Starting phenix.real_space_refine on Wed Mar 5 22:43:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1f_44077/03_2025/9b1f_44077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1f_44077/03_2025/9b1f_44077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b1f_44077/03_2025/9b1f_44077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1f_44077/03_2025/9b1f_44077.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1f_44077/03_2025/9b1f_44077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1f_44077/03_2025/9b1f_44077.cif" } resolution = 2.9 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2565 2.51 5 N 662 2.21 5 O 679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3936 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3922 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.71, per 1000 atoms: 0.94 Number of scatterers: 3936 At special positions: 0 Unit cell: (58.41, 85.668, 103.191, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 679 8.00 N 662 7.00 C 2565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 56 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 505.3 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 2 sheets defined 84.5% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.735A pdb=" N ASP A 97 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.547A pdb=" N TRP A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.927A pdb=" N GLY A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.583A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 221 removed outlier: 3.873A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 252 removed outlier: 3.894A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 264 through 273 removed outlier: 4.129A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 288 through 303 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.688A pdb=" N ALA A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 removed outlier: 5.377A pdb=" N GLU A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 removed outlier: 4.054A pdb=" N GLU A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.544A pdb=" N LEU A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 364 removed outlier: 4.320A pdb=" N ARG A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.883A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 373 through 400 removed outlier: 3.673A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix removed outlier: 3.651A pdb=" N GLY A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.710A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 456 removed outlier: 4.171A pdb=" N SER A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 482 removed outlier: 4.384A pdb=" N MET A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.650A pdb=" N VAL A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.662A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Proline residue: A 501 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 275 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 1.19 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: 1239 1.34 - 1.46: 926 1.46 - 1.58: 1823 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4035 Sorted by residual: bond pdb=" CA VAL A 500 " pdb=" CB VAL A 500 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.52e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" CA PRO A 75 " pdb=" C PRO A 75 " ideal model delta sigma weight residual 1.517 1.528 -0.011 9.30e-03 1.16e+04 1.34e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.425 -0.022 2.00e-02 2.50e+03 1.16e+00 ... (remaining 4030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 5017 0.92 - 1.84: 390 1.84 - 2.76: 52 2.76 - 3.69: 33 3.69 - 4.61: 12 Bond angle restraints: 5504 Sorted by residual: angle pdb=" C PHE A 380 " pdb=" N ILE A 381 " pdb=" CA ILE A 381 " ideal model delta sigma weight residual 120.47 116.59 3.88 1.58e+00 4.01e-01 6.04e+00 angle pdb=" CA TYR A 272 " pdb=" CB TYR A 272 " pdb=" CG TYR A 272 " ideal model delta sigma weight residual 113.90 118.20 -4.30 1.80e+00 3.09e-01 5.71e+00 angle pdb=" C PHE A 360 " pdb=" N PHE A 361 " pdb=" CA PHE A 361 " ideal model delta sigma weight residual 121.58 117.31 4.27 1.95e+00 2.63e-01 4.79e+00 angle pdb=" C ALA A 192 " pdb=" N PHE A 193 " pdb=" CA PHE A 193 " ideal model delta sigma weight residual 120.26 123.05 -2.79 1.34e+00 5.57e-01 4.33e+00 angle pdb=" CA ARG A 227 " pdb=" C ARG A 227 " pdb=" N PRO A 228 " ideal model delta sigma weight residual 120.77 118.78 1.99 9.70e-01 1.06e+00 4.22e+00 ... (remaining 5499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 2259 17.73 - 35.47: 113 35.47 - 53.20: 13 53.20 - 70.94: 3 70.94 - 88.67: 3 Dihedral angle restraints: 2391 sinusoidal: 919 harmonic: 1472 Sorted by residual: dihedral pdb=" CA PRO A 457 " pdb=" C PRO A 457 " pdb=" N THR A 458 " pdb=" CA THR A 458 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 54 " pdb=" C LEU A 54 " pdb=" N ASP A 55 " pdb=" CA ASP A 55 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA HIS A 398 " pdb=" C HIS A 398 " pdb=" N LEU A 399 " pdb=" CA LEU A 399 " ideal model delta harmonic sigma weight residual 180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.78e+00 ... (remaining 2388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 420 0.028 - 0.056: 149 0.056 - 0.084: 53 0.084 - 0.112: 23 0.112 - 0.140: 6 Chirality restraints: 651 Sorted by residual: chirality pdb=" CA PHE A 361 " pdb=" N PHE A 361 " pdb=" C PHE A 361 " pdb=" CB PHE A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA PRO A 501 " pdb=" N PRO A 501 " pdb=" C PRO A 501 " pdb=" CB PRO A 501 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 648 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 479 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 480 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 381 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C ILE A 381 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE A 381 " -0.008 2.00e-02 2.50e+03 pdb=" N GLY A 382 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 492 " 0.020 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO A 493 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " 0.017 5.00e-02 4.00e+02 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1195 2.83 - 3.35: 3949 3.35 - 3.86: 6339 3.86 - 4.38: 7558 4.38 - 4.90: 12633 Nonbonded interactions: 31674 Sorted by model distance: nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 451 " pdb=" O PRO A 512 " model vdw 2.326 3.040 nonbonded pdb=" OD1 ASN A 56 " pdb=" OG1 THR A 58 " model vdw 2.408 3.040 nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.444 3.040 nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.451 3.040 ... (remaining 31669 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: 3.600 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.940 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4035 Z= 0.258 Angle : 0.608 4.607 5504 Z= 0.335 Chirality : 0.037 0.140 651 Planarity : 0.004 0.033 684 Dihedral : 11.292 88.675 1435 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 0.97 (0.37), residues: 513 helix: 0.62 (0.26), residues: 378 sheet: None (None), residues: 0 loop : 1.20 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.015 0.002 PHE A 356 TYR 0.018 0.002 TYR A 272 ARG 0.004 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.380 Fit side-chains REVERT: A 73 SER cc_start: 0.8258 (t) cc_final: 0.7460 (m) REVERT: A 92 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6717 (mm110) REVERT: A 256 THR cc_start: 0.8603 (m) cc_final: 0.8365 (p) REVERT: A 281 ARG cc_start: 0.7673 (mtp-110) cc_final: 0.7352 (mtm-85) REVERT: A 470 MET cc_start: 0.7778 (mmt) cc_final: 0.7562 (tpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 1.0988 time to fit residues: 74.0674 Evaluate side-chains 46 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.180259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141596 restraints weight = 4215.549| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.79 r_work: 0.3533 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4035 Z= 0.222 Angle : 0.575 6.374 5504 Z= 0.296 Chirality : 0.040 0.134 651 Planarity : 0.005 0.035 684 Dihedral : 4.587 28.565 569 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.64 % Allowed : 7.21 % Favored : 90.14 % 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: 1.83 (0.38), residues: 513 helix: 1.27 (0.27), residues: 375 sheet: -1.11 (1.44), residues: 10 loop : 1.68 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.019 0.002 PHE A 266 TYR 0.025 0.002 TYR A 272 ARG 0.002 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.391 Fit side-chains REVERT: A 92 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6632 (mm110) REVERT: A 263 SER cc_start: 0.8132 (m) cc_final: 0.7867 (m) REVERT: A 272 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6032 (t80) REVERT: A 281 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7426 (mtm-85) REVERT: A 390 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.5180 (mtp) REVERT: A 470 MET cc_start: 0.7697 (mmt) cc_final: 0.7436 (tpp) outliers start: 11 outliers final: 3 residues processed: 53 average time/residue: 1.0352 time to fit residues: 57.3003 Evaluate side-chains 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 449 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.179264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.140755 restraints weight = 4161.649| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.80 r_work: 0.3543 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4035 Z= 0.234 Angle : 0.549 6.658 5504 Z= 0.278 Chirality : 0.040 0.160 651 Planarity : 0.005 0.037 684 Dihedral : 4.316 25.505 569 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.40 % Allowed : 10.10 % Favored : 87.50 % 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: 1.98 (0.38), residues: 513 helix: 1.42 (0.26), residues: 376 sheet: -1.72 (1.37), residues: 10 loop : 1.64 (0.63), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.017 0.002 PHE A 266 TYR 0.022 0.002 TYR A 272 ARG 0.007 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.382 Fit side-chains REVERT: A 17 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6775 (mm110) REVERT: A 73 SER cc_start: 0.8101 (t) cc_final: 0.7311 (m) REVERT: A 89 ARG cc_start: 0.7030 (ttm-80) cc_final: 0.6437 (mtt180) REVERT: A 92 GLN cc_start: 0.7118 (mm-40) cc_final: 0.6834 (mm-40) REVERT: A 263 SER cc_start: 0.8025 (m) cc_final: 0.7816 (m) REVERT: A 281 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7608 (mtm-85) REVERT: A 390 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.4970 (mtp) REVERT: A 449 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7522 (p) REVERT: A 470 MET cc_start: 0.7886 (mmt) cc_final: 0.7665 (tpp) outliers start: 10 outliers final: 3 residues processed: 52 average time/residue: 1.0812 time to fit residues: 58.4264 Evaluate side-chains 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 449 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.177480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139840 restraints weight = 4176.733| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.72 r_work: 0.3508 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4035 Z= 0.235 Angle : 0.566 8.084 5504 Z= 0.280 Chirality : 0.040 0.156 651 Planarity : 0.005 0.037 684 Dihedral : 4.222 23.494 569 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.16 % Allowed : 11.30 % Favored : 86.54 % 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: 2.05 (0.38), residues: 513 helix: 1.48 (0.27), residues: 377 sheet: -1.79 (1.39), residues: 10 loop : 1.65 (0.62), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.016 0.002 PHE A 266 TYR 0.022 0.002 TYR A 272 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.534 Fit side-chains REVERT: A 73 SER cc_start: 0.7961 (t) cc_final: 0.7113 (m) REVERT: A 89 ARG cc_start: 0.6967 (ttm-80) cc_final: 0.6365 (mtt180) REVERT: A 92 GLN cc_start: 0.7000 (mm-40) cc_final: 0.6699 (mm-40) REVERT: A 263 SER cc_start: 0.8120 (m) cc_final: 0.7907 (m) REVERT: A 272 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.6076 (t80) REVERT: A 281 ARG cc_start: 0.7733 (mtp-110) cc_final: 0.7417 (mtm-85) REVERT: A 449 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7336 (p) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 1.0913 time to fit residues: 57.9356 Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 449 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.190334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.155228 restraints weight = 4055.396| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.65 r_work: 0.3518 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4035 Z= 0.235 Angle : 0.548 7.059 5504 Z= 0.273 Chirality : 0.040 0.158 651 Planarity : 0.005 0.038 684 Dihedral : 4.094 20.274 569 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.37 % Allowed : 11.78 % Favored : 84.86 % 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: 2.04 (0.38), residues: 513 helix: 1.51 (0.27), residues: 376 sheet: -1.84 (1.40), residues: 10 loop : 1.51 (0.61), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.016 0.002 PHE A 266 TYR 0.022 0.002 TYR A 272 ARG 0.007 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.372 Fit side-chains REVERT: A 17 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6502 (mm110) REVERT: A 73 SER cc_start: 0.7949 (t) cc_final: 0.7098 (m) REVERT: A 89 ARG cc_start: 0.6957 (ttm-80) cc_final: 0.6433 (mtt180) REVERT: A 92 GLN cc_start: 0.7011 (mm-40) cc_final: 0.6714 (mm-40) REVERT: A 272 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6128 (t80) REVERT: A 281 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7429 (ttm-80) REVERT: A 449 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7328 (p) REVERT: A 470 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.6370 (ttt) outliers start: 14 outliers final: 4 residues processed: 53 average time/residue: 0.9813 time to fit residues: 54.3266 Evaluate side-chains 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 470 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 49 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.0050 chunk 38 optimal weight: 0.0570 overall best weight: 0.2512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.179290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.140381 restraints weight = 4196.828| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.85 r_work: 0.3512 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4035 Z= 0.151 Angle : 0.533 12.474 5504 Z= 0.258 Chirality : 0.038 0.144 651 Planarity : 0.004 0.036 684 Dihedral : 3.858 18.709 569 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.12 % Allowed : 12.98 % Favored : 83.89 % 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: 2.31 (0.38), residues: 513 helix: 1.78 (0.27), residues: 378 sheet: -1.89 (1.40), residues: 10 loop : 1.34 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.000 HIS A 139 PHE 0.013 0.001 PHE A 358 TYR 0.018 0.001 TYR A 272 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.384 Fit side-chains REVERT: A 17 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6716 (mm110) REVERT: A 89 ARG cc_start: 0.6841 (ttm-80) cc_final: 0.6534 (mtt-85) REVERT: A 92 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6540 (mm110) REVERT: A 281 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7271 (ttm-80) REVERT: A 390 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5816 (mmt) outliers start: 13 outliers final: 6 residues processed: 50 average time/residue: 1.0601 time to fit residues: 55.2470 Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 421 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.0370 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.178323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.139472 restraints weight = 4242.242| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.86 r_work: 0.3517 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4035 Z= 0.191 Angle : 0.543 12.214 5504 Z= 0.264 Chirality : 0.039 0.151 651 Planarity : 0.004 0.035 684 Dihedral : 3.850 17.376 569 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.88 % Allowed : 13.70 % Favored : 83.41 % 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: 2.27 (0.38), residues: 513 helix: 1.77 (0.27), residues: 378 sheet: -1.89 (1.46), residues: 10 loop : 1.26 (0.59), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.014 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.007 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.427 Fit side-chains REVERT: A 17 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6758 (mm110) REVERT: A 73 SER cc_start: 0.7869 (t) cc_final: 0.7024 (m) REVERT: A 89 ARG cc_start: 0.6872 (ttm-80) cc_final: 0.6291 (mtt180) REVERT: A 92 GLN cc_start: 0.6898 (mm-40) cc_final: 0.6592 (mm110) REVERT: A 231 MET cc_start: 0.7056 (tpp) cc_final: 0.6801 (tpt) REVERT: A 281 ARG cc_start: 0.7686 (mtp-110) cc_final: 0.7347 (ttm-80) REVERT: A 379 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8396 (ttt) REVERT: A 390 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.5852 (mmt) outliers start: 12 outliers final: 4 residues processed: 47 average time/residue: 1.0835 time to fit residues: 53.1287 Evaluate side-chains 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 0.0670 chunk 42 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.178495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139722 restraints weight = 4203.517| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.85 r_work: 0.3523 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4035 Z= 0.186 Angle : 0.539 11.538 5504 Z= 0.262 Chirality : 0.038 0.150 651 Planarity : 0.004 0.035 684 Dihedral : 3.795 15.868 569 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.64 % Allowed : 13.70 % Favored : 83.65 % 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: 2.23 (0.38), residues: 513 helix: 1.74 (0.27), residues: 379 sheet: -1.87 (1.48), residues: 10 loop : 1.24 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.000 HIS A 139 PHE 0.013 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.007 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.413 Fit side-chains REVERT: A 17 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6769 (mm110) REVERT: A 73 SER cc_start: 0.7850 (t) cc_final: 0.7007 (m) REVERT: A 87 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7944 (ptt180) REVERT: A 89 ARG cc_start: 0.6850 (ttm-80) cc_final: 0.6350 (mtt180) REVERT: A 92 GLN cc_start: 0.6915 (mm-40) cc_final: 0.6612 (mm110) REVERT: A 281 ARG cc_start: 0.7697 (mtp-110) cc_final: 0.7352 (ttm-80) REVERT: A 390 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.5885 (mmt) outliers start: 11 outliers final: 4 residues processed: 50 average time/residue: 1.1160 time to fit residues: 58.0993 Evaluate side-chains 50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.177108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.137718 restraints weight = 4227.064| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.92 r_work: 0.3492 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4035 Z= 0.229 Angle : 0.565 11.369 5504 Z= 0.276 Chirality : 0.040 0.163 651 Planarity : 0.005 0.036 684 Dihedral : 3.896 15.442 569 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.16 % Allowed : 14.66 % Favored : 83.17 % 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: 2.07 (0.37), residues: 513 helix: 1.64 (0.27), residues: 377 sheet: -1.90 (1.51), residues: 10 loop : 1.12 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.014 0.002 PHE A 358 TYR 0.022 0.002 TYR A 272 ARG 0.008 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.422 Fit side-chains REVERT: A 17 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6773 (mm110) REVERT: A 73 SER cc_start: 0.7897 (t) cc_final: 0.7047 (m) REVERT: A 87 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7984 (ptt180) REVERT: A 89 ARG cc_start: 0.6871 (ttm-80) cc_final: 0.6444 (mtt180) REVERT: A 92 GLN cc_start: 0.6912 (mm-40) cc_final: 0.6605 (mm110) REVERT: A 281 ARG cc_start: 0.7700 (mtp-110) cc_final: 0.7351 (ttm-80) REVERT: A 376 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7789 (mp) REVERT: A 390 MET cc_start: 0.6371 (OUTLIER) cc_final: 0.5891 (mmt) REVERT: A 470 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6101 (ttt) outliers start: 9 outliers final: 4 residues processed: 48 average time/residue: 1.1149 time to fit residues: 55.6785 Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 470 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.190444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.155604 restraints weight = 4040.361| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.63 r_work: 0.3516 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4035 Z= 0.243 Angle : 0.575 11.348 5504 Z= 0.282 Chirality : 0.040 0.161 651 Planarity : 0.005 0.036 684 Dihedral : 3.914 15.273 569 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.40 % Allowed : 14.18 % Favored : 83.41 % 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: 1.96 (0.37), residues: 513 helix: 1.58 (0.27), residues: 377 sheet: -2.03 (1.51), residues: 10 loop : 1.00 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.014 0.002 PHE A 358 TYR 0.022 0.002 TYR A 272 ARG 0.008 0.000 ARG A 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.459 Fit side-chains REVERT: A 17 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6816 (mm110) REVERT: A 73 SER cc_start: 0.7935 (OUTLIER) cc_final: 0.7112 (m) REVERT: A 87 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7970 (ptt180) REVERT: A 89 ARG cc_start: 0.6921 (ttm-80) cc_final: 0.6426 (mtt180) REVERT: A 92 GLN cc_start: 0.7021 (mm-40) cc_final: 0.6711 (mm110) REVERT: A 281 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.7443 (ttm-80) REVERT: A 390 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.6025 (mmt) REVERT: A 426 MET cc_start: 0.5796 (mpp) cc_final: 0.4383 (mmt) REVERT: A 470 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6230 (ttt) outliers start: 10 outliers final: 4 residues processed: 48 average time/residue: 1.1941 time to fit residues: 59.5842 Evaluate side-chains 51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 470 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.0270 chunk 27 optimal weight: 0.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.178075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.139520 restraints weight = 4206.167| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.84 r_work: 0.3479 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4035 Z= 0.186 Angle : 0.550 10.921 5504 Z= 0.269 Chirality : 0.038 0.145 651 Planarity : 0.005 0.038 684 Dihedral : 3.810 14.771 569 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.16 % Allowed : 14.42 % Favored : 83.41 % 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: 2.09 (0.37), residues: 513 helix: 1.70 (0.27), residues: 377 sheet: -2.13 (1.47), residues: 10 loop : 0.98 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.000 HIS A 139 PHE 0.013 0.001 PHE A 358 TYR 0.019 0.001 TYR A 272 ARG 0.008 0.000 ARG A 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3320.29 seconds wall clock time: 57 minutes 19.37 seconds (3439.37 seconds total)