Starting phenix.real_space_refine on Fri Aug 22 15:51:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpd_36476/08_2025/8jpd_36476_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpd_36476/08_2025/8jpd_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_36476/08_2025/8jpd_36476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpd_36476/08_2025/8jpd_36476.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpd_36476/08_2025/8jpd_36476_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpd_36476/08_2025/8jpd_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-2.0-5787/lib/python3.9/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: 1.50, per 1000 atoms: 0.29 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: 0.42 Conformation dependent library (CDL) restraints added in 523.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.21 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: 0.85 Time building geometry restraints manager: 0.57 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=" C HIS G 282 " pdb=" O HIS G 282 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.26e-02 6.30e+03 1.34e+01 ... (remaining 5317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 6951 1.41 - 2.83: 183 2.83 - 4.24: 50 4.24 - 5.66: 12 5.66 - 7.07: 2 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: 2881 17.84 - 35.69: 264 35.69 - 53.53: 42 53.53 - 71.37: 9 71.37 - 89.21: 6 Dihedral angle restraints: 3202 sinusoidal: 1284 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=" C23 STU G 701 " pdb=" C21 STU G 701 " pdb=" C22 STU G 701 " pdb=" N2 STU G 701 " ideal model delta sinusoidal sigma weight residual 76.33 141.41 -65.08 1 2.00e+01 2.50e-03 1.39e+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 ... (remaining 3199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 482 0.028 - 0.056: 199 0.056 - 0.084: 56 0.084 - 0.112: 28 0.112 - 0.141: 14 Chirality restraints: 779 Sorted by residual: 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 chirality pdb=" CA ILE G 323 " pdb=" N ILE G 323 " pdb=" C ILE G 323 " pdb=" CB ILE G 323 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE G 471 " pdb=" N ILE G 471 " pdb=" C ILE G 471 " pdb=" CB ILE G 471 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-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: 0.010 Normalize map: mean=0, sd=1: 3.220 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: 0.010 Process input model: 6.900 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 5322 Z= 0.247 Angle : 0.613 7.073 7198 Z= 0.365 Chirality : 0.038 0.141 779 Planarity : 0.005 0.068 924 Dihedral : 14.353 89.213 1962 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 aren 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 covalent geometry : bond 0.00396 ( 5322) covalent geometry : angle 0.61277 ( 7198) hydrogen bonds : bond 0.13983 ( 268) hydrogen bonds : angle 6.60525 ( 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 : 0.131 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: 0.5580 time to fit residues: 84.4306 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 : 0.166 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4044 r_free = 0.4044 target = 0.178094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143629 restraints weight = 6295.285| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.11 r_work: 0.3490 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5322 Z= 0.125 Angle : 0.569 5.759 7198 Z= 0.293 Chirality : 0.041 0.136 779 Planarity : 0.004 0.045 924 Dihedral : 5.342 62.786 725 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.55 % Allowed : 15.51 % Favored : 80.93 % 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 aren not related in a simple way. whole: 1.24 (0.34), residues: 656 helix: 1.49 (0.30), residues: 319 sheet: 0.44 (0.64), residues: 67 loop : 0.24 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 69 TYR 0.017 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 328 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5322) covalent geometry : angle 0.56887 ( 7198) hydrogen bonds : bond 0.03812 ( 268) hydrogen bonds : angle 4.89496 ( 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: 19 poor density : 92 time to evaluate : 0.117 Fit side-chains REVERT: G 15 MET cc_start: 0.4585 (tmt) cc_final: 0.4316 (tmt) REVERT: G 106 ARG cc_start: 0.6560 (ttt-90) cc_final: 0.5133 (tpt170) REVERT: G 114 MET cc_start: 0.7568 (tpt) cc_final: 0.7360 (tpt) REVERT: G 117 LEU cc_start: 0.7717 (mt) cc_final: 0.7494 (mp) REVERT: G 344 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7839 (mmmt) REVERT: G 648 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7476 (mtt-85) outliers start: 19 outliers final: 3 residues processed: 104 average time/residue: 0.5259 time to fit residues: 56.8414 Evaluate side-chains 78 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 344 LYS Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 648 ARG 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: 0.0980 chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 0.0030 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.0170 chunk 18 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.2228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 140 GLN G 155 GLN G 445 GLN G 459 GLN G 508 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.178576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144135 restraints weight = 6252.968| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.11 r_work: 0.3492 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5322 Z= 0.104 Angle : 0.525 5.876 7198 Z= 0.267 Chirality : 0.040 0.133 779 Planarity : 0.004 0.046 924 Dihedral : 5.198 62.596 722 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.99 % Allowed : 16.82 % Favored : 80.19 % 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 aren not related in a simple way. whole: 1.31 (0.34), residues: 656 helix: 1.56 (0.30), residues: 324 sheet: 0.43 (0.63), residues: 67 loop : 0.25 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 579 TYR 0.015 0.001 TYR G 651 PHE 0.010 0.001 PHE G 391 TRP 0.016 0.001 TRP G 590 HIS 0.002 0.000 HIS G 131 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 5322) covalent geometry : angle 0.52459 ( 7198) hydrogen bonds : bond 0.03400 ( 268) hydrogen bonds : angle 4.62504 ( 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 102 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: G 15 MET cc_start: 0.4618 (tmt) cc_final: 0.4343 (tmt) REVERT: G 106 ARG cc_start: 0.6585 (ttt-90) cc_final: 0.5318 (tpt170) REVERT: G 114 MET cc_start: 0.7710 (tpt) cc_final: 0.7440 (tpt) REVERT: G 515 GLU cc_start: 0.8563 (pm20) cc_final: 0.8223 (pt0) outliers start: 16 outliers final: 4 residues processed: 95 average time/residue: 0.4907 time to fit residues: 48.4632 Evaluate side-chains 77 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 155 GLN G 194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.170882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135362 restraints weight = 6257.852| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.12 r_work: 0.3380 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5322 Z= 0.153 Angle : 0.574 6.077 7198 Z= 0.293 Chirality : 0.041 0.134 779 Planarity : 0.004 0.046 924 Dihedral : 5.486 66.861 722 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.36 % Allowed : 18.50 % Favored : 78.13 % 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 aren not related in a simple way. whole: 1.24 (0.34), residues: 656 helix: 1.49 (0.30), residues: 322 sheet: 0.23 (0.61), residues: 71 loop : 0.30 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 69 TYR 0.017 0.002 TYR G 86 PHE 0.016 0.001 PHE G 391 TRP 0.021 0.002 TRP G 590 HIS 0.004 0.001 HIS G 282 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 5322) covalent geometry : angle 0.57414 ( 7198) hydrogen bonds : bond 0.03837 ( 268) hydrogen bonds : angle 4.65611 ( 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 102 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: G 17 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8088 (mtm) REVERT: G 48 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7977 (mt-10) REVERT: G 106 ARG cc_start: 0.6694 (ttt-90) cc_final: 0.5171 (tpt170) REVERT: G 363 GLN cc_start: 0.8192 (mt0) cc_final: 0.7934 (mt0) REVERT: G 380 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8347 (ttp) REVERT: G 504 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: G 515 GLU cc_start: 0.8573 (pm20) cc_final: 0.8354 (pm20) outliers start: 18 outliers final: 6 residues processed: 93 average time/residue: 0.4845 time to fit residues: 46.7598 Evaluate side-chains 82 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 290 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: 0.6980 chunk 59 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3938 r_free = 0.3938 target = 0.168747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133645 restraints weight = 6327.475| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.18 r_work: 0.3360 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5322 Z= 0.169 Angle : 0.597 7.281 7198 Z= 0.304 Chirality : 0.042 0.134 779 Planarity : 0.004 0.046 924 Dihedral : 5.491 66.599 722 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.99 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 aren not related in a simple way. whole: 1.11 (0.34), residues: 656 helix: 1.39 (0.30), residues: 323 sheet: 0.01 (0.61), residues: 71 loop : 0.29 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 69 TYR 0.010 0.002 TYR G 281 PHE 0.040 0.002 PHE G 572 TRP 0.014 0.001 TRP G 590 HIS 0.003 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 5322) covalent geometry : angle 0.59658 ( 7198) hydrogen bonds : bond 0.03842 ( 268) hydrogen bonds : angle 4.69592 ( 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 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8055 (mt-10) REVERT: G 48 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7961 (mt-10) REVERT: G 106 ARG cc_start: 0.6859 (ttt-90) cc_final: 0.5211 (tpt170) REVERT: G 363 GLN cc_start: 0.8198 (mt0) cc_final: 0.7923 (mt0) REVERT: G 380 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8379 (ttp) REVERT: G 504 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: G 515 GLU cc_start: 0.8562 (pm20) cc_final: 0.8339 (pm20) REVERT: G 624 ILE cc_start: 0.8466 (mm) cc_final: 0.8124 (tt) REVERT: G 653 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7529 (tp30) outliers start: 19 outliers final: 8 residues processed: 87 average time/residue: 0.5362 time to fit residues: 48.3692 Evaluate side-chains 77 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 290 SER Chi-restraints excluded: chain G residue 380 MET 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 602 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 60 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131864 restraints weight = 6255.921| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.19 r_work: 0.3329 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5322 Z= 0.186 Angle : 0.604 6.599 7198 Z= 0.310 Chirality : 0.043 0.136 779 Planarity : 0.004 0.045 924 Dihedral : 5.613 67.568 722 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.93 % Allowed : 19.63 % Favored : 76.45 % 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 aren not related in a simple way. whole: 0.94 (0.33), residues: 656 helix: 1.28 (0.30), residues: 325 sheet: -0.09 (0.61), residues: 71 loop : 0.13 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 69 TYR 0.011 0.002 TYR G 281 PHE 0.016 0.002 PHE G 391 TRP 0.016 0.001 TRP G 590 HIS 0.004 0.001 HIS G 282 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 5322) covalent geometry : angle 0.60445 ( 7198) hydrogen bonds : bond 0.04026 ( 268) hydrogen bonds : angle 4.76615 ( 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 89 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8126 (mt-10) REVERT: G 69 ARG cc_start: 0.8276 (ttt-90) cc_final: 0.8027 (ttt-90) REVERT: G 363 GLN cc_start: 0.8273 (mt0) cc_final: 0.7961 (mt0) REVERT: G 380 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8359 (ttp) REVERT: G 515 GLU cc_start: 0.8598 (pm20) cc_final: 0.8377 (pm20) REVERT: G 620 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8276 (mt) REVERT: G 653 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7709 (tp30) outliers start: 21 outliers final: 10 residues processed: 84 average time/residue: 0.5154 time to fit residues: 44.8727 Evaluate side-chains 77 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 290 SER Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 426 GLU 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 Chi-restraints excluded: chain G residue 620 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 18 optimal weight: 0.0370 chunk 38 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.168904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134214 restraints weight = 6262.696| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.16 r_work: 0.3370 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4270 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= 0.128 Angle : 0.558 6.815 7198 Z= 0.283 Chirality : 0.041 0.138 779 Planarity : 0.004 0.045 924 Dihedral : 5.359 64.755 722 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.80 % Allowed : 20.56 % Favored : 76.64 % 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 aren not related in a simple way. whole: 1.12 (0.34), residues: 656 helix: 1.51 (0.30), residues: 322 sheet: -0.28 (0.56), residues: 79 loop : 0.25 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 404 TYR 0.011 0.001 TYR G 281 PHE 0.013 0.001 PHE G 391 TRP 0.013 0.001 TRP G 590 HIS 0.002 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5322) covalent geometry : angle 0.55753 ( 7198) hydrogen bonds : bond 0.03480 ( 268) hydrogen bonds : angle 4.63376 ( 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 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8162 (mt-10) REVERT: G 106 ARG cc_start: 0.6989 (ttt-90) cc_final: 0.5325 (tpt170) REVERT: G 380 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8402 (ttp) REVERT: G 404 ARG cc_start: 0.6931 (mmm-85) cc_final: 0.6684 (mmm-85) REVERT: G 515 GLU cc_start: 0.8521 (pm20) cc_final: 0.8284 (pm20) outliers start: 15 outliers final: 9 residues processed: 85 average time/residue: 0.4890 time to fit residues: 43.2408 Evaluate side-chains 76 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 380 MET 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: 0.6980 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3941 r_free = 0.3941 target = 0.169499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134774 restraints weight = 6260.760| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.13 r_work: 0.3377 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5322 Z= 0.124 Angle : 0.555 7.355 7198 Z= 0.281 Chirality : 0.040 0.134 779 Planarity : 0.004 0.044 924 Dihedral : 5.311 64.948 722 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.80 % Allowed : 21.50 % Favored : 75.70 % 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 aren not related in a simple way. whole: 1.18 (0.34), residues: 656 helix: 1.58 (0.30), residues: 323 sheet: -0.25 (0.56), residues: 79 loop : 0.23 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 404 TYR 0.011 0.001 TYR G 281 PHE 0.013 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 covalent geometry : bond 0.00290 ( 5322) covalent geometry : angle 0.55511 ( 7198) hydrogen bonds : bond 0.03369 ( 268) hydrogen bonds : angle 4.56259 ( 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 87 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8156 (mt-10) REVERT: G 106 ARG cc_start: 0.6912 (ttt-90) cc_final: 0.5304 (tpt170) REVERT: G 380 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8376 (ttp) REVERT: G 404 ARG cc_start: 0.6853 (mmm-85) cc_final: 0.6638 (mmm-85) REVERT: G 515 GLU cc_start: 0.8481 (pm20) cc_final: 0.8262 (pm20) REVERT: G 620 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8252 (mt) outliers start: 15 outliers final: 9 residues processed: 84 average time/residue: 0.5384 time to fit residues: 47.0322 Evaluate side-chains 77 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 295 ILE Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 411 VAL 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 Chi-restraints excluded: chain G residue 620 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 chunk 49 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3953 r_free = 0.3953 target = 0.170505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135922 restraints weight = 6243.089| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.16 r_work: 0.3402 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4465 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 8.409 7198 Z= 0.276 Chirality : 0.040 0.137 779 Planarity : 0.004 0.044 924 Dihedral : 5.220 64.278 722 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.24 % Allowed : 22.99 % Favored : 74.77 % 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 aren not related in a simple way. whole: 1.25 (0.34), residues: 656 helix: 1.63 (0.30), residues: 323 sheet: -0.25 (0.58), residues: 77 loop : 0.28 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 404 TYR 0.011 0.001 TYR G 281 PHE 0.012 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 covalent geometry : bond 0.00268 ( 5322) covalent geometry : angle 0.54651 ( 7198) hydrogen bonds : bond 0.03209 ( 268) hydrogen bonds : angle 4.53026 ( 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 85 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8141 (mt-10) REVERT: G 106 ARG cc_start: 0.6909 (ttt-90) cc_final: 0.5362 (tpt170) REVERT: G 133 GLN cc_start: 0.8199 (mt0) cc_final: 0.7977 (mt0) REVERT: G 380 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8382 (ttp) REVERT: G 437 LEU cc_start: 0.8660 (tt) cc_final: 0.8426 (tp) REVERT: G 515 GLU cc_start: 0.8453 (pm20) cc_final: 0.8245 (pm20) REVERT: G 620 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8207 (mt) outliers start: 12 outliers final: 9 residues processed: 82 average time/residue: 0.5556 time to fit residues: 47.2188 Evaluate side-chains 81 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 290 SER Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 411 VAL 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 Chi-restraints excluded: chain G residue 620 LEU 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: 2.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3919 r_free = 0.3919 target = 0.167440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132325 restraints weight = 6353.646| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.16 r_work: 0.3318 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5322 Z= 0.186 Angle : 0.625 9.117 7198 Z= 0.314 Chirality : 0.042 0.142 779 Planarity : 0.004 0.045 924 Dihedral : 5.499 67.405 722 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.43 % Allowed : 22.80 % Favored : 74.77 % 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 aren not related in a simple way. whole: 1.07 (0.34), residues: 656 helix: 1.52 (0.30), residues: 323 sheet: -0.33 (0.60), residues: 73 loop : 0.13 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 404 TYR 0.012 0.002 TYR G 281 PHE 0.015 0.002 PHE G 391 TRP 0.012 0.001 TRP G 590 HIS 0.003 0.001 HIS G 282 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 5322) covalent geometry : angle 0.62490 ( 7198) hydrogen bonds : bond 0.03797 ( 268) hydrogen bonds : angle 4.67607 ( 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 82 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8163 (mt-10) REVERT: G 106 ARG cc_start: 0.6912 (ttt-90) cc_final: 0.5336 (tpt170) REVERT: G 133 GLN cc_start: 0.8245 (mt0) cc_final: 0.8016 (mt0) REVERT: G 380 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8339 (ttp) REVERT: G 437 LEU cc_start: 0.8685 (tt) cc_final: 0.8447 (tp) REVERT: G 515 GLU cc_start: 0.8526 (pm20) cc_final: 0.8311 (pm20) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 0.5095 time to fit residues: 41.8478 Evaluate side-chains 78 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 290 SER Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 385 LEU 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 574 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: 6.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 0.0570 chunk 19 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3940 r_free = 0.3940 target = 0.169342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134700 restraints weight = 6336.476| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.15 r_work: 0.3371 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5322 Z= 0.130 Angle : 0.578 8.900 7198 Z= 0.292 Chirality : 0.040 0.140 779 Planarity : 0.004 0.044 924 Dihedral : 5.314 64.919 722 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.24 % Allowed : 23.36 % 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 aren not related in a simple way. whole: 1.13 (0.34), residues: 656 helix: 1.58 (0.30), residues: 323 sheet: -0.28 (0.57), residues: 79 loop : 0.14 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 404 TYR 0.011 0.001 TYR G 281 PHE 0.014 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 covalent geometry : bond 0.00308 ( 5322) covalent geometry : angle 0.57826 ( 7198) hydrogen bonds : bond 0.03373 ( 268) hydrogen bonds : angle 4.57901 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.40 seconds wall clock time: 33 minutes 42.17 seconds (2022.17 seconds total)