Starting phenix.real_space_refine on Sun Apr 27 00:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1f_44077/04_2025/9b1f_44077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1f_44077/04_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_44077/04_2025/9b1f_44077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1f_44077/04_2025/9b1f_44077.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1f_44077/04_2025/9b1f_44077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1f_44077/04_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-5669/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: 4.16, per 1000 atoms: 1.06 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 454.8 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: 0.43 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: 1.13 Time building geometry restraints manager: 1.14 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.350 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:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- 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 4038 Z= 0.181 Angle : 0.611 4.607 5511 Z= 0.336 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 1) link_NAG-ASN : angle 0.97913 ( 3) hydrogen bonds : bond 0.14343 ( 275) hydrogen bonds : angle 6.11253 ( 795) SS BOND : bond 0.00159 ( 2) SS BOND : angle 2.01344 ( 4) covalent geometry : bond 0.00379 ( 4035) covalent geometry : angle 0.60839 ( 5504) *********************** 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 : 0.438 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: 1.1247 time to fit residues: 75.8425 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 : 0.393 ------------------------------------------------------------------------------- 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 4038 Z= 0.151 Angle : 0.577 6.374 5511 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 1) link_NAG-ASN : angle 0.96100 ( 3) hydrogen bonds : bond 0.05390 ( 275) hydrogen bonds : angle 4.69615 ( 795) SS BOND : bond 0.00060 ( 2) SS BOND : angle 1.71783 ( 4) covalent geometry : bond 0.00328 ( 4035) covalent geometry : angle 0.57500 ( 5504) *********************** 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 : 0.422 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: 1.0592 time to fit residues: 58.6016 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 : 0.465 ------------------------------------------------------------------------------- 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 4038 Z= 0.152 Angle : 0.551 6.658 5511 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 1) link_NAG-ASN : angle 0.84332 ( 3) hydrogen bonds : bond 0.05270 ( 275) hydrogen bonds : angle 4.58913 ( 795) SS BOND : bond 0.00131 ( 2) SS BOND : angle 1.59362 ( 4) covalent geometry : bond 0.00341 ( 4035) covalent geometry : angle 0.54890 ( 5504) *********************** 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 : 0.377 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: 1.1564 time to fit residues: 62.4608 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 : 0.469 ------------------------------------------------------------------------------- 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: 0.1980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.178422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.140755 restraints weight = 4173.352| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.73 r_work: 0.3534 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4038 Z= 0.137 Angle : 0.551 7.809 5511 Z= 0.272 Chirality : 0.039 0.148 651 Planarity : 0.005 0.036 684 Dihedral : 4.156 23.229 569 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.92 % Allowed : 11.78 % Favored : 86.30 % 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: 2.19 (0.38), residues: 513 helix: 1.58 (0.27), residues: 377 sheet: -1.81 (1.38), residues: 10 loop : 1.70 (0.63), 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 0.015 0.002 PHE A 266 TYR 0.021 0.002 TYR A 272 ARG 0.006 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 0.90210 ( 3) hydrogen bonds : bond 0.04882 ( 275) hydrogen bonds : angle 4.48027 ( 795) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.48370 ( 4) covalent geometry : bond 0.00303 ( 4035) covalent geometry : angle 0.54960 ( 5504) *********************** 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 52 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 1.066 Fit side-chains REVERT: A 17 GLN cc_start: 0.7287 (mm-40) cc_final: 0.6520 (mm-40) REVERT: A 89 ARG cc_start: 0.6937 (ttm-80) cc_final: 0.6340 (mtt180) REVERT: A 92 GLN cc_start: 0.6974 (mm-40) cc_final: 0.6675 (mm-40) REVERT: A 263 SER cc_start: 0.8098 (m) cc_final: 0.7877 (m) REVERT: A 272 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6095 (t80) REVERT: A 281 ARG cc_start: 0.7718 (mtp-110) cc_final: 0.7401 (mtm-85) REVERT: A 470 MET cc_start: 0.7716 (mmt) cc_final: 0.7420 (tpp) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 1.9260 time to fit residues: 96.4988 Evaluate side-chains 48 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.176802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.137954 restraints weight = 4277.864| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.85 r_work: 0.3479 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4038 Z= 0.142 Angle : 0.542 7.017 5511 Z= 0.269 Chirality : 0.039 0.157 651 Planarity : 0.005 0.038 684 Dihedral : 4.033 19.570 569 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.64 % Allowed : 11.78 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.38), residues: 513 helix: 1.58 (0.27), residues: 376 sheet: -1.78 (1.45), residues: 10 loop : 1.54 (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 0.008 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 1) link_NAG-ASN : angle 0.92665 ( 3) hydrogen bonds : bond 0.04886 ( 275) hydrogen bonds : angle 4.46399 ( 795) SS BOND : bond 0.00165 ( 2) SS BOND : angle 1.48452 ( 4) covalent geometry : bond 0.00320 ( 4035) covalent geometry : angle 0.54070 ( 5504) *********************** 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 56 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.397 Fit side-chains REVERT: A 73 SER cc_start: 0.7849 (t) cc_final: 0.6983 (m) REVERT: A 89 ARG cc_start: 0.6907 (ttm-80) cc_final: 0.6547 (mtt-85) REVERT: A 92 GLN cc_start: 0.6873 (mm-40) cc_final: 0.6576 (mm-40) REVERT: A 263 SER cc_start: 0.8165 (m) cc_final: 0.7960 (m) REVERT: A 272 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.5954 (t80) REVERT: A 281 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7276 (ttm-80) REVERT: A 390 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5970 (mpp) REVERT: A 449 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7123 (p) REVERT: A 470 MET cc_start: 0.7597 (mmt) cc_final: 0.6265 (ttt) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 1.5575 time to fit residues: 85.5800 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 : 0.389 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain A residue 376 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.0060 chunk 38 optimal weight: 0.1980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.178193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.139492 restraints weight = 4197.078| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.83 r_work: 0.3547 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4038 Z= 0.122 Angle : 0.539 12.777 5511 Z= 0.261 Chirality : 0.038 0.153 651 Planarity : 0.004 0.036 684 Dihedral : 3.859 17.328 569 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.12 % Allowed : 12.74 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.38), residues: 513 helix: 1.72 (0.27), residues: 377 sheet: -1.84 (1.49), residues: 10 loop : 1.34 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.013 0.001 PHE A 266 TYR 0.019 0.001 TYR A 272 ARG 0.007 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 1) link_NAG-ASN : angle 0.91824 ( 3) hydrogen bonds : bond 0.04480 ( 275) hydrogen bonds : angle 4.38143 ( 795) SS BOND : bond 0.00147 ( 2) SS BOND : angle 1.35685 ( 4) covalent geometry : bond 0.00265 ( 4035) covalent geometry : angle 0.53801 ( 5504) *********************** 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 57 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.416 Fit side-chains REVERT: A 17 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6302 (mm110) REVERT: A 73 SER cc_start: 0.7939 (t) cc_final: 0.7117 (m) REVERT: A 89 ARG cc_start: 0.6918 (ttm-80) cc_final: 0.6657 (mtt-85) REVERT: A 92 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6664 (mm110) REVERT: A 281 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.7467 (ttm-80) REVERT: A 390 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.5908 (mmt) REVERT: A 470 MET cc_start: 0.7739 (mmt) cc_final: 0.6499 (ttt) outliers start: 13 outliers final: 6 residues processed: 49 average time/residue: 1.0635 time to fit residues: 54.2822 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 : 0.414 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.177842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.139089 restraints weight = 4232.925| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.85 r_work: 0.3514 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4038 Z= 0.129 Angle : 0.547 12.340 5511 Z= 0.264 Chirality : 0.039 0.154 651 Planarity : 0.004 0.035 684 Dihedral : 3.843 16.195 569 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.40 % Allowed : 13.46 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.38), residues: 513 helix: 1.70 (0.27), residues: 378 sheet: -1.88 (1.51), residues: 10 loop : 1.32 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 1) link_NAG-ASN : angle 0.92606 ( 3) hydrogen bonds : bond 0.04597 ( 275) hydrogen bonds : angle 4.37404 ( 795) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.36983 ( 4) covalent geometry : bond 0.00284 ( 4035) covalent geometry : angle 0.54531 ( 5504) *********************** 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 53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.479 Fit side-chains REVERT: A 17 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6484 (mm110) REVERT: A 73 SER cc_start: 0.7896 (t) cc_final: 0.7060 (m) REVERT: A 89 ARG cc_start: 0.6853 (ttm-80) cc_final: 0.6589 (mtt-85) REVERT: A 92 GLN cc_start: 0.6930 (mm-40) cc_final: 0.6627 (mm110) REVERT: A 281 ARG cc_start: 0.7720 (mtp-110) cc_final: 0.7379 (ttm-80) REVERT: A 379 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8399 (ttt) REVERT: A 390 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.5877 (mmt) REVERT: A 470 MET cc_start: 0.7649 (mmt) cc_final: 0.6359 (ttt) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 1.6293 time to fit residues: 81.2191 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 : 1.010 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 0.0060 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.178469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.139873 restraints weight = 4230.924| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.85 r_work: 0.3541 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4038 Z= 0.124 Angle : 0.543 11.699 5511 Z= 0.263 Chirality : 0.038 0.153 651 Planarity : 0.004 0.035 684 Dihedral : 3.828 14.876 569 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.92 % Allowed : 14.42 % 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: 2.22 (0.38), residues: 513 helix: 1.72 (0.27), residues: 378 sheet: -1.93 (1.50), residues: 10 loop : 1.30 (0.59), residues: 125 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 0.007 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 1) link_NAG-ASN : angle 0.93604 ( 3) hydrogen bonds : bond 0.04487 ( 275) hydrogen bonds : angle 4.36008 ( 795) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.33191 ( 4) covalent geometry : bond 0.00269 ( 4035) covalent geometry : angle 0.54194 ( 5504) *********************** 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 53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.428 Fit side-chains REVERT: A 73 SER cc_start: 0.7908 (t) cc_final: 0.7082 (m) REVERT: A 87 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7996 (ptt180) REVERT: A 89 ARG cc_start: 0.6856 (ttm-80) cc_final: 0.6624 (mtt-85) REVERT: A 92 GLN cc_start: 0.6955 (mm-40) cc_final: 0.6657 (mm110) REVERT: A 281 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.7425 (ttm-80) REVERT: A 390 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.5952 (mmt) REVERT: A 470 MET cc_start: 0.7725 (mmt) cc_final: 0.6459 (ttt) outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 1.1666 time to fit residues: 60.5893 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 : 0.380 ------------------------------------------------------------------------------- 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 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 421 LEU 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: 0.8980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.175847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137349 restraints weight = 4215.082| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.83 r_work: 0.3488 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4038 Z= 0.155 Angle : 0.578 11.638 5511 Z= 0.283 Chirality : 0.040 0.162 651 Planarity : 0.005 0.036 684 Dihedral : 3.931 15.478 569 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 2.01 (0.37), residues: 513 helix: 1.57 (0.27), residues: 375 sheet: -1.98 (1.51), residues: 10 loop : 1.22 (0.58), residues: 128 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 1) link_NAG-ASN : angle 1.02032 ( 3) hydrogen bonds : bond 0.05078 ( 275) hydrogen bonds : angle 4.49151 ( 795) SS BOND : bond 0.00197 ( 2) SS BOND : angle 1.49384 ( 4) covalent geometry : bond 0.00362 ( 4035) covalent geometry : angle 0.57679 ( 5504) *********************** 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 52 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.417 Fit side-chains REVERT: A 73 SER cc_start: 0.7960 (OUTLIER) cc_final: 0.7135 (m) REVERT: A 89 ARG cc_start: 0.6956 (ttm-80) cc_final: 0.6439 (mtt180) REVERT: A 92 GLN cc_start: 0.6984 (mm-40) cc_final: 0.6699 (mm-40) REVERT: A 281 ARG cc_start: 0.7805 (mtp-110) cc_final: 0.7461 (ttm-80) REVERT: A 376 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8027 (mp) REVERT: A 390 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6054 (mmt) REVERT: A 470 MET cc_start: 0.7739 (mmt) cc_final: 0.6527 (ttt) outliers start: 11 outliers final: 4 residues processed: 49 average time/residue: 1.0843 time to fit residues: 55.3327 Evaluate side-chains 48 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 73 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 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 = 0.4139 r_free = 0.4139 target = 0.190535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.155675 restraints weight = 4023.310| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.63 r_work: 0.3518 rms_B_bonded: 2.04 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: 0.7793 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4038 Z= 0.149 Angle : 0.580 11.502 5511 Z= 0.283 Chirality : 0.040 0.159 651 Planarity : 0.005 0.039 684 Dihedral : 3.907 15.288 569 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.68 % Allowed : 14.90 % 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: 1.94 (0.37), residues: 513 helix: 1.53 (0.27), residues: 375 sheet: -2.06 (1.51), residues: 10 loop : 1.14 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 1.06014 ( 3) hydrogen bonds : bond 0.04982 ( 275) hydrogen bonds : angle 4.48813 ( 795) SS BOND : bond 0.00190 ( 2) SS BOND : angle 1.46473 ( 4) covalent geometry : bond 0.00345 ( 4035) covalent geometry : angle 0.57858 ( 5504) ********************** 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 50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.414 Fit side-chains REVERT: A 73 SER cc_start: 0.7926 (OUTLIER) cc_final: 0.7093 (m) REVERT: A 89 ARG cc_start: 0.6947 (ttm-80) cc_final: 0.6433 (mtt180) REVERT: A 92 GLN cc_start: 0.6989 (mm-40) cc_final: 0.6703 (mm-40) REVERT: A 281 ARG cc_start: 0.7802 (mtp-110) cc_final: 0.7461 (ttm-80) REVERT: A 376 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8029 (mp) REVERT: A 390 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6028 (mmt) REVERT: A 426 MET cc_start: 0.5732 (mpp) cc_final: 0.4360 (mmt) REVERT: A 470 MET cc_start: 0.7677 (mmt) cc_final: 0.6496 (ttt) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 1.1630 time to fit residues: 58.0989 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 : 0.365 ------------------------------------------------------------------------------- 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 73 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.191079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156352 restraints weight = 3966.136| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.63 r_work: 0.3530 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4038 Z= 0.144 Angle : 0.573 11.284 5511 Z= 0.280 Chirality : 0.039 0.150 651 Planarity : 0.005 0.038 684 Dihedral : 3.877 15.078 569 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.92 % Allowed : 14.90 % 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: 1.84 (0.38), residues: 513 helix: 1.44 (0.27), residues: 381 sheet: -2.07 (1.52), residues: 10 loop : 1.14 (0.60), residues: 122 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 0.021 0.002 TYR A 272 ARG 0.008 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 1) link_NAG-ASN : angle 1.07709 ( 3) hydrogen bonds : bond 0.04895 ( 275) hydrogen bonds : angle 4.48203 ( 795) SS BOND : bond 0.00179 ( 2) SS BOND : angle 1.44094 ( 4) covalent geometry : bond 0.00329 ( 4035) covalent geometry : angle 0.57194 ( 5504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3807.38 seconds wall clock time: 67 minutes 45.61 seconds (4065.61 seconds total)