Starting phenix.real_space_refine on Wed Jul 1 23:32:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2d_38851/07_2026/8y2d_38851.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2d_38851/07_2026/8y2d_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_38851/07_2026/8y2d_38851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2d_38851/07_2026/8y2d_38851.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2d_38851/07_2026/8y2d_38851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2d_38851/07_2026/8y2d_38851.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.068 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 15 Ad-hoc single atom residues: {' NA': 2, ' CL': 1} Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 3} Chain breaks: 3 Time building chain proxies: 0.73, per 1000 atoms: 0.17 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: 0.31 Conformation dependent library (CDL) restraints added in 141.6 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: 0.08 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: 0.38 Time building geometry restraints manager: 0.43 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 3.210 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 3.210 nonbonded pdb=" O ALA A 77 " pdb="NA NA A 702 " model vdw 2.292 3.210 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.780 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 4313 Z= 0.121 Angle : 0.505 5.405 5888 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (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 ARG 0.004 0.000 ARG A 125 TYR 0.021 0.001 TYR A 303 PHE 0.011 0.001 PHE A 412 TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 4312) covalent geometry : angle 0.50532 / 0.26 ( 5886) SS BOND : bond 0.00121 / 0.06 ( 1) SS BOND : angle 0.26733 / 0.16 ( 2) hydrogen bonds : bond 0.14199 / 9.87 ( 256) hydrogen bonds : angle 4.16593 / 2.96 ( 747) *********************** 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 : 0.141 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3618 time to fit residues: 19.6447 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 : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3428 r_free = 0.3428 target = 0.130822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110186 restraints weight = 5142.718| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.70 r_work: 0.3101 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4313 Z= 0.124 Angle : 0.514 7.494 5888 Z= 0.262 Chirality : 0.038 0.120 665 Planarity : 0.004 0.043 721 Dihedral : 3.964 25.438 570 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.16 % Allowed : 23.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.38), residues: 522 helix: 1.57 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.72 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.010 0.001 TYR A 575 PHE 0.012 0.001 PHE A 412 TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 4312) covalent geometry : angle 0.51415 / 0.26 ( 5886) SS BOND : bond 0.00147 / 0.08 ( 1) SS BOND : angle 0.35805 / 0.21 ( 2) hydrogen bonds : bond 0.05419 / 3.64 ( 256) hydrogen bonds : angle 3.77180 / 2.67 ( 747) *********************** 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 61 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.089 Fit side-chains REVERT: A 510 GLN cc_start: 0.7112 (tp40) cc_final: 0.6602 (mp-120) REVERT: A 610 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6782 (ttm110) outliers start: 14 outliers final: 5 residues processed: 57 average time/residue: 0.3627 time to fit residues: 21.5481 Evaluate side-chains 46 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.091 ------------------------------------------------------------------------------- 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 398 ILE 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 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3415 r_free = 0.3415 target = 0.129659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109267 restraints weight = 5110.285| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.67 r_work: 0.3070 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4313 Z= 0.147 Angle : 0.542 6.560 5888 Z= 0.279 Chirality : 0.039 0.123 665 Planarity : 0.004 0.044 721 Dihedral : 4.128 25.137 570 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.84 % Allowed : 23.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.38), residues: 522 helix: 1.48 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.92 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.015 0.001 TYR A 303 PHE 0.016 0.001 PHE A 412 TRP 0.011 0.001 TRP A 132 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4312) covalent geometry : angle 0.54198 / 0.28 ( 5886) SS BOND : bond 0.00225 / 0.12 ( 1) SS BOND : angle 0.35944 / 0.21 ( 2) hydrogen bonds : bond 0.06012 / 4.02 ( 256) hydrogen bonds : angle 3.91541 / 2.76 ( 747) *********************** 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 58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.127 Fit side-chains REVERT: A 232 ASP cc_start: 0.8381 (t0) cc_final: 0.8177 (t0) REVERT: A 272 MET cc_start: 0.7101 (ttm) cc_final: 0.6119 (tmt) REVERT: A 593 TYR cc_start: 0.7805 (m-80) cc_final: 0.7544 (m-80) REVERT: A 610 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6732 (ttm110) outliers start: 17 outliers final: 10 residues processed: 53 average time/residue: 0.3483 time to fit residues: 19.4563 Evaluate side-chains 51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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 493 ILE 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 20 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3522 r_free = 0.3522 target = 0.137255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117264 restraints weight = 4992.409| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.70 r_work: 0.3094 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4313 Z= 0.117 Angle : 0.492 6.280 5888 Z= 0.255 Chirality : 0.037 0.116 665 Planarity : 0.004 0.042 721 Dihedral : 4.008 24.577 570 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.38), residues: 522 helix: 1.61 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.91 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.009 0.001 TYR A 343 PHE 0.011 0.001 PHE A 412 TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4312) covalent geometry : angle 0.49192 / 0.25 ( 5886) SS BOND : bond 0.00118 / 0.06 ( 1) SS BOND : angle 0.47803 / 0.25 ( 2) hydrogen bonds : bond 0.05165 / 3.46 ( 256) hydrogen bonds : angle 3.84963 / 2.72 ( 747) *********************** 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 57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.154 Fit side-chains REVERT: A 226 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7681 (mt0) REVERT: A 232 ASP cc_start: 0.8312 (t0) cc_final: 0.8086 (t0) REVERT: A 593 TYR cc_start: 0.7764 (m-80) cc_final: 0.7517 (m-80) REVERT: A 610 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6705 (ttm110) outliers start: 15 outliers final: 7 residues processed: 51 average time/residue: 0.3694 time to fit residues: 19.8434 Evaluate side-chains 51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 355 LEU Chi-restraints excluded: chain A residue 398 ILE 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 6 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 14 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3453 r_free = 0.3453 target = 0.132757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112295 restraints weight = 5111.765| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.68 r_work: 0.3113 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4313 Z= 0.106 Angle : 0.469 5.727 5888 Z= 0.242 Chirality : 0.037 0.117 665 Planarity : 0.004 0.041 721 Dihedral : 3.888 24.093 570 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.61 % Allowed : 23.93 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.38), residues: 522 helix: 1.74 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.89 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.017 0.001 TYR A 303 PHE 0.009 0.001 PHE A 412 TRP 0.009 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 4312) covalent geometry : angle 0.46906 / 0.24 ( 5886) SS BOND : bond 0.00146 / 0.08 ( 1) SS BOND : angle 0.65655 / 0.35 ( 2) hydrogen bonds : bond 0.04692 / 3.14 ( 256) hydrogen bonds : angle 3.79623 / 2.68 ( 747) *********************** 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 62 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.158 Fit side-chains REVERT: A 226 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: A 232 ASP cc_start: 0.8273 (t0) cc_final: 0.8012 (t0) REVERT: A 510 GLN cc_start: 0.7060 (tp40) cc_final: 0.6533 (OUTLIER) REVERT: A 593 TYR cc_start: 0.7746 (m-80) cc_final: 0.7516 (m-80) REVERT: A 610 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6687 (ttm110) outliers start: 16 outliers final: 8 residues processed: 57 average time/residue: 0.3763 time to fit residues: 22.4585 Evaluate side-chains 56 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.087 ------------------------------------------------------------------------------- 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 398 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 493 ILE 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 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3464 r_free = 0.3464 target = 0.133252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112769 restraints weight = 5168.271| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.71 r_work: 0.3105 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4313 Z= 0.109 Angle : 0.475 5.752 5888 Z= 0.245 Chirality : 0.037 0.116 665 Planarity : 0.004 0.041 721 Dihedral : 3.869 24.024 570 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.93 % Allowed : 24.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.38), residues: 522 helix: 1.61 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.90 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.017 0.001 TYR A 303 PHE 0.010 0.001 PHE A 412 TRP 0.010 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 4312) covalent geometry : angle 0.47475 / 0.24 ( 5886) SS BOND : bond 0.00170 / 0.09 ( 1) SS BOND : angle 0.40730 / 0.22 ( 2) hydrogen bonds : bond 0.04801 / 3.22 ( 256) hydrogen bonds : angle 3.80670 / 2.68 ( 747) *********************** 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 61 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.148 Fit side-chains REVERT: A 232 ASP cc_start: 0.8274 (t0) cc_final: 0.8012 (t0) REVERT: A 250 LEU cc_start: 0.8020 (tp) cc_final: 0.7682 (tp) REVERT: A 510 GLN cc_start: 0.7069 (tp40) cc_final: 0.6556 (OUTLIER) REVERT: A 593 TYR cc_start: 0.7742 (m-80) cc_final: 0.7504 (m-80) REVERT: A 610 ARG cc_start: 0.7163 (ttp80) cc_final: 0.6694 (ttm110) outliers start: 13 outliers final: 8 residues processed: 57 average time/residue: 0.3706 time to fit residues: 22.1071 Evaluate side-chains 51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 454 LEU Chi-restraints excluded: chain A residue 493 ILE 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 35 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 0.0370 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3437 r_free = 0.3437 target = 0.130776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.110501 restraints weight = 5146.997| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.69 r_work: 0.3069 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4313 Z= 0.159 Angle : 0.553 5.758 5888 Z= 0.286 Chirality : 0.039 0.125 665 Planarity : 0.004 0.043 721 Dihedral : 4.149 24.584 570 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.39 % Allowed : 23.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.38), residues: 522 helix: 1.49 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -2.00 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 344 TYR 0.017 0.002 TYR A 303 PHE 0.017 0.002 PHE A 412 TRP 0.012 0.001 TRP A 132 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 4312) covalent geometry : angle 0.55262 / 0.29 ( 5886) SS BOND : bond 0.00314 / 0.17 ( 1) SS BOND : angle 0.55445 / 0.30 ( 2) hydrogen bonds : bond 0.06259 / 4.18 ( 256) hydrogen bonds : angle 4.00118 / 2.82 ( 747) *********************** 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 59 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.124 Fit side-chains REVERT: A 232 ASP cc_start: 0.8372 (t0) cc_final: 0.8099 (t0) REVERT: A 250 LEU cc_start: 0.8103 (tp) cc_final: 0.7704 (tp) REVERT: A 272 MET cc_start: 0.7038 (ttm) cc_final: 0.6113 (tmt) REVERT: A 593 TYR cc_start: 0.7796 (m-80) cc_final: 0.7548 (m-80) REVERT: A 610 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6708 (ttm110) outliers start: 15 outliers final: 9 residues processed: 55 average time/residue: 0.3799 time to fit residues: 21.8688 Evaluate side-chains 52 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 342 CYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 398 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3524 r_free = 0.3524 target = 0.137550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.117476 restraints weight = 5003.423| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.70 r_work: 0.3109 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4313 Z= 0.114 Angle : 0.489 5.883 5888 Z= 0.254 Chirality : 0.037 0.116 665 Planarity : 0.004 0.043 721 Dihedral : 4.009 24.412 570 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.48 % Allowed : 23.93 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.38), residues: 522 helix: 1.66 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.95 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.010 0.001 TYR A 343 PHE 0.010 0.001 PHE A 412 TRP 0.010 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 4312) covalent geometry : angle 0.48922 / 0.25 ( 5886) SS BOND : bond 0.00168 / 0.09 ( 1) SS BOND : angle 0.39726 / 0.22 ( 2) hydrogen bonds : bond 0.05041 / 3.38 ( 256) hydrogen bonds : angle 3.88495 / 2.74 ( 747) *********************** 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 53 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.130 Fit side-chains REVERT: A 232 ASP cc_start: 0.8297 (t0) cc_final: 0.8039 (t0) REVERT: A 250 LEU cc_start: 0.8046 (tp) cc_final: 0.7678 (tp) REVERT: A 272 MET cc_start: 0.6962 (ttm) cc_final: 0.6005 (tmt) REVERT: A 441 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.5830 (pp) REVERT: A 593 TYR cc_start: 0.7758 (m-80) cc_final: 0.7538 (m-80) REVERT: A 610 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6671 (ttm110) outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 0.3613 time to fit residues: 18.8583 Evaluate side-chains 51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 300 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3466 r_free = 0.3466 target = 0.133991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113332 restraints weight = 5152.528| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.70 r_work: 0.3120 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4313 Z= 0.100 Angle : 0.459 5.537 5888 Z= 0.236 Chirality : 0.036 0.118 665 Planarity : 0.004 0.042 721 Dihedral : 3.812 23.694 570 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.03 % Allowed : 24.38 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (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 ARG 0.002 0.000 ARG A 125 TYR 0.021 0.001 TYR A 303 PHE 0.007 0.001 PHE A 412 TRP 0.009 0.001 TRP A 132 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 4312) covalent geometry : angle 0.45912 / 0.24 ( 5886) SS BOND : bond 0.00120 / 0.06 ( 1) SS BOND : angle 0.33233 / 0.19 ( 2) hydrogen bonds : bond 0.04316 / 2.89 ( 256) hydrogen bonds : angle 3.76444 / 2.65 ( 747) *********************** 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 53 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.115 Fit side-chains REVERT: A 232 ASP cc_start: 0.8261 (t0) cc_final: 0.8004 (t0) REVERT: A 250 LEU cc_start: 0.7990 (tp) cc_final: 0.7628 (tp) REVERT: A 441 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.5701 (pp) REVERT: A 593 TYR cc_start: 0.7717 (m-80) cc_final: 0.7488 (m-80) REVERT: A 610 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6639 (ttm110) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.3244 time to fit residues: 17.3708 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 : 0.139 ------------------------------------------------------------------------------- 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 300 VAL 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 34 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3448 r_free = 0.3448 target = 0.132372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111736 restraints weight = 5064.968| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.69 r_work: 0.3133 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4313 Z= 0.114 Angle : 0.488 5.592 5888 Z= 0.250 Chirality : 0.037 0.116 665 Planarity : 0.004 0.042 721 Dihedral : 3.856 23.886 570 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.03 % Allowed : 24.38 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.38), residues: 522 helix: 1.61 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.90 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.019 0.001 TYR A 303 PHE 0.010 0.001 PHE A 412 TRP 0.010 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 4312) covalent geometry : angle 0.48811 / 0.25 ( 5886) SS BOND : bond 0.00169 / 0.09 ( 1) SS BOND : angle 0.38514 / 0.22 ( 2) hydrogen bonds : bond 0.04861 / 3.25 ( 256) hydrogen bonds : angle 3.80375 / 2.67 ( 747) ********************** 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 51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.091 Fit side-chains REVERT: A 232 ASP cc_start: 0.8292 (t0) cc_final: 0.8008 (t0) REVERT: A 250 LEU cc_start: 0.8018 (tp) cc_final: 0.7652 (tp) REVERT: A 272 MET cc_start: 0.6947 (ttm) cc_final: 0.5972 (tmt) REVERT: A 441 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.5754 (pp) REVERT: A 593 TYR cc_start: 0.7733 (m-80) cc_final: 0.7496 (m-80) REVERT: A 610 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6645 (ttm110) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.3692 time to fit residues: 18.9655 Evaluate side-chains 51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 300 VAL 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 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3463 r_free = 0.3463 target = 0.133389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112844 restraints weight = 5082.067| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.69 r_work: 0.3134 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4313 Z= 0.112 Angle : 0.486 5.585 5888 Z= 0.249 Chirality : 0.037 0.116 665 Planarity : 0.004 0.042 721 Dihedral : 3.871 24.016 570 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.03 % Allowed : 24.38 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.38), residues: 522 helix: 1.61 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.91 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.020 0.001 TYR A 303 PHE 0.010 0.001 PHE A 412 TRP 0.010 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 4312) covalent geometry : angle 0.48592 / 0.25 ( 5886) SS BOND : bond 0.00178 / 0.09 ( 1) SS BOND : angle 0.37744 / 0.22 ( 2) hydrogen bonds : bond 0.04821 / 3.23 ( 256) hydrogen bonds : angle 3.80601 / 2.67 ( 747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1123.30 seconds wall clock time: 19 minutes 51.87 seconds (1191.87 seconds total)