Starting phenix.real_space_refine on Mon Jan 13 21:45:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2d_38851/01_2025/8y2d_38851.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2d_38851/01_2025/8y2d_38851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y2d_38851/01_2025/8y2d_38851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2d_38851/01_2025/8y2d_38851.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2d_38851/01_2025/8y2d_38851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2d_38851/01_2025/8y2d_38851.cif" } resolution = 2.8 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= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 23 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2791 2.51 5 N 658 2.21 5 O 714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4189 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4171 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 504} Chain breaks: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 18 Unusual residues: {' CL': 1, ' NA': 2, 'LDP': 1} Classifications: {'undetermined': 4, 'water': 4} Link IDs: {None: 7} Time building chain proxies: 3.22, per 1000 atoms: 0.77 Number of scatterers: 4189 At special positions: 0 Unit cell: (71.4, 68, 92.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 23 16.00 Na 2 11.00 O 714 8.00 N 658 7.00 C 2791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " distance=2.03 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: 1.15 Conformation dependent library (CDL) restraints added in 487.6 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 78.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 68 through 78 removed outlier: 3.986A pdb=" N SER A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 4.008A pdb=" N VAL A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 98 through 125 removed outlier: 5.078A pdb=" N MET A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.761A pdb=" N TRP A 132 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 133 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 134 " --> pdb=" O VAL A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 129 through 134' Processing helix chain 'A' and resid 140 through 170 removed outlier: 3.573A pdb=" N VAL A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 237 through 255 removed outlier: 3.507A pdb=" N ALA A 242 " --> pdb=" O TRP A 238 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 287 removed outlier: 4.119A pdb=" N THR A 271 " --> pdb=" O TRP A 267 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Proline residue: A 273 - end of helix removed outlier: 3.638A pdb=" N THR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.900A pdb=" N GLY A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 323 Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.566A pdb=" N ALA A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 375 removed outlier: 3.679A pdb=" N ASP A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.872A pdb=" N TYR A 394 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.628A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 461 Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.947A pdb=" N THR A 465 " --> pdb=" O PHE A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 467 through 479 removed outlier: 4.024A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 498 removed outlier: 4.135A pdb=" N LEU A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 517 through 542 removed outlier: 5.247A pdb=" N SER A 528 " --> pdb=" O TRP A 524 " (cutoff:3.500A) Proline residue: A 529 - end of helix Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.659A pdb=" N ASN A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 removed outlier: 4.091A pdb=" N ILE A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 removed outlier: 3.632A pdb=" N TYR A 548 " --> pdb=" O TYR A 551 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1247 1.34 - 1.46: 1054 1.46 - 1.58: 1977 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4312 Sorted by residual: bond pdb=" CG PRO A 584 " pdb=" CD PRO A 584 " ideal model delta sigma weight residual 1.503 1.557 -0.054 3.40e-02 8.65e+02 2.51e+00 bond pdb=" C8 LDP A 701 " pdb=" N1 LDP A 701 " ideal model delta sigma weight residual 1.456 1.484 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" CB PRO A 584 " pdb=" CG PRO A 584 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.40e-01 bond pdb=" C7 LDP A 701 " pdb=" C8 LDP A 701 " ideal model delta sigma weight residual 1.528 1.511 0.017 2.00e-02 2.50e+03 6.90e-01 bond pdb=" C LEU A 583 " pdb=" N PRO A 584 " ideal model delta sigma weight residual 1.328 1.337 -0.009 1.25e-02 6.40e+03 5.74e-01 ... (remaining 4307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 5670 1.08 - 2.16: 152 2.16 - 3.24: 44 3.24 - 4.32: 10 4.32 - 5.40: 10 Bond angle restraints: 5886 Sorted by residual: angle pdb=" CA TYR A 88 " pdb=" CB TYR A 88 " pdb=" CG TYR A 88 " ideal model delta sigma weight residual 113.90 118.53 -4.63 1.80e+00 3.09e-01 6.61e+00 angle pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" CD PRO A 584 " ideal model delta sigma weight residual 112.00 109.32 2.68 1.40e+00 5.10e-01 3.67e+00 angle pdb=" N PRO A 584 " pdb=" CA PRO A 584 " pdb=" C PRO A 584 " ideal model delta sigma weight residual 111.03 114.44 -3.41 1.78e+00 3.16e-01 3.66e+00 angle pdb=" CA TYR A 343 " pdb=" CB TYR A 343 " pdb=" CG TYR A 343 " ideal model delta sigma weight residual 113.90 117.16 -3.26 1.80e+00 3.09e-01 3.29e+00 angle pdb=" C CYS A 342 " pdb=" N TYR A 343 " pdb=" CA TYR A 343 " ideal model delta sigma weight residual 120.44 122.71 -2.27 1.30e+00 5.92e-01 3.06e+00 ... (remaining 5881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 2057 15.65 - 31.29: 260 31.29 - 46.94: 87 46.94 - 62.59: 23 62.59 - 78.23: 2 Dihedral angle restraints: 2429 sinusoidal: 908 harmonic: 1521 Sorted by residual: dihedral pdb=" CA ALA A 397 " pdb=" C ALA A 397 " pdb=" N ILE A 398 " pdb=" CA ILE A 398 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LEU A 526 " pdb=" C LEU A 526 " pdb=" N VAL A 527 " pdb=" CA VAL A 527 " ideal model delta harmonic sigma weight residual 180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG A 443 " pdb=" CD ARG A 443 " pdb=" NE ARG A 443 " pdb=" CZ ARG A 443 " ideal model delta sinusoidal sigma weight residual -90.00 -134.37 44.37 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 2426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 361 0.024 - 0.047: 177 0.047 - 0.071: 85 0.071 - 0.095: 24 0.095 - 0.118: 18 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA VAL A 377 " pdb=" N VAL A 377 " pdb=" C VAL A 377 " pdb=" CB VAL A 377 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA PRO A 136 " pdb=" N PRO A 136 " pdb=" C PRO A 136 " pdb=" CB PRO A 136 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ASP A 232 " pdb=" N ASP A 232 " pdb=" C ASP A 232 " pdb=" CB ASP A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 662 not shown) Planarity restraints: 721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 523 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C CYS A 523 " -0.032 2.00e-02 2.50e+03 pdb=" O CYS A 523 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP A 524 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 494 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.77e+00 pdb=" C GLY A 494 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY A 494 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 495 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 186 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 187 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " -0.023 5.00e-02 4.00e+02 ... (remaining 718 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 836 2.77 - 3.30: 3722 3.30 - 3.84: 6918 3.84 - 4.37: 7768 4.37 - 4.90: 14147 Nonbonded interactions: 33391 Sorted by model distance: nonbonded pdb=" O VAL A 78 " pdb="NA NA A 703 " model vdw 2.240 2.470 nonbonded pdb=" O HOH A 802 " pdb=" O HOH A 804 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASN A 82 " pdb="NA NA A 702 " model vdw 2.277 2.470 nonbonded pdb=" O ALA A 77 " pdb="NA NA A 702 " model vdw 2.292 2.470 nonbonded pdb=" NH2 ARG A 125 " pdb=" O ASN A 336 " model vdw 2.305 3.120 ... (remaining 33386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.003 0.054 4312 Z= 0.178 Angle : 0.505 5.405 5886 Z= 0.264 Chirality : 0.037 0.118 665 Planarity : 0.004 0.041 721 Dihedral : 16.286 78.233 1454 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 25.28 % Favored : 74.72 % 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 (0.38), residues: 522 helix: 1.59 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.43 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 PHE 0.011 0.001 PHE A 412 TYR 0.021 0.001 TYR A 303 ARG 0.004 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.461 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 1.1060 time to fit residues: 60.1039 Evaluate side-chains 44 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.0020 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111564 restraints weight = 5082.612| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.68 r_work: 0.3084 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4312 Z= 0.200 Angle : 0.531 7.205 5886 Z= 0.271 Chirality : 0.038 0.122 665 Planarity : 0.004 0.045 721 Dihedral : 4.042 25.586 570 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.61 % Allowed : 23.02 % Favored : 73.36 % 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: 0.90 (0.38), residues: 522 helix: 1.51 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.74 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 PHE 0.014 0.001 PHE A 412 TYR 0.011 0.001 TYR A 575 ARG 0.003 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.473 Fit side-chains REVERT: A 610 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6728 (ttm110) outliers start: 16 outliers final: 7 residues processed: 54 average time/residue: 0.9919 time to fit residues: 56.3422 Evaluate side-chains 49 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 1 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** 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 = 0.3538 r_free = 0.3538 target = 0.138753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.118688 restraints weight = 5009.790| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.70 r_work: 0.3122 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4312 Z= 0.159 Angle : 0.482 6.134 5886 Z= 0.248 Chirality : 0.037 0.117 665 Planarity : 0.004 0.042 721 Dihedral : 3.950 24.719 570 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.16 % Allowed : 23.70 % Favored : 73.14 % 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 (0.38), residues: 522 helix: 1.67 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.81 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 PHE 0.010 0.001 PHE A 412 TYR 0.015 0.001 TYR A 303 ARG 0.003 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.446 Fit side-chains REVERT: A 593 TYR cc_start: 0.7749 (m-80) cc_final: 0.7486 (m-80) REVERT: A 610 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6685 (ttm110) outliers start: 14 outliers final: 7 residues processed: 50 average time/residue: 0.9575 time to fit residues: 50.3413 Evaluate side-chains 49 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.0070 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** 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 = 0.3435 r_free = 0.3435 target = 0.130991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110623 restraints weight = 5075.768| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.67 r_work: 0.3073 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4312 Z= 0.206 Angle : 0.521 6.051 5886 Z= 0.269 Chirality : 0.038 0.121 665 Planarity : 0.004 0.043 721 Dihedral : 4.069 24.700 570 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.39 % Allowed : 23.70 % Favored : 72.91 % 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: 0.94 (0.38), residues: 522 helix: 1.57 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.85 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.003 0.001 HIS A 165 PHE 0.015 0.001 PHE A 412 TYR 0.015 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.424 Fit side-chains REVERT: A 250 LEU cc_start: 0.8032 (tp) cc_final: 0.7677 (tp) REVERT: A 272 MET cc_start: 0.6998 (ttm) cc_final: 0.6035 (tmt) REVERT: A 593 TYR cc_start: 0.7764 (m-80) cc_final: 0.7518 (m-80) REVERT: A 610 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6687 (ttm110) outliers start: 15 outliers final: 9 residues processed: 53 average time/residue: 0.9343 time to fit residues: 52.1886 Evaluate side-chains 50 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** 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 = 0.3448 r_free = 0.3448 target = 0.132332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111623 restraints weight = 5202.035| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.71 r_work: 0.3112 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4312 Z= 0.155 Angle : 0.479 5.931 5886 Z= 0.247 Chirality : 0.037 0.116 665 Planarity : 0.004 0.041 721 Dihedral : 3.962 24.378 570 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.93 % Allowed : 23.70 % Favored : 73.36 % 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 (0.38), residues: 522 helix: 1.76 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.87 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 PHE 0.009 0.001 PHE A 412 TYR 0.009 0.001 TYR A 343 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.413 Fit side-chains REVERT: A 250 LEU cc_start: 0.8004 (tp) cc_final: 0.7647 (tp) REVERT: A 510 GLN cc_start: 0.7087 (tp40) cc_final: 0.6568 (OUTLIER) REVERT: A 593 TYR cc_start: 0.7718 (m-80) cc_final: 0.7489 (m-80) REVERT: A 610 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6706 (ttm110) outliers start: 13 outliers final: 8 residues processed: 58 average time/residue: 1.0630 time to fit residues: 64.4083 Evaluate side-chains 51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** 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 = 0.3427 r_free = 0.3427 target = 0.130252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109855 restraints weight = 5032.381| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.67 r_work: 0.3061 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4312 Z= 0.232 Angle : 0.541 5.715 5886 Z= 0.280 Chirality : 0.039 0.124 665 Planarity : 0.004 0.043 721 Dihedral : 4.136 24.574 570 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.61 % Allowed : 23.48 % Favored : 72.91 % 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: 0.86 (0.38), residues: 522 helix: 1.53 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.92 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.003 0.001 HIS A 165 PHE 0.016 0.002 PHE A 412 TYR 0.016 0.001 TYR A 303 ARG 0.001 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.489 Fit side-chains REVERT: A 250 LEU cc_start: 0.8119 (tp) cc_final: 0.7728 (tp) REVERT: A 272 MET cc_start: 0.7057 (ttm) cc_final: 0.6125 (tmt) REVERT: A 593 TYR cc_start: 0.7814 (m-80) cc_final: 0.7584 (m-80) REVERT: A 610 ARG cc_start: 0.7208 (ttp80) cc_final: 0.6733 (ttm110) outliers start: 16 outliers final: 9 residues processed: 56 average time/residue: 0.9361 time to fit residues: 55.0822 Evaluate side-chains 52 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 511 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** 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 = 0.3518 r_free = 0.3518 target = 0.137034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116933 restraints weight = 5008.450| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.70 r_work: 0.3072 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4312 Z= 0.171 Angle : 0.501 5.855 5886 Z= 0.259 Chirality : 0.038 0.116 665 Planarity : 0.004 0.042 721 Dihedral : 4.042 24.476 570 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.16 % Allowed : 24.15 % Favored : 72.69 % 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: 0.99 (0.38), residues: 522 helix: 1.67 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.94 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 PHE 0.011 0.001 PHE A 412 TYR 0.010 0.001 TYR A 575 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.425 Fit side-chains REVERT: A 226 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: A 250 LEU cc_start: 0.8058 (tp) cc_final: 0.7665 (tp) REVERT: A 272 MET cc_start: 0.6973 (ttm) cc_final: 0.6005 (tmt) REVERT: A 510 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6617 (mp10) REVERT: A 610 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6648 (ttm110) outliers start: 14 outliers final: 9 residues processed: 54 average time/residue: 0.9343 time to fit residues: 53.0128 Evaluate side-chains 54 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** 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 = 0.3508 r_free = 0.3508 target = 0.136187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116129 restraints weight = 4977.218| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.69 r_work: 0.3060 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4312 Z= 0.200 Angle : 0.521 5.758 5886 Z= 0.269 Chirality : 0.038 0.123 665 Planarity : 0.004 0.043 721 Dihedral : 4.080 24.438 570 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.39 % Allowed : 23.93 % Favored : 72.69 % 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: 0.90 (0.38), residues: 522 helix: 1.57 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.92 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 PHE 0.013 0.001 PHE A 412 TYR 0.018 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.414 Fit side-chains REVERT: A 226 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: A 250 LEU cc_start: 0.8088 (tp) cc_final: 0.7692 (tp) REVERT: A 272 MET cc_start: 0.7002 (ttm) cc_final: 0.6044 (tmt) REVERT: A 510 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6620 (mp10) REVERT: A 593 TYR cc_start: 0.7884 (m-80) cc_final: 0.7609 (m-80) REVERT: A 610 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6677 (ttm110) outliers start: 15 outliers final: 10 residues processed: 54 average time/residue: 0.9343 time to fit residues: 53.0511 Evaluate side-chains 54 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** 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 = 0.3462 r_free = 0.3462 target = 0.133292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.112898 restraints weight = 5048.751| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.68 r_work: 0.3101 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4312 Z= 0.157 Angle : 0.486 5.820 5886 Z= 0.251 Chirality : 0.037 0.133 665 Planarity : 0.004 0.044 721 Dihedral : 3.961 24.177 570 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.16 % Allowed : 24.15 % Favored : 72.69 % 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: 1.00 (0.38), residues: 522 helix: 1.60 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.89 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.001 0.000 HIS A 165 PHE 0.009 0.001 PHE A 412 TYR 0.019 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.435 Fit side-chains REVERT: A 250 LEU cc_start: 0.8054 (tp) cc_final: 0.7653 (tp) REVERT: A 272 MET cc_start: 0.6983 (ttm) cc_final: 0.6011 (tmt) REVERT: A 510 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6615 (mp10) REVERT: A 593 TYR cc_start: 0.7822 (m-80) cc_final: 0.7618 (m-80) REVERT: A 610 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6655 (ttm110) outliers start: 14 outliers final: 7 residues processed: 55 average time/residue: 0.9224 time to fit residues: 53.3814 Evaluate side-chains 52 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** 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 = 0.3488 r_free = 0.3488 target = 0.135109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.114829 restraints weight = 5062.656| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.68 r_work: 0.3111 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4312 Z= 0.143 Angle : 0.474 5.577 5886 Z= 0.244 Chirality : 0.037 0.124 665 Planarity : 0.004 0.044 721 Dihedral : 3.832 23.783 570 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.26 % Allowed : 25.06 % Favored : 72.69 % 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 (0.38), residues: 522 helix: 1.68 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.87 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 PHE 0.008 0.001 PHE A 412 TYR 0.019 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.454 Fit side-chains REVERT: A 250 LEU cc_start: 0.8003 (tp) cc_final: 0.7650 (tp) REVERT: A 393 ILE cc_start: 0.7332 (mm) cc_final: 0.7126 (tp) REVERT: A 441 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.5722 (pp) REVERT: A 610 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6654 (ttm110) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 1.0293 time to fit residues: 59.3538 Evaluate side-chains 52 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 0.0020 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** 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 = 0.3471 r_free = 0.3471 target = 0.134514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.113865 restraints weight = 5061.249| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.69 r_work: 0.3127 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4312 Z= 0.131 Angle : 0.464 5.836 5886 Z= 0.238 Chirality : 0.037 0.124 665 Planarity : 0.004 0.043 721 Dihedral : 3.759 23.586 570 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.03 % Allowed : 25.28 % Favored : 72.69 % 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: 1.20 (0.38), residues: 522 helix: 1.75 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.81 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.001 0.000 HIS A 165 PHE 0.007 0.001 PHE A 534 TYR 0.019 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.53 seconds wall clock time: 49 minutes 25.73 seconds (2965.73 seconds total)