Starting phenix.real_space_refine on Sat May 10 06:21:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpd_36476/05_2025/8jpd_36476_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpd_36476/05_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_36476/05_2025/8jpd_36476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpd_36476/05_2025/8jpd_36476.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpd_36476/05_2025/8jpd_36476_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpd_36476/05_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-5687/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: 4.09, per 1000 atoms: 0.79 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: 2.57 Conformation dependent library (CDL) restraints added in 678.1 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: 0.63 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: 1.72 Time building geometry restraints manager: 1.87 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: 1.900 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.080 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:14.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.730 ------------------------------------------------------------------------------- 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= 0.247 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 : 4.50 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 Details of bonding type rmsd hydrogen bonds : bond 0.13983 ( 268) hydrogen bonds : angle 6.60525 ( 768) covalent geometry : bond 0.00396 ( 5322) covalent geometry : angle 0.61277 ( 7198) *********************** 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 : 0.549 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: 1.2938 time to fit residues: 195.9148 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 = 0.138407 restraints weight = 6150.066| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.10 r_work: 0.3421 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- 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= 0.161 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 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 268) hydrogen bonds : angle 4.92206 ( 768) covalent geometry : bond 0.00364 ( 5322) covalent geometry : angle 0.60499 ( 7198) *********************** 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 : 0.572 Fit side-chains REVERT: G 106 ARG cc_start: 0.6711 (ttt-90) cc_final: 0.5155 (tpt170) REVERT: G 114 MET cc_start: 0.7738 (tpt) cc_final: 0.7380 (tpt) REVERT: G 117 LEU cc_start: 0.7851 (mt) cc_final: 0.7651 (mp) REVERT: G 135 HIS cc_start: 0.7046 (m-70) cc_final: 0.6829 (m90) REVERT: G 380 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8037 (ttt) REVERT: G 572 PHE cc_start: 0.3830 (m-80) cc_final: 0.3615 (t80) REVERT: G 648 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7715 (mtt180) outliers start: 22 outliers final: 6 residues processed: 107 average time/residue: 1.3047 time to fit residues: 144.9629 Evaluate side-chains 80 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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: 0.1980 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: 3.9990 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 155 GLN 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 = 0.3963 r_free = 0.3963 target = 0.170802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135305 restraints weight = 6173.522| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.12 r_work: 0.3382 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5322 Z= 0.151 Angle : 0.574 6.076 7198 Z= 0.294 Chirality : 0.041 0.136 779 Planarity : 0.004 0.046 924 Dihedral : 5.520 66.242 722 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.93 % Allowed : 17.01 % Favored : 79.07 % 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: 1.13 (0.34), residues: 656 helix: 1.45 (0.30), residues: 322 sheet: 0.08 (0.60), residues: 71 loop : 0.21 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 590 HIS 0.005 0.001 HIS G 194 PHE 0.013 0.001 PHE G 391 TYR 0.011 0.001 TYR G 651 ARG 0.004 0.000 ARG G 431 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 268) hydrogen bonds : angle 4.70719 ( 768) covalent geometry : bond 0.00347 ( 5322) covalent geometry : angle 0.57422 ( 7198) *********************** 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 111 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: G 48 GLU cc_start: 0.8209 (mt-10) cc_final: 0.8008 (mt-10) REVERT: G 106 ARG cc_start: 0.6764 (ttt-90) cc_final: 0.5202 (tpt170) REVERT: G 114 MET cc_start: 0.8092 (tpt) cc_final: 0.7556 (tpt) REVERT: G 135 HIS cc_start: 0.7383 (m-70) cc_final: 0.7155 (m90) REVERT: G 344 LYS cc_start: 0.8337 (mmpt) cc_final: 0.8125 (mmmt) REVERT: G 363 GLN cc_start: 0.8216 (mt0) cc_final: 0.7893 (mt0) REVERT: G 504 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: G 515 GLU cc_start: 0.8550 (pm20) cc_final: 0.8346 (pm20) REVERT: G 648 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7611 (mtt180) REVERT: G 653 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7388 (tp30) outliers start: 21 outliers final: 2 residues processed: 105 average time/residue: 1.3671 time to fit residues: 148.8047 Evaluate side-chains 72 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 192 SER 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: 0.6980 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133863 restraints weight = 6375.301| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.22 r_work: 0.3347 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5322 Z= 0.148 Angle : 0.569 6.059 7198 Z= 0.292 Chirality : 0.041 0.131 779 Planarity : 0.004 0.046 924 Dihedral : 5.485 65.858 722 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.74 % Allowed : 18.88 % Favored : 77.38 % 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: 1.10 (0.34), residues: 656 helix: 1.43 (0.30), residues: 322 sheet: -0.04 (0.59), residues: 71 loop : 0.22 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 590 HIS 0.004 0.001 HIS G 194 PHE 0.046 0.002 PHE G 572 TYR 0.011 0.001 TYR G 281 ARG 0.005 0.000 ARG G 69 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 268) hydrogen bonds : angle 4.63474 ( 768) covalent geometry : bond 0.00350 ( 5322) covalent geometry : angle 0.56938 ( 7198) *********************** 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 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.646 Fit side-chains REVERT: G 15 MET cc_start: 0.5551 (tmt) cc_final: 0.4891 (mmt) REVERT: G 36 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: G 48 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7966 (mt-10) REVERT: G 106 ARG cc_start: 0.6782 (ttt-90) cc_final: 0.5253 (tpt170) REVERT: G 363 GLN cc_start: 0.8227 (mt0) cc_final: 0.7915 (mt0) REVERT: G 380 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8366 (ttp) REVERT: G 431 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7794 (mtp85) REVERT: G 504 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: G 515 GLU cc_start: 0.8565 (pm20) cc_final: 0.8351 (pm20) REVERT: G 624 ILE cc_start: 0.8443 (mm) cc_final: 0.8085 (tt) REVERT: G 648 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7636 (mtt180) REVERT: G 653 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7550 (tp30) outliers start: 20 outliers final: 5 residues processed: 89 average time/residue: 1.4310 time to fit residues: 132.3944 Evaluate side-chains 77 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 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: 10.0000 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 459 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 = 0.168993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133943 restraints weight = 6265.551| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.19 r_work: 0.3362 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5322 Z= 0.144 Angle : 0.564 6.114 7198 Z= 0.287 Chirality : 0.041 0.135 779 Planarity : 0.004 0.045 924 Dihedral : 5.434 65.836 722 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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 (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: 1.10 (0.34), residues: 656 helix: 1.45 (0.30), residues: 323 sheet: -0.06 (0.60), residues: 71 loop : 0.19 (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 194 PHE 0.021 0.001 PHE G 572 TYR 0.011 0.001 TYR G 281 ARG 0.003 0.000 ARG G 69 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 268) hydrogen bonds : angle 4.66930 ( 768) covalent geometry : bond 0.00339 ( 5322) covalent geometry : angle 0.56403 ( 7198) *********************** 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 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: G 36 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: G 48 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7902 (mt-10) REVERT: G 69 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8093 (ttt-90) REVERT: G 90 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7816 (mptt) REVERT: G 106 ARG cc_start: 0.6839 (ttt-90) cc_final: 0.5181 (tpt170) REVERT: G 363 GLN cc_start: 0.8206 (mt0) cc_final: 0.7917 (mt0) REVERT: G 380 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8357 (ttp) REVERT: G 504 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: G 515 GLU cc_start: 0.8531 (pm20) cc_final: 0.8305 (pm20) REVERT: G 624 ILE cc_start: 0.8403 (mm) cc_final: 0.8159 (tt) REVERT: G 648 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7670 (mtt180) REVERT: G 653 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7612 (tp30) outliers start: 18 outliers final: 6 residues processed: 87 average time/residue: 1.3983 time to fit residues: 126.2910 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 : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 GLU 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 504 GLU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 540 LYS Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain G residue 648 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 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 = 0.3901 r_free = 0.3901 target = 0.165849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129649 restraints weight = 6183.071| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.22 r_work: 0.3297 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4083 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= 0.182 Angle : 0.602 6.953 7198 Z= 0.305 Chirality : 0.042 0.134 779 Planarity : 0.004 0.044 924 Dihedral : 5.569 67.237 722 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.30 % Allowed : 19.25 % 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: 1.05 (0.34), residues: 656 helix: 1.43 (0.30), residues: 322 sheet: -0.18 (0.59), residues: 71 loop : 0.18 (0.40), residues: 263 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 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 268) hydrogen bonds : angle 4.71628 ( 768) covalent geometry : bond 0.00437 ( 5322) covalent geometry : angle 0.60220 ( 7198) *********************** 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: 23 poor density : 66 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: G 48 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7914 (mt-10) REVERT: G 69 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8056 (ttt-90) REVERT: G 363 GLN cc_start: 0.8234 (mt0) cc_final: 0.7953 (mt0) REVERT: G 380 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8370 (ttp) REVERT: G 507 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.7914 (ttm110) REVERT: G 515 GLU cc_start: 0.8559 (pm20) cc_final: 0.8328 (pm20) REVERT: G 648 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7667 (mtt180) REVERT: G 653 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7718 (tp30) outliers start: 23 outliers final: 10 residues processed: 83 average time/residue: 1.3127 time to fit residues: 113.4317 Evaluate side-chains 77 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 229 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.167146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131452 restraints weight = 6143.272| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.19 r_work: 0.3338 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5322 Z= 0.140 Angle : 0.561 6.859 7198 Z= 0.285 Chirality : 0.041 0.133 779 Planarity : 0.004 0.044 924 Dihedral : 5.414 65.524 722 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.36 % Allowed : 21.12 % Favored : 75.51 % 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: 1.51 (0.30), residues: 322 sheet: -0.39 (0.56), residues: 79 loop : 0.18 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 590 HIS 0.003 0.001 HIS G 262 PHE 0.014 0.001 PHE G 391 TYR 0.012 0.001 TYR G 281 ARG 0.003 0.000 ARG G 69 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 268) hydrogen bonds : angle 4.60581 ( 768) covalent geometry : bond 0.00328 ( 5322) covalent geometry : angle 0.56086 ( 7198) *********************** 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 91 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: G 48 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7841 (mt-10) REVERT: G 69 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7997 (ttt-90) REVERT: G 106 ARG cc_start: 0.6917 (ttt-90) cc_final: 0.5238 (tpt170) REVERT: G 363 GLN cc_start: 0.8252 (mt0) cc_final: 0.7955 (mt0) REVERT: G 380 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8398 (ttp) REVERT: G 504 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7804 (mm-30) REVERT: G 515 GLU cc_start: 0.8522 (pm20) cc_final: 0.8281 (pm20) REVERT: G 648 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7772 (mtt180) REVERT: G 653 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7755 (tp30) outliers start: 18 outliers final: 9 residues processed: 86 average time/residue: 1.4124 time to fit residues: 126.1212 Evaluate side-chains 79 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 229 MET 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: 0.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.167550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132528 restraints weight = 6216.767| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.17 r_work: 0.3343 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4371 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= 0.150 Angle : 0.580 7.583 7198 Z= 0.293 Chirality : 0.041 0.136 779 Planarity : 0.004 0.044 924 Dihedral : 5.460 66.492 722 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.18 % Allowed : 22.24 % 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: 1.04 (0.34), residues: 656 helix: 1.49 (0.30), residues: 322 sheet: -0.56 (0.56), residues: 79 loop : 0.23 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 590 HIS 0.003 0.001 HIS G 262 PHE 0.015 0.001 PHE G 391 TYR 0.016 0.001 TYR G 651 ARG 0.007 0.001 ARG G 404 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 268) hydrogen bonds : angle 4.63997 ( 768) covalent geometry : bond 0.00355 ( 5322) covalent geometry : angle 0.57985 ( 7198) *********************** 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: 17 poor density : 71 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: G 48 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7892 (mt-10) REVERT: G 380 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8400 (ttp) REVERT: G 404 ARG cc_start: 0.6899 (mmm-85) cc_final: 0.6657 (mmm-85) REVERT: G 437 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8468 (tp) REVERT: G 504 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7903 (mm-30) REVERT: G 515 GLU cc_start: 0.8543 (pm20) cc_final: 0.8317 (pm20) REVERT: G 648 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7766 (mtt180) outliers start: 17 outliers final: 10 residues processed: 82 average time/residue: 1.4932 time to fit residues: 127.0391 Evaluate side-chains 78 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 229 MET 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 437 LEU 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: 0.5980 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.168535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133790 restraints weight = 6194.616| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.15 r_work: 0.3368 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5322 Z= 0.128 Angle : 0.565 8.349 7198 Z= 0.284 Chirality : 0.040 0.139 779 Planarity : 0.004 0.044 924 Dihedral : 5.328 65.064 722 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.36 % Allowed : 22.80 % 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: 1.06 (0.34), residues: 656 helix: 1.53 (0.30), residues: 322 sheet: -0.58 (0.55), residues: 81 loop : 0.22 (0.41), residues: 253 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 0.020 0.001 TYR G 651 ARG 0.007 0.000 ARG G 404 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 268) hydrogen bonds : angle 4.59684 ( 768) covalent geometry : bond 0.00299 ( 5322) covalent geometry : angle 0.56516 ( 7198) *********************** 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 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: G 48 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7839 (mt-10) REVERT: G 106 ARG cc_start: 0.6952 (ttt-90) cc_final: 0.5338 (tpt170) REVERT: G 380 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8386 (ttp) REVERT: G 404 ARG cc_start: 0.6821 (mmm-85) cc_final: 0.6603 (mmm-85) REVERT: G 437 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8436 (tp) REVERT: G 471 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8984 (mm) REVERT: G 504 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7861 (mm-30) REVERT: G 515 GLU cc_start: 0.8481 (pm20) cc_final: 0.8258 (pm20) REVERT: G 579 ARG cc_start: 0.8243 (mtp85) cc_final: 0.8035 (mtt-85) REVERT: G 648 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7788 (mtt180) outliers start: 18 outliers final: 9 residues processed: 84 average time/residue: 1.2865 time to fit residues: 112.4844 Evaluate side-chains 80 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 426 GLU Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 460 MET Chi-restraints excluded: chain G residue 471 ILE 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 624 ILE 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: 0.8980 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 48 optimal weight: 0.0040 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 14 optimal weight: 0.0040 overall best weight: 0.3404 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.170805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136314 restraints weight = 6220.210| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.16 r_work: 0.3407 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4523 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= 0.110 Angle : 0.554 9.128 7198 Z= 0.278 Chirality : 0.040 0.137 779 Planarity : 0.004 0.043 924 Dihedral : 5.193 64.068 722 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.06 % Allowed : 24.11 % 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: 1.15 (0.34), residues: 656 helix: 1.55 (0.30), residues: 323 sheet: -0.37 (0.56), residues: 79 loop : 0.26 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 590 HIS 0.002 0.001 HIS G 262 PHE 0.011 0.001 PHE G 391 TYR 0.011 0.001 TYR G 281 ARG 0.007 0.000 ARG G 404 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 268) hydrogen bonds : angle 4.51406 ( 768) covalent geometry : bond 0.00254 ( 5322) covalent geometry : angle 0.55437 ( 7198) ********************** 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 87 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: G 15 MET cc_start: 0.5474 (tmt) cc_final: 0.4890 (pp-130) REVERT: G 48 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7827 (mt-10) REVERT: G 106 ARG cc_start: 0.6814 (ttt-90) cc_final: 0.5272 (tpt170) REVERT: G 380 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8374 (ttp) REVERT: G 437 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8466 (tp) REVERT: G 471 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8985 (mm) REVERT: G 504 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7826 (mm-30) REVERT: G 515 GLU cc_start: 0.8429 (pm20) cc_final: 0.8111 (pt0) REVERT: G 648 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7720 (mtt180) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 1.4518 time to fit residues: 126.3629 Evaluate side-chains 79 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 437 LEU Chi-restraints excluded: chain G residue 460 MET Chi-restraints excluded: chain G residue 471 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.167733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132746 restraints weight = 6256.545| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.15 r_work: 0.3338 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4629 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= 0.159 Angle : 0.603 8.982 7198 Z= 0.303 Chirality : 0.041 0.143 779 Planarity : 0.004 0.044 924 Dihedral : 5.432 66.850 722 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.80 % Allowed : 24.11 % 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: 1.10 (0.34), residues: 656 helix: 1.50 (0.30), residues: 323 sheet: -0.51 (0.58), residues: 79 loop : 0.31 (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 282 PHE 0.014 0.001 PHE G 391 TYR 0.022 0.002 TYR G 651 ARG 0.008 0.001 ARG G 404 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 268) hydrogen bonds : angle 4.61896 ( 768) covalent geometry : bond 0.00381 ( 5322) covalent geometry : angle 0.60331 ( 7198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4831.48 seconds wall clock time: 83 minutes 41.45 seconds (5021.45 seconds total)