Starting phenix.real_space_refine on Fri May 9 21:43:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1f_44077/05_2025/9b1f_44077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1f_44077/05_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_44077/05_2025/9b1f_44077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1f_44077/05_2025/9b1f_44077.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1f_44077/05_2025/9b1f_44077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1f_44077/05_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-5687/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: 3.78, per 1000 atoms: 0.96 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: 1.05 Conformation dependent library (CDL) restraints added in 514.0 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: 0.38 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: 1.05 Time building geometry restraints manager: 1.22 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: 2.850 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.690 Find NCS groups from input model: 0.030 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:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.080 ------------------------------------------------------------------------------- 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 : 0.384 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: 1.0852 time to fit residues: 73.1687 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 = 54)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.141561 restraints weight = 4215.547| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.80 r_work: 0.3537 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- 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 : 0.387 Fit side-chains REVERT: A 92 GLN cc_start: 0.7008 (mm-40) cc_final: 0.6636 (mm110) REVERT: A 263 SER cc_start: 0.8135 (m) cc_final: 0.7870 (m) REVERT: A 272 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6028 (t80) REVERT: A 281 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7427 (mtm-85) REVERT: A 390 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.5174 (mtp) REVERT: A 470 MET cc_start: 0.7701 (mmt) cc_final: 0.7439 (tpp) outliers start: 11 outliers final: 3 residues processed: 53 average time/residue: 1.0608 time to fit residues: 58.6825 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 : 0.462 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.176981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.139099 restraints weight = 4175.439| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.75 r_work: 0.3535 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4038 Z= 0.166 Angle : 0.569 7.069 5511 Z= 0.288 Chirality : 0.041 0.154 651 Planarity : 0.005 0.037 684 Dihedral : 4.405 26.117 569 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.40 % Allowed : 9.86 % Favored : 87.74 % 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: 1.31 (0.26), residues: 376 sheet: -1.69 (1.38), residues: 10 loop : 1.58 (0.62), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.003 0.001 HIS A 139 PHE 0.018 0.002 PHE A 266 TYR 0.023 0.002 TYR A 272 ARG 0.006 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 1) link_NAG-ASN : angle 0.90301 ( 3) hydrogen bonds : bond 0.05524 ( 275) hydrogen bonds : angle 4.65954 ( 795) SS BOND : bond 0.00144 ( 2) SS BOND : angle 1.64350 ( 4) covalent geometry : bond 0.00382 ( 4035) covalent geometry : angle 0.56772 ( 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 : 0.419 Fit side-chains REVERT: A 17 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6718 (mm110) REVERT: A 73 SER cc_start: 0.8092 (t) cc_final: 0.7290 (m) REVERT: A 89 ARG cc_start: 0.6990 (ttm-80) cc_final: 0.6390 (mtt180) REVERT: A 92 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6802 (mm-40) REVERT: A 263 SER cc_start: 0.8057 (m) cc_final: 0.7843 (m) REVERT: A 272 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6208 (t80) REVERT: A 281 ARG cc_start: 0.7879 (mtp-110) cc_final: 0.7545 (mtm-85) REVERT: A 390 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.5020 (mtp) REVERT: A 449 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7486 (p) REVERT: A 470 MET cc_start: 0.7833 (mmt) cc_final: 0.7599 (tpp) outliers start: 10 outliers final: 3 residues processed: 53 average time/residue: 1.1304 time to fit residues: 62.4850 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 : 0.412 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 5 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.180977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.142839 restraints weight = 4156.155| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.78 r_work: 0.3552 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4038 Z= 0.121 Angle : 0.534 7.294 5511 Z= 0.264 Chirality : 0.038 0.148 651 Planarity : 0.004 0.035 684 Dihedral : 4.116 23.705 569 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.92 % Allowed : 11.54 % 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: 2.31 (0.38), residues: 513 helix: 1.68 (0.27), residues: 377 sheet: -1.84 (1.36), residues: 10 loop : 1.71 (0.63), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.000 HIS A 139 PHE 0.014 0.001 PHE A 266 TYR 0.020 0.001 TYR A 272 ARG 0.006 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 1) link_NAG-ASN : angle 0.88207 ( 3) hydrogen bonds : bond 0.04605 ( 275) hydrogen bonds : angle 4.43663 ( 795) SS BOND : bond 0.00111 ( 2) SS BOND : angle 1.42179 ( 4) covalent geometry : bond 0.00250 ( 4035) covalent geometry : angle 0.53229 ( 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 53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.417 Fit side-chains REVERT: A 17 GLN cc_start: 0.7254 (mm-40) cc_final: 0.6500 (mm-40) REVERT: A 89 ARG cc_start: 0.6888 (ttm-80) cc_final: 0.6311 (mtt180) REVERT: A 92 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6695 (mm110) REVERT: A 263 SER cc_start: 0.8094 (m) cc_final: 0.7874 (m) REVERT: A 281 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7430 (mtm-85) REVERT: A 470 MET cc_start: 0.7728 (mmt) cc_final: 0.7449 (tpp) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 1.1314 time to fit residues: 56.5033 Evaluate side-chains 48 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 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 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: 0.6980 chunk 42 optimal weight: 0.7980 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: 0.6980 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.177812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140072 restraints weight = 4275.465| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.75 r_work: 0.3522 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2470 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= 0.147 Angle : 0.546 7.176 5511 Z= 0.271 Chirality : 0.039 0.159 651 Planarity : 0.005 0.037 684 Dihedral : 4.066 20.724 569 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.40 % Allowed : 12.26 % Favored : 85.34 % 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: 2.18 (0.38), residues: 513 helix: 1.59 (0.27), residues: 376 sheet: -1.87 (1.40), residues: 10 loop : 1.62 (0.61), residues: 127 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 0.017 0.002 PHE A 266 TYR 0.023 0.002 TYR A 272 ARG 0.007 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 1) link_NAG-ASN : angle 0.89008 ( 3) hydrogen bonds : bond 0.04978 ( 275) hydrogen bonds : angle 4.48949 ( 795) SS BOND : bond 0.00163 ( 2) SS BOND : angle 1.51595 ( 4) covalent geometry : bond 0.00331 ( 4035) covalent geometry : angle 0.54439 ( 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 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.362 Fit side-chains REVERT: A 73 SER cc_start: 0.7957 (t) cc_final: 0.7117 (m) REVERT: A 89 ARG cc_start: 0.6973 (ttm-80) cc_final: 0.6399 (mtt180) REVERT: A 92 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6730 (mm-40) REVERT: A 281 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.7427 (ttm-80) REVERT: A 470 MET cc_start: 0.7723 (mmt) cc_final: 0.6517 (ttt) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 1.0616 time to fit residues: 56.4268 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 : 0.378 ------------------------------------------------------------------------------- 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 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 421 LEU 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: 0.9980 chunk 46 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.191792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156779 restraints weight = 3989.061| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.64 r_work: 0.3536 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2589 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= 0.131 Angle : 0.552 13.132 5511 Z= 0.267 Chirality : 0.039 0.151 651 Planarity : 0.004 0.036 684 Dihedral : 3.931 18.349 569 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.88 % Allowed : 12.50 % Favored : 84.62 % 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: 2.15 (0.38), residues: 513 helix: 1.64 (0.27), residues: 377 sheet: -1.86 (1.42), residues: 10 loop : 1.39 (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 0.014 0.001 PHE A 266 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 0.00214 ( 1) link_NAG-ASN : angle 0.92095 ( 3) hydrogen bonds : bond 0.04691 ( 275) hydrogen bonds : angle 4.42872 ( 795) SS BOND : bond 0.00164 ( 2) SS BOND : angle 1.41011 ( 4) covalent geometry : bond 0.00290 ( 4035) covalent geometry : angle 0.55067 ( 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 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.400 Fit side-chains REVERT: A 17 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6317 (mm110) REVERT: A 73 SER cc_start: 0.7909 (t) cc_final: 0.7069 (m) REVERT: A 89 ARG cc_start: 0.6908 (ttm-80) cc_final: 0.6326 (mtt180) REVERT: A 92 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6651 (mm110) REVERT: A 281 ARG cc_start: 0.7728 (mtp-110) cc_final: 0.7389 (ttm-80) REVERT: A 390 MET cc_start: 0.6036 (mmm) cc_final: 0.5313 (mmt) REVERT: A 470 MET cc_start: 0.7654 (mmt) cc_final: 0.6412 (ttt) outliers start: 12 outliers final: 6 residues processed: 48 average time/residue: 1.1513 time to fit residues: 57.4223 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 : 0.381 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 22 optimal weight: 0.0370 chunk 42 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.178173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.139517 restraints weight = 4231.149| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.82 r_work: 0.3502 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4038 Z= 0.122 Angle : 0.537 12.072 5511 Z= 0.261 Chirality : 0.038 0.153 651 Planarity : 0.004 0.035 684 Dihedral : 3.846 16.998 569 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.40 % Allowed : 13.94 % 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: 2.26 (0.38), residues: 513 helix: 1.72 (0.27), residues: 378 sheet: -1.94 (1.45), residues: 10 loop : 1.41 (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 0.020 0.001 TYR A 272 ARG 0.007 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 1) link_NAG-ASN : angle 0.91578 ( 3) hydrogen bonds : bond 0.04529 ( 275) hydrogen bonds : angle 4.37331 ( 795) SS BOND : bond 0.00141 ( 2) SS BOND : angle 1.36470 ( 4) covalent geometry : bond 0.00262 ( 4035) covalent geometry : angle 0.53571 ( 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 54 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.431 Fit side-chains REVERT: A 17 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6594 (mm110) REVERT: A 89 ARG cc_start: 0.6855 (ttm-80) cc_final: 0.6254 (mtt180) REVERT: A 92 GLN cc_start: 0.6876 (mm-40) cc_final: 0.6563 (mm110) REVERT: A 281 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7288 (ttm-80) REVERT: A 379 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8368 (ttt) REVERT: A 390 MET cc_start: 0.5898 (mmm) cc_final: 0.5213 (mmt) REVERT: A 470 MET cc_start: 0.7578 (mmt) cc_final: 0.6237 (ttt) outliers start: 10 outliers final: 4 residues processed: 49 average time/residue: 1.1079 time to fit residues: 56.5068 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 : 0.415 ------------------------------------------------------------------------------- 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 320 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 34 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.176845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.138105 restraints weight = 4211.209| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.84 r_work: 0.3480 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: 0.7706 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4038 Z= 0.146 Angle : 0.553 11.650 5511 Z= 0.270 Chirality : 0.039 0.159 651 Planarity : 0.005 0.036 684 Dihedral : 3.882 15.530 569 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.40 % Allowed : 13.70 % 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: 2.11 (0.38), residues: 513 helix: 1.63 (0.27), residues: 377 sheet: -1.98 (1.48), residues: 10 loop : 1.30 (0.59), 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 16 TYR 0.022 0.002 TYR A 272 ARG 0.007 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 0.96607 ( 3) hydrogen bonds : bond 0.04839 ( 275) hydrogen bonds : angle 4.43953 ( 795) SS BOND : bond 0.00188 ( 2) SS BOND : angle 1.44198 ( 4) covalent geometry : bond 0.00336 ( 4035) covalent geometry : angle 0.55127 ( 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 52 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.374 Fit side-chains REVERT: A 17 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7068 (mm-40) REVERT: A 73 SER cc_start: 0.7827 (t) cc_final: 0.6969 (m) REVERT: A 87 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7913 (ptt180) REVERT: A 89 ARG cc_start: 0.6844 (ttm-80) cc_final: 0.6263 (mtt180) REVERT: A 92 GLN cc_start: 0.6883 (mm-40) cc_final: 0.6564 (mm110) REVERT: A 281 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7287 (ttm-80) REVERT: A 379 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8405 (ttt) REVERT: A 390 MET cc_start: 0.5894 (mmm) cc_final: 0.5198 (mmt) REVERT: A 470 MET cc_start: 0.7562 (mmt) cc_final: 0.6236 (ttt) outliers start: 10 outliers final: 5 residues processed: 47 average time/residue: 1.1388 time to fit residues: 55.6375 Evaluate side-chains 50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 379 MET Chi-restraints excluded: chain A residue 384 VAL 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: 0.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 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 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.176992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138363 restraints weight = 4195.093| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.84 r_work: 0.3508 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4038 Z= 0.138 Angle : 0.549 11.282 5511 Z= 0.269 Chirality : 0.039 0.157 651 Planarity : 0.005 0.036 684 Dihedral : 3.837 15.169 569 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.40 % Allowed : 13.70 % 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: 2.09 (0.37), residues: 513 helix: 1.64 (0.27), residues: 377 sheet: -2.06 (1.48), residues: 10 loop : 1.20 (0.59), 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 0.014 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 0.00177 ( 1) link_NAG-ASN : angle 0.97748 ( 3) hydrogen bonds : bond 0.04785 ( 275) hydrogen bonds : angle 4.43790 ( 795) SS BOND : bond 0.00182 ( 2) SS BOND : angle 1.41486 ( 4) covalent geometry : bond 0.00313 ( 4035) covalent geometry : angle 0.54752 ( 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 53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.377 Fit side-chains REVERT: A 17 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6855 (mm110) REVERT: A 73 SER cc_start: 0.7958 (t) cc_final: 0.7142 (m) REVERT: A 87 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8013 (ptt180) REVERT: A 89 ARG cc_start: 0.6916 (ttm-80) cc_final: 0.6523 (mtt180) REVERT: A 92 GLN cc_start: 0.7031 (mm-40) cc_final: 0.6720 (mm110) REVERT: A 281 ARG cc_start: 0.7833 (mtp-110) cc_final: 0.7496 (ttm-80) REVERT: A 390 MET cc_start: 0.6050 (mmm) cc_final: 0.3977 (ptm) REVERT: A 470 MET cc_start: 0.7736 (mmt) cc_final: 0.6528 (ttt) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 1.0996 time to fit residues: 56.0698 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 : 0.362 ------------------------------------------------------------------------------- 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 421 LEU 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: 0.6980 chunk 45 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.177783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138644 restraints weight = 4244.845| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.90 r_work: 0.3489 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4038 Z= 0.126 Angle : 0.535 10.968 5511 Z= 0.263 Chirality : 0.038 0.148 651 Planarity : 0.005 0.038 684 Dihedral : 3.769 14.865 569 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.68 % Allowed : 14.66 % 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: 2.17 (0.38), residues: 513 helix: 1.71 (0.27), residues: 377 sheet: -2.08 (1.46), residues: 10 loop : 1.20 (0.59), 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 0.014 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.008 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 0.95715 ( 3) hydrogen bonds : bond 0.04596 ( 275) hydrogen bonds : angle 4.39417 ( 795) SS BOND : bond 0.00161 ( 2) SS BOND : angle 1.36045 ( 4) covalent geometry : bond 0.00277 ( 4035) covalent geometry : angle 0.53391 ( 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 49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.372 Fit side-chains REVERT: A 73 SER cc_start: 0.7923 (OUTLIER) cc_final: 0.7103 (m) REVERT: A 89 ARG cc_start: 0.6879 (ttm-80) cc_final: 0.6467 (mtt180) REVERT: A 92 GLN cc_start: 0.6978 (mm-40) cc_final: 0.6667 (mm110) REVERT: A 281 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.7444 (ttm-80) REVERT: A 376 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7818 (mp) REVERT: A 390 MET cc_start: 0.5951 (mmm) cc_final: 0.3911 (ptm) REVERT: A 470 MET cc_start: 0.7686 (mmt) cc_final: 0.6427 (ttt) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 1.0434 time to fit residues: 51.1738 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 : 0.389 ------------------------------------------------------------------------------- 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 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.0970 chunk 6 optimal weight: 0.0020 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.2786 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.181041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.142266 restraints weight = 4193.375| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.85 r_work: 0.3520 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4038 Z= 0.108 Angle : 0.506 10.345 5511 Z= 0.248 Chirality : 0.037 0.135 651 Planarity : 0.004 0.038 684 Dihedral : 3.586 13.611 569 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.76 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: 2.41 (0.38), residues: 513 helix: 1.88 (0.27), residues: 379 sheet: -2.13 (1.43), residues: 10 loop : 1.30 (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 0.017 0.001 TYR A 272 ARG 0.007 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 1) link_NAG-ASN : angle 0.96143 ( 3) hydrogen bonds : bond 0.04023 ( 275) hydrogen bonds : angle 4.24795 ( 795) SS BOND : bond 0.00120 ( 2) SS BOND : angle 1.22208 ( 4) covalent geometry : bond 0.00221 ( 4035) covalent geometry : angle 0.50486 ( 5504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3368.93 seconds wall clock time: 59 minutes 0.44 seconds (3540.44 seconds total)