Starting phenix.real_space_refine on Thu Jul 2 01:33:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpd_36476/07_2026/8jpd_36476_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpd_36476/07_2026/8jpd_36476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpd_36476/07_2026/8jpd_36476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpd_36476/07_2026/8jpd_36476.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpd_36476/07_2026/8jpd_36476_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpd_36476/07_2026/8jpd_36476_neut.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3330 2.51 5 N 891 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s 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: 5198 Number of models: 1 Model: "" Number of chains: 2 Chain: "G" Number of atoms: 5163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5163 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 28, 'TRANS': 629} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'STU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.30, per 1000 atoms: 0.25 Number of scatterers: 5198 At special positions: 0 Unit cell: (81.576, 104.648, 88.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 940 8.00 N 891 7.00 C 3330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 158.6 milliseconds 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 55.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'G' and resid 3 through 19 Processing helix chain 'G' and resid 23 through 28 removed outlier: 3.633A pdb=" N ALA G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 38 No H-bonds generated for 'chain 'G' and resid 36 through 38' Processing helix chain 'G' and resid 39 through 49 removed outlier: 4.176A pdb=" N LYS G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 60 Processing helix chain 'G' and resid 61 through 76 removed outlier: 3.764A pdb=" N LEU G 76 " --> pdb=" O CYS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 94 removed outlier: 3.687A pdb=" N LYS G 94 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 113 removed outlier: 4.148A pdb=" N VAL G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 119 Processing helix chain 'G' and resid 125 through 138 removed outlier: 3.700A pdb=" N LYS G 138 " --> pdb=" O GLY G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 158 Processing helix chain 'G' and resid 159 through 168 removed outlier: 3.509A pdb=" N GLN G 163 " --> pdb=" O GLY G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 183 Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'G' and resid 224 through 230 Processing helix chain 'G' and resid 232 through 248 removed outlier: 3.779A pdb=" N THR G 248 " --> pdb=" O SER G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 287 removed outlier: 3.517A pdb=" N HIS G 282 " --> pdb=" O ASP G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 311 removed outlier: 4.156A pdb=" N PHE G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR G 297 " --> pdb=" O ASP G 293 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 321 No H-bonds generated for 'chain 'G' and resid 319 through 321' Processing helix chain 'G' and resid 358 through 363 Processing helix chain 'G' and resid 370 through 387 removed outlier: 3.981A pdb=" N TRP G 374 " --> pdb=" O SER G 370 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE G 375 " --> pdb=" O SER G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 403 Processing helix chain 'G' and resid 404 through 408 removed outlier: 3.911A pdb=" N THR G 408 " --> pdb=" O MET G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 429 Processing helix chain 'G' and resid 443 through 449 removed outlier: 3.723A pdb=" N VAL G 447 " --> pdb=" O GLY G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 454 Processing helix chain 'G' and resid 457 through 464 Processing helix chain 'G' and resid 481 through 486 Processing helix chain 'G' and resid 489 through 494 Processing helix chain 'G' and resid 499 through 504 Processing helix chain 'G' and resid 505 through 507 No H-bonds generated for 'chain 'G' and resid 505 through 507' Processing helix chain 'G' and resid 513 through 525 Processing helix chain 'G' and resid 525 through 548 Processing helix chain 'G' and resid 636 through 659 Processing sheet with id=AA1, first strand: chain 'G' and resid 191 through 200 removed outlier: 4.646A pdb=" N GLY G 207 " --> pdb=" O HIS G 194 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE G 196 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL G 205 " --> pdb=" O ILE G 196 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLY G 198 " --> pdb=" O GLY G 203 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY G 203 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR G 259 " --> pdb=" O ILE G 270 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP G 272 " --> pdb=" O MET G 257 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N MET G 257 " --> pdb=" O ASP G 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'G' and resid 323 through 325 Processing sheet with id=AA4, first strand: chain 'G' and resid 597 through 602 removed outlier: 4.740A pdb=" N SER G 599 " --> pdb=" O TRP G 590 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP G 590 " --> pdb=" O SER G 599 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR G 582 " --> pdb=" O GLU G 589 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR G 580 " --> pdb=" O ARG G 591 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET G 561 " --> pdb=" O LEU G 583 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 768 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: 0.87 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 860 1.30 - 1.42: 1385 1.42 - 1.55: 3016 1.55 - 1.68: 2 1.68 - 1.81: 59 Bond restraints: 5322 Sorted by residual: bond pdb=" C ASP G 637 " pdb=" O ASP G 637 " ideal model delta sigma weight residual 1.243 1.179 0.063 9.90e-03 1.02e+04 4.11e+01 bond pdb=" C ILE G 529 " pdb=" O ILE G 529 " ideal model delta sigma weight residual 1.237 1.167 0.070 1.13e-02 7.83e+03 3.81e+01 bond pdb=" C TRP G 590 " pdb=" O TRP G 590 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.25e-02 6.40e+03 2.79e+01 bond pdb=" C GLN G 598 " pdb=" O GLN G 598 " ideal model delta sigma weight residual 1.234 1.179 0.055 1.22e-02 6.72e+03 2.05e+01 bond pdb=" C19 STU G 701 " pdb=" N3 STU G 701 " ideal model delta sigma weight residual 1.422 1.347 0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 5317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6996 1.64 - 3.28: 147 3.28 - 4.92: 44 4.92 - 6.56: 6 6.56 - 8.20: 5 Bond angle restraints: 7198 Sorted by residual: angle pdb=" N ILE G 529 " pdb=" CA ILE G 529 " pdb=" C ILE G 529 " ideal model delta sigma weight residual 110.42 104.79 5.63 9.60e-01 1.09e+00 3.44e+01 angle pdb=" N SER G 636 " pdb=" CA SER G 636 " pdb=" C SER G 636 " ideal model delta sigma weight residual 109.50 102.43 7.07 1.58e+00 4.01e-01 2.00e+01 angle pdb=" CA ILE G 529 " pdb=" C ILE G 529 " pdb=" N ASN G 530 " ideal model delta sigma weight residual 116.89 121.57 -4.68 1.11e+00 8.12e-01 1.78e+01 angle pdb=" CA ILE G 529 " pdb=" C ILE G 529 " pdb=" O ILE G 529 " ideal model delta sigma weight residual 121.17 116.71 4.46 1.06e+00 8.90e-01 1.77e+01 angle pdb=" N THR G 533 " pdb=" CA THR G 533 " pdb=" C THR G 533 " ideal model delta sigma weight residual 111.07 107.23 3.84 1.07e+00 8.73e-01 1.29e+01 ... (remaining 7193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2903 17.84 - 35.69: 267 35.69 - 53.53: 42 53.53 - 71.37: 7 71.37 - 89.21: 6 Dihedral angle restraints: 3225 sinusoidal: 1307 harmonic: 1918 Sorted by residual: dihedral pdb=" CA LYS G 567 " pdb=" C LYS G 567 " pdb=" N MET G 568 " pdb=" CA MET G 568 " ideal model delta harmonic sigma weight residual 180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA THR G 524 " pdb=" C THR G 524 " pdb=" N VAL G 525 " pdb=" CA VAL G 525 " ideal model delta harmonic sigma weight residual -180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA MET G 568 " pdb=" C MET G 568 " pdb=" N GLY G 569 " pdb=" CA GLY G 569 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 3222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 713 0.071 - 0.142: 64 0.142 - 0.212: 0 0.212 - 0.283: 0 0.283 - 0.354: 2 Chirality restraints: 779 Sorted by residual: chirality pdb=" C25 STU G 701 " pdb=" C24 STU G 701 " pdb=" N3 STU G 701 " pdb=" O4 STU G 701 " both_signs ideal model delta sigma weight residual False 2.34 1.99 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C21 STU G 701 " pdb=" C26 STU G 701 " pdb=" N2 STU G 701 " pdb=" O4 STU G 701 " both_signs ideal model delta sigma weight residual False 2.79 2.44 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA TRP G 590 " pdb=" N TRP G 590 " pdb=" C TRP G 590 " pdb=" CB TRP G 590 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 776 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP G 590 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C TRP G 590 " -0.061 2.00e-02 2.50e+03 pdb=" O TRP G 590 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG G 591 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 635 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ASP G 635 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP G 635 " -0.022 2.00e-02 2.50e+03 pdb=" N SER G 636 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 637 " 0.044 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO G 638 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 638 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 638 " 0.039 5.00e-02 4.00e+02 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1403 2.81 - 3.33: 5005 3.33 - 3.85: 8453 3.85 - 4.38: 10150 4.38 - 4.90: 17643 Nonbonded interactions: 42654 Sorted by model distance: nonbonded pdb=" O THR G 406 " pdb=" NH2 ARG G 431 " model vdw 2.283 3.120 nonbonded pdb=" OD1 ASP G 326 " pdb=" N HIS G 330 " model vdw 2.303 3.120 nonbonded pdb=" O PHE G 417 " pdb=" NH1 ARG G 422 " model vdw 2.321 3.120 nonbonded pdb=" O ASP G 455 " pdb=" OD1 ASP G 455 " model vdw 2.332 3.040 nonbonded pdb=" O SER G 350 " pdb=" OG SER G 350 " model vdw 2.349 3.040 ... (remaining 42649 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: 3.010 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.750 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:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 5322 Z= 0.280 Angle : 0.664 8.202 7198 Z= 0.375 Chirality : 0.042 0.354 779 Planarity : 0.005 0.068 924 Dihedral : 14.219 89.213 1985 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.37 % Allowed : 6.92 % Favored : 92.71 % 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: 0.83 (0.33), residues: 656 helix: 1.14 (0.30), residues: 308 sheet: 0.50 (0.65), residues: 66 loop : 0.03 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 516 TYR 0.025 0.001 TYR G 651 PHE 0.016 0.001 PHE G 296 TRP 0.026 0.002 TRP G 590 HIS 0.009 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.28 ( 5322) covalent geometry : angle 0.66449 / 0.37 ( 7198) hydrogen bonds : bond 0.13983 / 8.76 ( 268) hydrogen bonds : angle 6.60525 / 4.68 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: G 92 TYR cc_start: 0.7487 (t80) cc_final: 0.7242 (t80) REVERT: G 106 ARG cc_start: 0.6852 (ttt-90) cc_final: 0.5785 (tpt170) REVERT: G 568 MET cc_start: 0.5623 (tpt) cc_final: 0.5361 (mmp) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.5743 time to fit residues: 86.9609 Evaluate side-chains 88 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 636 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 0.0270 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN G 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.178005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143524 restraints weight = 6277.166| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.10 r_work: 0.3490 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5322 Z= 0.122 Angle : 0.557 4.965 7198 Z= 0.290 Chirality : 0.041 0.136 779 Planarity : 0.004 0.046 924 Dihedral : 4.688 25.488 748 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.74 % Allowed : 14.95 % Favored : 81.31 % 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: 1.22 (0.33), residues: 656 helix: 1.47 (0.30), residues: 319 sheet: 0.48 (0.65), residues: 67 loop : 0.23 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 591 TYR 0.016 0.001 TYR G 651 PHE 0.012 0.001 PHE G 391 TRP 0.019 0.001 TRP G 590 HIS 0.003 0.001 HIS G 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 5322) covalent geometry : angle 0.55745 / 0.29 ( 7198) hydrogen bonds : bond 0.03723 / 2.44 ( 268) hydrogen bonds : angle 4.84788 / 3.38 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.203 Fit side-chains REVERT: G 15 MET cc_start: 0.4592 (tmt) cc_final: 0.4337 (tmt) REVERT: G 106 ARG cc_start: 0.6550 (ttt-90) cc_final: 0.5131 (tpt170) REVERT: G 117 LEU cc_start: 0.7751 (mt) cc_final: 0.7530 (mp) outliers start: 20 outliers final: 3 residues processed: 104 average time/residue: 0.6057 time to fit residues: 65.4318 Evaluate side-chains 77 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 512 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.0270 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 140 GLN G 155 GLN G 194 HIS G 445 GLN G 459 GLN G 508 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.173558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138428 restraints weight = 6228.063| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.12 r_work: 0.3423 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5322 Z= 0.132 Angle : 0.540 5.398 7198 Z= 0.279 Chirality : 0.040 0.136 779 Planarity : 0.004 0.046 924 Dihedral : 4.567 19.901 745 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.36 % Allowed : 17.01 % Favored : 79.63 % 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: 1.30 (0.34), residues: 656 helix: 1.55 (0.30), residues: 322 sheet: 0.11 (0.61), residues: 71 loop : 0.37 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 579 TYR 0.014 0.001 TYR G 651 PHE 0.013 0.001 PHE G 391 TRP 0.018 0.002 TRP G 590 HIS 0.003 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 5322) covalent geometry : angle 0.54018 / 0.28 ( 7198) hydrogen bonds : bond 0.03812 / 2.47 ( 268) hydrogen bonds : angle 4.67573 / 3.24 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: G 15 MET cc_start: 0.4979 (tmt) cc_final: 0.4362 (mmp) REVERT: G 106 ARG cc_start: 0.6652 (ttt-90) cc_final: 0.5208 (tpt170) REVERT: G 380 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8308 (ttt) REVERT: G 504 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: G 515 GLU cc_start: 0.8549 (pm20) cc_final: 0.8221 (pt0) REVERT: G 572 PHE cc_start: 0.3982 (m-80) cc_final: 0.3754 (t80) outliers start: 18 outliers final: 4 residues processed: 100 average time/residue: 0.5287 time to fit residues: 55.0404 Evaluate side-chains 78 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 504 GLU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 602 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 59 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 140 GLN G 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133830 restraints weight = 6228.003| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.21 r_work: 0.3324 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5322 Z= 0.133 Angle : 0.551 7.218 7198 Z= 0.284 Chirality : 0.041 0.131 779 Planarity : 0.004 0.047 924 Dihedral : 4.652 20.086 745 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.55 % Allowed : 18.50 % Favored : 77.94 % 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: 1.24 (0.34), residues: 656 helix: 1.50 (0.30), residues: 322 sheet: 0.18 (0.61), residues: 71 loop : 0.31 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 69 TYR 0.010 0.001 TYR G 281 PHE 0.013 0.001 PHE G 391 TRP 0.019 0.001 TRP G 590 HIS 0.004 0.001 HIS G 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 5322) covalent geometry : angle 0.55145 / 0.28 ( 7198) hydrogen bonds : bond 0.03560 / 2.31 ( 268) hydrogen bonds : angle 4.60716 / 3.18 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: G 15 MET cc_start: 0.5344 (tmt) cc_final: 0.4705 (mmt) REVERT: G 88 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: G 106 ARG cc_start: 0.6633 (ttt-90) cc_final: 0.5157 (tpt170) REVERT: G 363 GLN cc_start: 0.8219 (mt0) cc_final: 0.7916 (mt0) REVERT: G 380 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8347 (ttt) REVERT: G 504 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: G 572 PHE cc_start: 0.4149 (m-80) cc_final: 0.3938 (t80) outliers start: 19 outliers final: 5 residues processed: 92 average time/residue: 0.5736 time to fit residues: 54.9731 Evaluate side-chains 79 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 504 GLU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 602 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 48 optimal weight: 0.0770 chunk 59 optimal weight: 0.0370 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.172113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137229 restraints weight = 6318.504| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.16 r_work: 0.3394 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5322 Z= 0.112 Angle : 0.531 8.087 7198 Z= 0.271 Chirality : 0.040 0.134 779 Planarity : 0.004 0.046 924 Dihedral : 4.466 20.108 745 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.74 % Allowed : 18.32 % Favored : 77.94 % 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: 1.24 (0.34), residues: 656 helix: 1.54 (0.30), residues: 322 sheet: 0.10 (0.61), residues: 71 loop : 0.27 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 69 TYR 0.010 0.001 TYR G 281 PHE 0.013 0.001 PHE G 391 TRP 0.013 0.001 TRP G 590 HIS 0.003 0.001 HIS G 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 5322) covalent geometry : angle 0.53101 / 0.27 ( 7198) hydrogen bonds : bond 0.03324 / 2.16 ( 268) hydrogen bonds : angle 4.57849 / 3.14 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: G 15 MET cc_start: 0.5155 (tmt) cc_final: 0.4548 (pp-130) REVERT: G 48 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7953 (mt-10) REVERT: G 106 ARG cc_start: 0.6820 (ttt-90) cc_final: 0.5289 (tpt170) REVERT: G 344 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8178 (mmpt) REVERT: G 363 GLN cc_start: 0.8206 (mt0) cc_final: 0.7922 (mt0) REVERT: G 409 MET cc_start: 0.6899 (mpm) cc_final: 0.6636 (mpt) REVERT: G 437 LEU cc_start: 0.8486 (tp) cc_final: 0.8277 (tp) REVERT: G 504 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: G 515 GLU cc_start: 0.8501 (pm20) cc_final: 0.8280 (pm20) REVERT: G 624 ILE cc_start: 0.8418 (mm) cc_final: 0.8084 (tt) REVERT: G 653 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7462 (tp30) outliers start: 20 outliers final: 8 residues processed: 93 average time/residue: 0.5501 time to fit residues: 53.2391 Evaluate side-chains 83 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 460 MET Chi-restraints excluded: chain G residue 504 GLU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain G residue 602 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.166744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131240 restraints weight = 6269.293| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.16 r_work: 0.3326 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5322 Z= 0.212 Angle : 0.641 7.700 7198 Z= 0.328 Chirality : 0.044 0.135 779 Planarity : 0.004 0.044 924 Dihedral : 5.084 22.963 745 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.18 % Allowed : 20.93 % Favored : 75.89 % 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: 0.91 (0.34), residues: 656 helix: 1.25 (0.30), residues: 325 sheet: -0.18 (0.60), residues: 71 loop : 0.16 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 392 TYR 0.011 0.002 TYR G 281 PHE 0.036 0.002 PHE G 572 TRP 0.015 0.002 TRP G 590 HIS 0.004 0.001 HIS G 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 ( 5322) covalent geometry : angle 0.64074 / 0.33 ( 7198) hydrogen bonds : bond 0.04289 / 2.73 ( 268) hydrogen bonds : angle 4.82788 / 3.30 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.201 Fit side-chains REVERT: G 48 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7967 (mt-10) REVERT: G 192 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8683 (p) REVERT: G 344 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8286 (mmpt) REVERT: G 363 GLN cc_start: 0.8298 (mt0) cc_final: 0.7998 (mt0) REVERT: G 409 MET cc_start: 0.7210 (mpm) cc_final: 0.6845 (mpt) REVERT: G 437 LEU cc_start: 0.8494 (tp) cc_final: 0.8268 (tp) REVERT: G 515 GLU cc_start: 0.8623 (pm20) cc_final: 0.8403 (pm20) REVERT: G 653 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7692 (tp30) outliers start: 17 outliers final: 8 residues processed: 82 average time/residue: 0.5624 time to fit residues: 48.0181 Evaluate side-chains 73 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain G residue 602 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 HIS ** 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 = 0.3906 r_free = 0.3906 target = 0.166447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129659 restraints weight = 6240.968| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.18 r_work: 0.3303 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5322 Z= 0.161 Angle : 0.587 7.972 7198 Z= 0.301 Chirality : 0.042 0.136 779 Planarity : 0.004 0.044 924 Dihedral : 4.848 21.163 745 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.80 % Allowed : 22.24 % Favored : 74.95 % 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: 0.93 (0.34), residues: 656 helix: 1.39 (0.30), residues: 322 sheet: -0.35 (0.58), residues: 73 loop : 0.07 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 404 TYR 0.011 0.001 TYR G 281 PHE 0.021 0.001 PHE G 572 TRP 0.013 0.001 TRP G 590 HIS 0.003 0.001 HIS G 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 5322) covalent geometry : angle 0.58740 / 0.30 ( 7198) hydrogen bonds : bond 0.03763 / 2.41 ( 268) hydrogen bonds : angle 4.73758 / 3.24 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.187 Fit side-chains REVERT: G 36 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: G 192 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8634 (p) REVERT: G 344 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8256 (mmpt) REVERT: G 404 ARG cc_start: 0.6983 (mmm-85) cc_final: 0.6752 (mmm-85) REVERT: G 515 GLU cc_start: 0.8497 (pm20) cc_final: 0.8261 (pm20) outliers start: 15 outliers final: 8 residues processed: 76 average time/residue: 0.5057 time to fit residues: 40.1830 Evaluate side-chains 71 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 460 MET Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain G residue 602 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 19 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.0010 chunk 59 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 HIS ** 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 = 0.3931 r_free = 0.3931 target = 0.168743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132323 restraints weight = 6255.068| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.20 r_work: 0.3334 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5322 Z= 0.117 Angle : 0.543 7.937 7198 Z= 0.278 Chirality : 0.040 0.137 779 Planarity : 0.004 0.044 924 Dihedral : 4.553 20.811 745 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.62 % Allowed : 22.99 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.34), residues: 656 helix: 1.49 (0.30), residues: 323 sheet: -0.44 (0.55), residues: 79 loop : 0.19 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 404 TYR 0.017 0.001 TYR G 651 PHE 0.014 0.001 PHE G 572 TRP 0.012 0.001 TRP G 590 HIS 0.002 0.001 HIS G 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5322) covalent geometry : angle 0.54293 / 0.28 ( 7198) hydrogen bonds : bond 0.03346 / 2.17 ( 268) hydrogen bonds : angle 4.60776 / 3.15 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.157 Fit side-chains REVERT: G 15 MET cc_start: 0.5393 (tmt) cc_final: 0.4718 (pp-130) REVERT: G 48 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7821 (mt-10) REVERT: G 106 ARG cc_start: 0.6741 (ttt-90) cc_final: 0.5130 (tpt170) REVERT: G 344 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8282 (mmpt) REVERT: G 404 ARG cc_start: 0.6907 (mmm-85) cc_final: 0.6704 (mmm-85) REVERT: G 437 LEU cc_start: 0.8324 (tp) cc_final: 0.8090 (tp) REVERT: G 515 GLU cc_start: 0.8432 (pm20) cc_final: 0.8202 (pm20) outliers start: 14 outliers final: 6 residues processed: 83 average time/residue: 0.5106 time to fit residues: 44.1301 Evaluate side-chains 74 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 602 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 0.0970 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 41 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 HIS ** 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 = 0.3934 r_free = 0.3934 target = 0.168951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132610 restraints weight = 6226.679| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.19 r_work: 0.3310 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5322 Z= 0.115 Angle : 0.547 8.582 7198 Z= 0.277 Chirality : 0.040 0.136 779 Planarity : 0.004 0.044 924 Dihedral : 4.477 20.523 745 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.50 % Allowed : 25.05 % Favored : 73.46 % 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: 1.11 (0.34), residues: 656 helix: 1.50 (0.30), residues: 323 sheet: -0.32 (0.56), residues: 79 loop : 0.26 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 404 TYR 0.016 0.001 TYR G 651 PHE 0.013 0.001 PHE G 391 TRP 0.011 0.001 TRP G 590 HIS 0.002 0.001 HIS G 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 5322) covalent geometry : angle 0.54673 / 0.28 ( 7198) hydrogen bonds : bond 0.03289 / 2.13 ( 268) hydrogen bonds : angle 4.60078 / 3.14 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.205 Fit side-chains REVERT: G 15 MET cc_start: 0.5326 (tmt) cc_final: 0.4662 (pp-130) REVERT: G 48 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7740 (mt-10) REVERT: G 106 ARG cc_start: 0.6634 (ttt-90) cc_final: 0.5057 (tpt170) REVERT: G 344 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8272 (mmpt) REVERT: G 404 ARG cc_start: 0.6942 (mmm-85) cc_final: 0.6736 (mmm-85) REVERT: G 437 LEU cc_start: 0.8296 (tp) cc_final: 0.8078 (tp) REVERT: G 515 GLU cc_start: 0.8385 (pm20) cc_final: 0.8167 (pm20) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.5413 time to fit residues: 44.5115 Evaluate side-chains 73 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 602 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 HIS ** 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 = 0.3905 r_free = 0.3905 target = 0.166195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129128 restraints weight = 6317.698| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.29 r_work: 0.3301 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5322 Z= 0.182 Angle : 0.620 9.248 7198 Z= 0.312 Chirality : 0.042 0.144 779 Planarity : 0.004 0.045 924 Dihedral : 4.755 20.701 745 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.06 % Allowed : 24.86 % Favored : 73.08 % 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: 1.00 (0.34), residues: 656 helix: 1.39 (0.30), residues: 323 sheet: -0.29 (0.60), residues: 71 loop : 0.16 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 311 TYR 0.014 0.002 TYR G 651 PHE 0.015 0.002 PHE G 391 TRP 0.011 0.001 TRP G 590 HIS 0.003 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 ( 5322) covalent geometry : angle 0.62025 / 0.31 ( 7198) hydrogen bonds : bond 0.03790 / 2.43 ( 268) hydrogen bonds : angle 4.73065 / 3.23 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.160 Fit side-chains REVERT: G 48 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7799 (mt-10) REVERT: G 344 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8287 (mmpt) REVERT: G 437 LEU cc_start: 0.8341 (tp) cc_final: 0.8125 (tp) REVERT: G 515 GLU cc_start: 0.8465 (pm20) cc_final: 0.8246 (pm20) outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 0.5388 time to fit residues: 41.7229 Evaluate side-chains 69 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 602 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 HIS ** 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 = 0.3911 r_free = 0.3911 target = 0.166870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130089 restraints weight = 6315.957| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.20 r_work: 0.3308 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5322 Z= 0.153 Angle : 0.597 8.902 7198 Z= 0.302 Chirality : 0.042 0.145 779 Planarity : 0.004 0.047 924 Dihedral : 4.721 20.727 745 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.87 % Allowed : 25.42 % Favored : 72.71 % 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: 0.96 (0.34), residues: 656 helix: 1.36 (0.30), residues: 322 sheet: -0.43 (0.58), residues: 77 loop : 0.21 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 311 TYR 0.015 0.002 TYR G 651 PHE 0.015 0.001 PHE G 391 TRP 0.012 0.001 TRP G 590 HIS 0.003 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 5322) covalent geometry : angle 0.59711 / 0.30 ( 7198) hydrogen bonds : bond 0.03648 / 2.35 ( 268) hydrogen bonds : angle 4.70655 / 3.21 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.32 seconds wall clock time: 39 minutes 22.19 seconds (2362.19 seconds total)