 0.3198 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3898 Z= 0.121 Angle : 0.587 15.153 5315 Z= 0.280 Chirality : 0.038 0.153 636 Planarity : 0.004 0.043 644 Dihedral : 5.863 47.505 570 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.26 % Allowed : 19.90 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.41), residues: 495 helix: 2.19 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.29 (0.62), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.013 0.001 TYR A 17 PHE 0.024 0.002 PHE A 12 TRP 0.007 0.001 TRP A 255 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 3897) covalent geometry : angle 0.58706 / 0.28 ( 5313) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 0.33164 / 0.19 ( 2) hydrogen bonds : bond 0.02898 / 1.90 ( 265) hydrogen bonds : angle 4.06302 / 2.95 ( 792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.128 Fit side-chains REVERT: A 17 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: A 23 MET cc_start: 0.7780 (tpp) cc_final: 0.7500 (tpt) REVERT: A 178 TYR cc_start: 0.7961 (m-80) cc_final: 0.7496 (m-10) REVERT: A 423 ILE cc_start: 0.8903 (mm) cc_final: 0.8619 (mt) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.0564 time to fit residues: 4.2350 Evaluate side-chains 57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 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 = 0.3572 r_free = 0.3572 target = 0.133073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110182 restraints weight = 5277.271| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.67 r_work: 0.3171 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3898 Z= 0.156 Angle : 0.604 15.103 5315 Z= 0.288 Chirality : 0.039 0.152 636 Planarity : 0.005 0.044 644 Dihedral : 5.810 45.937 570 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.76 % Allowed : 19.90 % Favored : 78.34 % 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: 1.87 (0.41), residues: 495 helix: 2.11 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.36 (0.62), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.012 0.001 TYR A 17 PHE 0.026 0.002 PHE A 12 TRP 0.005 0.001 TRP A 559 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 3897) covalent geometry : angle 0.60427 / 0.29 ( 5313) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 0.35320 / 0.20 ( 2) hydrogen bonds : bond 0.03112 / 2.04 ( 265) hydrogen bonds : angle 4.14481 / 3.01 ( 792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1135.92 seconds wall clock time: 20 minutes 10.61 seconds (1210.61 seconds total)