Starting phenix.real_space_refine on Thu Mar 6 07:30:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpd_36476/03_2025/8jpd_36476_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpd_36476/03_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_36476/03_2025/8jpd_36476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpd_36476/03_2025/8jpd_36476.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpd_36476/03_2025/8jpd_36476_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpd_36476/03_2025/8jpd_36476_neut.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 4, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} 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: 4.36, per 1000 atoms: 0.84 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: 1.27 Conformation dependent library (CDL) restraints added in 594.1 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: 0.60 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: 1.69 Time building geometry restraints manager: 1.50 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: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.730 ------------------------------------------------------------------------------- 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= 0.255 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 : 4.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.002 TRP G 590 HIS 0.009 0.001 HIS G 282 PHE 0.016 0.001 PHE G 296 TYR 0.025 0.001 TYR G 651 ARG 0.010 0.001 ARG G 516 *********************** 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 : 0.608 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: 1.3964 time to fit residues: 211.3026 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 : 0.600 ------------------------------------------------------------------------------- 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 54 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 G 508 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.173241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138416 restraints weight = 6150.065| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.09 r_work: 0.3419 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2610 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= 0.238 Angle : 0.605 5.404 7198 Z= 0.313 Chirality : 0.043 0.137 779 Planarity : 0.004 0.046 924 Dihedral : 5.543 64.812 725 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.11 % Allowed : 15.14 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.33), residues: 656 helix: 1.38 (0.30), residues: 320 sheet: 0.36 (0.64), residues: 67 loop : 0.22 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 590 HIS 0.004 0.001 HIS G 282 PHE 0.016 0.001 PHE G 391 TYR 0.016 0.002 TYR G 651 ARG 0.003 0.001 ARG G 404 *********************** 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 115 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.599 Fit side-chains REVERT: G 106 ARG cc_start: 0.6717 (ttt-90) cc_final: 0.5161 (tpt170) REVERT: G 114 MET cc_start: 0.7745 (tpt) cc_final: 0.7392 (tpt) REVERT: G 135 HIS cc_start: 0.7051 (m-70) cc_final: 0.6837 (m90) REVERT: G 380 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8039 (ttt) REVERT: G 572 PHE cc_start: 0.3827 (m-80) cc_final: 0.3622 (t80) REVERT: G 648 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7720 (mtt180) outliers start: 22 outliers final: 6 residues processed: 107 average time/residue: 1.2702 time to fit residues: 141.3092 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 : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 150 ILE 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 512 THR Chi-restraints excluded: chain G residue 602 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 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 445 GLN G 459 GLN G 508 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.169760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134399 restraints weight = 6171.593| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.11 r_work: 0.3364 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3385 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= 0.255 Angle : 0.592 6.128 7198 Z= 0.304 Chirality : 0.042 0.139 779 Planarity : 0.004 0.046 924 Dihedral : 5.638 67.268 722 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.74 % Allowed : 17.38 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.34), residues: 656 helix: 1.39 (0.30), residues: 321 sheet: -0.10 (0.59), residues: 73 loop : 0.20 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 590 HIS 0.006 0.001 HIS G 194 PHE 0.015 0.001 PHE G 391 TYR 0.011 0.001 TYR G 651 ARG 0.004 0.001 ARG G 431 *********************** 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 108 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8046 (mt-10) REVERT: G 48 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7997 (mt-10) REVERT: G 106 ARG cc_start: 0.6796 (ttt-90) cc_final: 0.5204 (tpt170) REVERT: G 344 LYS cc_start: 0.8325 (mmpt) cc_final: 0.8115 (mmmt) REVERT: G 363 GLN cc_start: 0.8232 (mt0) cc_final: 0.7901 (mt0) REVERT: G 504 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: G 648 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7682 (mtt180) REVERT: G 653 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7444 (tp30) outliers start: 20 outliers final: 3 residues processed: 101 average time/residue: 1.3807 time to fit residues: 144.8676 Evaluate side-chains 74 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 192 SER 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 648 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.168075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131689 restraints weight = 6354.238| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.28 r_work: 0.3332 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3701 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= 0.205 Angle : 0.558 6.091 7198 Z= 0.285 Chirality : 0.041 0.131 779 Planarity : 0.004 0.046 924 Dihedral : 5.449 65.273 722 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.99 % Allowed : 19.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.34), residues: 656 helix: 1.41 (0.30), residues: 323 sheet: 0.03 (0.60), residues: 71 loop : 0.21 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 590 HIS 0.003 0.001 HIS G 194 PHE 0.039 0.001 PHE G 572 TYR 0.011 0.001 TYR G 281 ARG 0.004 0.000 ARG G 69 *********************** 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 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: G 15 MET cc_start: 0.5512 (tmt) cc_final: 0.4790 (mmt) REVERT: G 36 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8070 (mt-10) REVERT: G 48 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7914 (mt-10) REVERT: G 88 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: G 106 ARG cc_start: 0.6699 (ttt-90) cc_final: 0.5165 (tpt170) REVERT: G 192 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8594 (p) REVERT: G 363 GLN cc_start: 0.8201 (mt0) cc_final: 0.7886 (mt0) REVERT: G 380 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8377 (ttp) REVERT: G 504 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: G 624 ILE cc_start: 0.8430 (mm) cc_final: 0.8068 (tt) REVERT: G 648 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7567 (mtt180) REVERT: G 653 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7547 (tp30) outliers start: 16 outliers final: 4 residues processed: 88 average time/residue: 1.3360 time to fit residues: 122.0715 Evaluate side-chains 78 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 426 GLU 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 648 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 49 optimal weight: 0.0670 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.0020 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5126 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.170023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135114 restraints weight = 6276.011| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.19 r_work: 0.3370 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5322 Z= 0.179 Angle : 0.541 6.128 7198 Z= 0.275 Chirality : 0.040 0.133 779 Planarity : 0.004 0.045 924 Dihedral : 5.334 64.907 722 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.55 % Allowed : 18.69 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.34), residues: 656 helix: 1.50 (0.30), residues: 323 sheet: 0.01 (0.60), residues: 71 loop : 0.23 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 590 HIS 0.003 0.001 HIS G 194 PHE 0.020 0.001 PHE G 572 TYR 0.011 0.001 TYR G 281 ARG 0.004 0.000 ARG G 69 *********************** 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 98 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8091 (mt-10) REVERT: G 69 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8067 (ttt-90) REVERT: G 106 ARG cc_start: 0.6848 (ttt-90) cc_final: 0.5196 (tpt170) REVERT: G 363 GLN cc_start: 0.8201 (mt0) cc_final: 0.7900 (mt0) REVERT: G 380 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8383 (ttp) REVERT: G 409 MET cc_start: 0.7056 (mpm) cc_final: 0.6826 (mpt) REVERT: G 504 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: G 624 ILE cc_start: 0.8400 (mm) cc_final: 0.8164 (tt) REVERT: G 648 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7653 (mtt180) REVERT: G 653 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7615 (tp30) outliers start: 19 outliers final: 4 residues processed: 92 average time/residue: 1.3514 time to fit residues: 129.5736 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 : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 295 ILE 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 540 LYS Chi-restraints excluded: chain G residue 648 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.167219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131893 restraints weight = 6227.127| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.16 r_work: 0.3330 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5322 Z= 0.284 Angle : 0.606 7.430 7198 Z= 0.306 Chirality : 0.043 0.135 779 Planarity : 0.004 0.044 924 Dihedral : 5.568 67.494 722 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.18 % Allowed : 20.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.34), residues: 656 helix: 1.43 (0.30), residues: 323 sheet: -0.15 (0.60), residues: 71 loop : 0.18 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 590 HIS 0.003 0.001 HIS G 282 PHE 0.016 0.002 PHE G 391 TYR 0.012 0.002 TYR G 281 ARG 0.003 0.000 ARG G 69 *********************** 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 81 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8161 (mt-10) REVERT: G 69 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8069 (ttt-90) REVERT: G 380 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8370 (ttp) REVERT: G 572 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6362 (t80) REVERT: G 648 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7684 (mtt180) REVERT: G 653 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7713 (tp30) outliers start: 17 outliers final: 7 residues processed: 77 average time/residue: 1.3971 time to fit residues: 111.9030 Evaluate side-chains 74 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG 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 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 572 PHE Chi-restraints excluded: chain G residue 648 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.167411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131501 restraints weight = 6141.362| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.22 r_work: 0.3317 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5322 Z= 0.208 Angle : 0.559 7.017 7198 Z= 0.283 Chirality : 0.041 0.136 779 Planarity : 0.004 0.044 924 Dihedral : 5.399 65.572 722 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 : 2.99 % Allowed : 21.68 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.34), residues: 656 helix: 1.50 (0.30), residues: 323 sheet: -0.34 (0.57), residues: 77 loop : 0.24 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 590 HIS 0.003 0.001 HIS G 286 PHE 0.014 0.001 PHE G 391 TYR 0.012 0.001 TYR G 281 ARG 0.003 0.000 ARG G 69 *********************** 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 87 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8153 (mt-10) REVERT: G 69 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8002 (ttt-90) REVERT: G 106 ARG cc_start: 0.6856 (ttt-90) cc_final: 0.5207 (tpt170) REVERT: G 380 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8401 (ttp) REVERT: G 648 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7693 (mtt180) REVERT: G 653 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7757 (tp30) outliers start: 16 outliers final: 8 residues processed: 83 average time/residue: 1.4088 time to fit residues: 121.5909 Evaluate side-chains 79 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG 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 426 GLU Chi-restraints excluded: chain G residue 460 MET Chi-restraints excluded: chain G residue 511 LEU 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 648 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131531 restraints weight = 6210.604| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.24 r_work: 0.3334 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5322 Z= 0.203 Angle : 0.563 8.078 7198 Z= 0.283 Chirality : 0.041 0.137 779 Planarity : 0.004 0.044 924 Dihedral : 5.359 65.590 722 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.80 % Allowed : 22.62 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.34), residues: 656 helix: 1.55 (0.30), residues: 323 sheet: -0.47 (0.57), residues: 79 loop : 0.29 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 590 HIS 0.003 0.001 HIS G 286 PHE 0.014 0.001 PHE G 391 TYR 0.017 0.001 TYR G 651 ARG 0.008 0.000 ARG G 404 *********************** 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 88 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8137 (mt-10) REVERT: G 69 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7941 (ttt-90) REVERT: G 106 ARG cc_start: 0.6771 (ttt-90) cc_final: 0.5143 (tpt170) REVERT: G 380 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8386 (ttp) REVERT: G 404 ARG cc_start: 0.6892 (mmm-85) cc_final: 0.6644 (mmm-85) REVERT: G 437 LEU cc_start: 0.8548 (tp) cc_final: 0.8259 (tp) REVERT: G 648 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7673 (mtt180) outliers start: 15 outliers final: 8 residues processed: 84 average time/residue: 1.4391 time to fit residues: 125.5110 Evaluate side-chains 78 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG 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 426 GLU Chi-restraints excluded: chain G residue 460 MET Chi-restraints excluded: chain G residue 511 LEU 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 648 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 0.0040 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3937 r_free = 0.3937 target = 0.168870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134016 restraints weight = 6206.369| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.20 r_work: 0.3358 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4441 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= 0.194 Angle : 0.570 9.229 7198 Z= 0.284 Chirality : 0.041 0.138 779 Planarity : 0.004 0.044 924 Dihedral : 5.310 65.318 722 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.62 % Allowed : 23.55 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.34), residues: 656 helix: 1.58 (0.30), residues: 323 sheet: -0.35 (0.58), residues: 77 loop : 0.26 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 590 HIS 0.003 0.001 HIS G 194 PHE 0.013 0.001 PHE G 391 TYR 0.017 0.001 TYR G 651 ARG 0.008 0.000 ARG G 404 *********************** 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 84 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8151 (mt-10) REVERT: G 69 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8066 (ttt-90) REVERT: G 106 ARG cc_start: 0.6886 (ttt-90) cc_final: 0.5291 (tpt170) REVERT: G 380 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8397 (ttp) REVERT: G 404 ARG cc_start: 0.6784 (mmm-85) cc_final: 0.6566 (mmm-85) REVERT: G 437 LEU cc_start: 0.8648 (tp) cc_final: 0.8348 (tp) REVERT: G 471 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8981 (mm) REVERT: G 648 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7722 (mtt180) outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 1.3834 time to fit residues: 114.9674 Evaluate side-chains 82 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 288 VAL 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 426 GLU Chi-restraints excluded: chain G residue 460 MET Chi-restraints excluded: chain G residue 471 ILE Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 572 PHE Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain G residue 648 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3946 r_free = 0.3946 target = 0.169476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134748 restraints weight = 6207.225| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.15 r_work: 0.3376 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5322 Z= 0.196 Angle : 0.580 9.087 7198 Z= 0.289 Chirality : 0.040 0.140 779 Planarity : 0.004 0.044 924 Dihedral : 5.308 65.394 722 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.99 % Allowed : 23.36 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.34), residues: 656 helix: 1.56 (0.30), residues: 323 sheet: -0.42 (0.57), residues: 81 loop : 0.28 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 590 HIS 0.002 0.001 HIS G 282 PHE 0.013 0.001 PHE G 391 TYR 0.016 0.001 TYR G 651 ARG 0.007 0.000 ARG G 404 ********************** 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 86 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8154 (mt-10) REVERT: G 106 ARG cc_start: 0.6860 (ttt-90) cc_final: 0.5282 (tpt170) REVERT: G 380 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8352 (ttp) REVERT: G 404 ARG cc_start: 0.6812 (mmm-85) cc_final: 0.6607 (mmm-85) REVERT: G 437 LEU cc_start: 0.8640 (tp) cc_final: 0.8368 (tp) REVERT: G 471 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8989 (mm) REVERT: G 648 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7744 (mtt180) outliers start: 16 outliers final: 11 residues processed: 81 average time/residue: 1.4027 time to fit residues: 117.8388 Evaluate side-chains 81 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 288 VAL 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 426 GLU Chi-restraints excluded: chain G residue 460 MET Chi-restraints excluded: chain G residue 471 ILE Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 572 PHE Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain G residue 648 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131811 restraints weight = 6268.751| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.16 r_work: 0.3332 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4581 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= 0.264 Angle : 0.614 9.080 7198 Z= 0.308 Chirality : 0.042 0.144 779 Planarity : 0.004 0.045 924 Dihedral : 5.506 67.284 722 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.18 % Allowed : 23.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.34), residues: 656 helix: 1.42 (0.30), residues: 325 sheet: -0.41 (0.60), residues: 73 loop : 0.09 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 590 HIS 0.003 0.001 HIS G 282 PHE 0.016 0.001 PHE G 391 TYR 0.018 0.002 TYR G 651 ARG 0.011 0.001 ARG G 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4996.35 seconds wall clock time: 85 minutes 37.05 seconds (5137.05 seconds total)