Starting phenix.real_space_refine on Tue Mar 3 12:39:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7w_33672/03_2026/7y7w_33672.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7w_33672/03_2026/7y7w_33672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7w_33672/03_2026/7y7w_33672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7w_33672/03_2026/7y7w_33672.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7w_33672/03_2026/7y7w_33672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7w_33672/03_2026/7y7w_33672.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2844 2.51 5 N 655 2.21 5 O 774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4310 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 22, 'TRANS': 506} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 100 Unusual residues: {' CL': 1, ' NA': 2, 'ABU': 1, 'NAG': 3} Classifications: {'undetermined': 7, 'water': 48} Link IDs: {None: 54} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.17, per 1000 atoms: 0.27 Number of scatterers: 4310 At special positions: 0 Unit cell: (67.115, 72.5275, 95.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 774 8.00 N 655 7.00 C 2844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.08 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 Links applied NAG-ASN " NAG A 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 300.2 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 966 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 82.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.734A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.743A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 154 removed outlier: 3.990A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 4.051A pdb=" N GLN A 163 " --> pdb=" O PRO A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 239 through 259 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.579A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.941A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 Processing helix chain 'A' and resid 315 through 350 removed outlier: 3.709A pdb=" N ASP A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 362 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.766A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 436 through 440 removed outlier: 4.174A pdb=" N THR A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 454 removed outlier: 4.096A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 474 removed outlier: 3.683A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 502 removed outlier: 4.487A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 530 through 546 removed outlier: 3.637A pdb=" N GLN A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.550A pdb=" N MET A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 569 removed outlier: 4.460A pdb=" N VAL A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 283 hydrogen bonds defined for protein. 822 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: 0.54 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: 1.16 - 1.29: 620 1.29 - 1.42: 1312 1.42 - 1.55: 2407 1.55 - 1.68: 0 1.68 - 1.81: 54 Bond restraints: 4393 Sorted by residual: bond pdb=" C ASP A 395 " pdb=" O ASP A 395 " ideal model delta sigma weight residual 1.237 1.165 0.072 1.19e-02 7.06e+03 3.64e+01 bond pdb=" C PHE A 53 " pdb=" O PHE A 53 " ideal model delta sigma weight residual 1.237 1.183 0.053 1.19e-02 7.06e+03 2.01e+01 bond pdb=" C SER A 396 " pdb=" O SER A 396 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.17e-02 7.31e+03 1.85e+01 bond pdb=" C ILE A 394 " pdb=" O ILE A 394 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" CG ASP A 395 " pdb=" OD1 ASP A 395 " ideal model delta sigma weight residual 1.249 1.193 0.056 1.90e-02 2.77e+03 8.75e+00 ... (remaining 4388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 5835 2.22 - 4.45: 128 4.45 - 6.67: 14 6.67 - 8.89: 4 8.89 - 11.12: 1 Bond angle restraints: 5982 Sorted by residual: angle pdb=" CA ASP A 395 " pdb=" CB ASP A 395 " pdb=" CG ASP A 395 " ideal model delta sigma weight residual 112.60 119.69 -7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.42 -11.12 2.00e+00 2.50e-01 3.09e+01 angle pdb=" N PHE A 53 " pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 111.36 105.81 5.55 1.09e+00 8.42e-01 2.59e+01 angle pdb=" CA ILE A 394 " pdb=" C ILE A 394 " pdb=" O ILE A 394 " ideal model delta sigma weight residual 120.85 115.79 5.06 1.06e+00 8.90e-01 2.28e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.58 -8.08 1.70e+00 3.46e-01 2.26e+01 ... (remaining 5977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2177 17.95 - 35.90: 257 35.90 - 53.86: 63 53.86 - 71.81: 15 71.81 - 89.76: 6 Dihedral angle restraints: 2518 sinusoidal: 995 harmonic: 1523 Sorted by residual: dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -49.63 -36.37 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta harmonic sigma weight residual 180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 663 0.277 - 0.554: 1 0.554 - 0.831: 0 0.831 - 1.108: 0 1.108 - 1.385: 2 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.80e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.21 -1.19 2.00e-01 2.50e+01 3.54e+01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 663 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.101 2.00e-02 2.50e+03 1.71e-01 3.66e+02 pdb=" CG ASN A 181 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.307 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.134 2.00e-02 2.50e+03 1.38e-01 2.40e+02 pdb=" CG ASN A 184 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " -0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.203 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.064 2.00e-02 2.50e+03 6.39e-02 5.11e+01 pdb=" CG ASN A 176 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.098 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.077 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 40 2.51 - 3.10: 3259 3.10 - 3.70: 7029 3.70 - 4.30: 10384 4.30 - 4.90: 16710 Nonbonded interactions: 37422 Sorted by model distance: nonbonded pdb=" O HOH A 805 " pdb=" O HOH A 828 " model vdw 1.907 3.040 nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 806 " model vdw 2.000 3.040 nonbonded pdb=" OE1 GLU A 101 " pdb=" O HOH A 801 " model vdw 2.008 3.040 nonbonded pdb=" O LEU A 298 " pdb=" O HOH A 802 " model vdw 2.030 3.040 nonbonded pdb=" OG1 THR A 290 " pdb=" O HOH A 803 " model vdw 2.045 3.040 ... (remaining 37417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 0.152 4397 Z= 0.332 Angle : 0.906 25.457 5993 Z= 0.500 Chirality : 0.084 1.385 666 Planarity : 0.005 0.042 725 Dihedral : 17.204 89.759 1549 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.11 % Allowed : 26.73 % Favored : 72.16 % 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: 0.06 (0.36), residues: 527 helix: 0.63 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -1.32 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 277 TYR 0.020 0.002 TYR A 72 PHE 0.026 0.003 PHE A 398 TRP 0.017 0.002 TRP A 500 HIS 0.007 0.002 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 4393) covalent geometry : angle 0.77718 ( 5982) SS BOND : bond 0.04738 ( 1) SS BOND : angle 5.56522 ( 2) hydrogen bonds : bond 0.13634 ( 283) hydrogen bonds : angle 6.49136 ( 822) link_NAG-ASN : bond 0.10743 ( 3) link_NAG-ASN : angle 11.75899 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.171 Fit side-chains REVERT: A 51 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6421 (p90) REVERT: A 121 MET cc_start: 0.8983 (ptm) cc_final: 0.8730 (ptp) REVERT: A 163 GLN cc_start: 0.8134 (mt0) cc_final: 0.7193 (pm20) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 0.5684 time to fit residues: 38.2837 Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 338 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 163 GLN A 198 HIS A 483 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.090922 restraints weight = 4660.002| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.49 r_work: 0.2874 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4397 Z= 0.149 Angle : 0.662 12.312 5993 Z= 0.328 Chirality : 0.046 0.370 666 Planarity : 0.004 0.040 725 Dihedral : 6.896 59.923 643 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.68 % Allowed : 20.71 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.37), residues: 527 helix: 1.42 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.33 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 50 TYR 0.020 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.013 0.001 TRP A 116 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4393) covalent geometry : angle 0.61507 ( 5982) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.65583 ( 2) hydrogen bonds : bond 0.05657 ( 283) hydrogen bonds : angle 4.62615 ( 822) link_NAG-ASN : bond 0.01089 ( 3) link_NAG-ASN : angle 6.34311 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.160 Fit side-chains REVERT: A 72 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8118 (p90) REVERT: A 163 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: A 560 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6522 (mttm) REVERT: A 566 ARG cc_start: 0.6885 (mtp85) cc_final: 0.6300 (mmm-85) REVERT: A 572 GLN cc_start: 0.5933 (OUTLIER) cc_final: 0.5666 (mm110) outliers start: 21 outliers final: 11 residues processed: 74 average time/residue: 0.5245 time to fit residues: 40.3623 Evaluate side-chains 67 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.092668 restraints weight = 4599.724| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.59 r_work: 0.2873 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4397 Z= 0.134 Angle : 0.602 10.125 5993 Z= 0.302 Chirality : 0.045 0.337 666 Planarity : 0.004 0.038 725 Dihedral : 6.035 49.562 641 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.90 % Allowed : 20.49 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.36), residues: 527 helix: 1.68 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.38 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.019 0.002 TYR A 72 PHE 0.031 0.002 PHE A 398 TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4393) covalent geometry : angle 0.57103 ( 5982) SS BOND : bond 0.00400 ( 1) SS BOND : angle 0.87769 ( 2) hydrogen bonds : bond 0.05345 ( 283) hydrogen bonds : angle 4.44806 ( 822) link_NAG-ASN : bond 0.01231 ( 3) link_NAG-ASN : angle 4.95526 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.153 Fit side-chains REVERT: A 72 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8230 (p90) REVERT: A 163 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8292 (mm-40) REVERT: A 384 LEU cc_start: 0.7739 (pp) cc_final: 0.7275 (mp) outliers start: 22 outliers final: 12 residues processed: 72 average time/residue: 0.4796 time to fit residues: 36.0553 Evaluate side-chains 66 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.091024 restraints weight = 4536.839| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.48 r_work: 0.2875 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4397 Z= 0.139 Angle : 0.586 8.453 5993 Z= 0.298 Chirality : 0.045 0.292 666 Planarity : 0.004 0.038 725 Dihedral : 5.500 31.974 641 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.12 % Allowed : 20.94 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.36), residues: 527 helix: 1.77 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.39 (0.46), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.021 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4393) covalent geometry : angle 0.56394 ( 5982) SS BOND : bond 0.00103 ( 1) SS BOND : angle 1.72449 ( 2) hydrogen bonds : bond 0.05497 ( 283) hydrogen bonds : angle 4.41668 ( 822) link_NAG-ASN : bond 0.01058 ( 3) link_NAG-ASN : angle 4.08462 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.110 Fit side-chains REVERT: A 72 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8168 (p90) outliers start: 23 outliers final: 15 residues processed: 73 average time/residue: 0.4413 time to fit residues: 33.6805 Evaluate side-chains 67 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.091680 restraints weight = 4595.308| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.49 r_work: 0.2883 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4397 Z= 0.130 Angle : 0.549 7.716 5993 Z= 0.283 Chirality : 0.043 0.265 666 Planarity : 0.004 0.037 725 Dihedral : 4.953 31.216 641 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.23 % Allowed : 20.94 % Favored : 74.83 % 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: 1.60 (0.37), residues: 527 helix: 1.91 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.27 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 566 TYR 0.019 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4393) covalent geometry : angle 0.53250 ( 5982) SS BOND : bond 0.00079 ( 1) SS BOND : angle 1.02649 ( 2) hydrogen bonds : bond 0.05223 ( 283) hydrogen bonds : angle 4.33229 ( 822) link_NAG-ASN : bond 0.00955 ( 3) link_NAG-ASN : angle 3.41613 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.099 Fit side-chains REVERT: A 72 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8091 (p90) outliers start: 19 outliers final: 14 residues processed: 72 average time/residue: 0.4443 time to fit residues: 33.4772 Evaluate side-chains 70 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 0.0270 chunk 50 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.091868 restraints weight = 4723.067| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.49 r_work: 0.2884 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4397 Z= 0.127 Angle : 0.541 7.666 5993 Z= 0.278 Chirality : 0.043 0.254 666 Planarity : 0.004 0.036 725 Dihedral : 4.775 31.791 641 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.45 % Allowed : 21.38 % Favored : 74.16 % 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: 1.65 (0.37), residues: 527 helix: 1.94 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.25 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.020 0.002 TYR A 72 PHE 0.031 0.002 PHE A 398 TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4393) covalent geometry : angle 0.52831 ( 5982) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.76391 ( 2) hydrogen bonds : bond 0.05168 ( 283) hydrogen bonds : angle 4.30918 ( 822) link_NAG-ASN : bond 0.00837 ( 3) link_NAG-ASN : angle 3.03034 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.170 Fit side-chains REVERT: A 72 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8119 (p90) outliers start: 20 outliers final: 14 residues processed: 76 average time/residue: 0.4940 time to fit residues: 39.1216 Evaluate side-chains 67 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.090891 restraints weight = 4615.434| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.49 r_work: 0.2871 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4397 Z= 0.137 Angle : 0.553 7.627 5993 Z= 0.286 Chirality : 0.044 0.247 666 Planarity : 0.004 0.036 725 Dihedral : 4.803 32.130 641 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.68 % Allowed : 20.49 % Favored : 74.83 % 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: 1.62 (0.37), residues: 527 helix: 1.91 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.25 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.022 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.009 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4393) covalent geometry : angle 0.54226 ( 5982) SS BOND : bond 0.00133 ( 1) SS BOND : angle 0.69412 ( 2) hydrogen bonds : bond 0.05415 ( 283) hydrogen bonds : angle 4.35916 ( 822) link_NAG-ASN : bond 0.00786 ( 3) link_NAG-ASN : angle 2.84070 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.175 Fit side-chains REVERT: A 72 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8079 (p90) REVERT: A 163 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8391 (mm-40) outliers start: 21 outliers final: 14 residues processed: 69 average time/residue: 0.4221 time to fit residues: 30.5666 Evaluate side-chains 67 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.090994 restraints weight = 4636.106| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.48 r_work: 0.2872 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4397 Z= 0.137 Angle : 0.560 7.582 5993 Z= 0.291 Chirality : 0.044 0.238 666 Planarity : 0.004 0.036 725 Dihedral : 4.779 32.158 641 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.79 % Allowed : 21.38 % Favored : 74.83 % 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: 1.62 (0.37), residues: 527 helix: 1.92 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.021 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.009 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4393) covalent geometry : angle 0.55009 ( 5982) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.83370 ( 2) hydrogen bonds : bond 0.05381 ( 283) hydrogen bonds : angle 4.35161 ( 822) link_NAG-ASN : bond 0.00756 ( 3) link_NAG-ASN : angle 2.70557 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.169 Fit side-chains REVERT: A 72 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8211 (p90) REVERT: A 163 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8370 (mm-40) outliers start: 17 outliers final: 14 residues processed: 66 average time/residue: 0.4587 time to fit residues: 31.7170 Evaluate side-chains 67 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.091444 restraints weight = 4683.029| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.50 r_work: 0.2880 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4397 Z= 0.129 Angle : 0.547 7.487 5993 Z= 0.284 Chirality : 0.043 0.243 666 Planarity : 0.004 0.036 725 Dihedral : 4.717 32.109 641 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.23 % Allowed : 20.94 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.37), residues: 527 helix: 1.95 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.22 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.020 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4393) covalent geometry : angle 0.53719 ( 5982) SS BOND : bond 0.00177 ( 1) SS BOND : angle 0.56627 ( 2) hydrogen bonds : bond 0.05220 ( 283) hydrogen bonds : angle 4.32217 ( 822) link_NAG-ASN : bond 0.00737 ( 3) link_NAG-ASN : angle 2.66110 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.138 Fit side-chains REVERT: A 72 TYR cc_start: 0.9137 (OUTLIER) cc_final: 0.8158 (p90) REVERT: A 309 TYR cc_start: 0.8298 (m-80) cc_final: 0.8078 (m-80) outliers start: 19 outliers final: 15 residues processed: 69 average time/residue: 0.4647 time to fit residues: 33.5515 Evaluate side-chains 68 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.092385 restraints weight = 4644.292| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.47 r_work: 0.2893 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4397 Z= 0.125 Angle : 0.540 7.491 5993 Z= 0.281 Chirality : 0.043 0.242 666 Planarity : 0.004 0.036 725 Dihedral : 4.639 31.924 641 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.34 % Allowed : 21.83 % Favored : 74.83 % 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: 1.71 (0.37), residues: 527 helix: 1.96 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.17 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 211 TYR 0.019 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.011 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4393) covalent geometry : angle 0.53070 ( 5982) SS BOND : bond 0.00120 ( 1) SS BOND : angle 0.59492 ( 2) hydrogen bonds : bond 0.05066 ( 283) hydrogen bonds : angle 4.29593 ( 822) link_NAG-ASN : bond 0.00716 ( 3) link_NAG-ASN : angle 2.60255 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.169 Fit side-chains REVERT: A 72 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8081 (p90) outliers start: 15 outliers final: 13 residues processed: 66 average time/residue: 0.4791 time to fit residues: 33.0881 Evaluate side-chains 67 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.090678 restraints weight = 4677.456| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.50 r_work: 0.2869 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4397 Z= 0.139 Angle : 0.558 7.543 5993 Z= 0.291 Chirality : 0.044 0.240 666 Planarity : 0.004 0.036 725 Dihedral : 4.694 32.494 641 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.56 % Allowed : 21.60 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.37), residues: 527 helix: 1.94 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.21 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.022 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.010 0.001 TRP A 146 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4393) covalent geometry : angle 0.54933 ( 5982) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.67638 ( 2) hydrogen bonds : bond 0.05433 ( 283) hydrogen bonds : angle 4.34368 ( 822) link_NAG-ASN : bond 0.00702 ( 3) link_NAG-ASN : angle 2.54300 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1786.65 seconds wall clock time: 31 minutes 8.86 seconds (1868.86 seconds total)