Starting phenix.real_space_refine on Thu Jun 5 00:49:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hez_34705/06_2025/8hez_34705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hez_34705/06_2025/8hez_34705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hez_34705/06_2025/8hez_34705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hez_34705/06_2025/8hez_34705.map" model { file = "/net/cci-nas-00/data/ceres_data/8hez_34705/06_2025/8hez_34705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hez_34705/06_2025/8hez_34705.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 37 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3129 2.51 5 N 769 2.21 5 O 802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4739 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4461 Classifications: {'peptide': 582} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 554} Chain breaks: 1 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 47 Unusual residues: {' NA': 1, 'LE6': 1, 'NAG': 1} Classifications: {'undetermined': 3, 'water': 4} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.23, per 1000 atoms: 0.68 Number of scatterers: 4739 At special positions: 0 Unit cell: (74.1469, 76.3602, 90.7469, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 37 16.00 Na 1 11.00 O 802 8.00 N 769 7.00 C 3129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.08 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.11 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.09 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.01 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 801 " - " ASN A 250 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 528.0 milliseconds 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 82.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 22 through 47 removed outlier: 4.000A pdb=" N ILE A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 58 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.837A pdb=" N PHE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 removed outlier: 3.761A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.056A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.675A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 175 through 192 removed outlier: 4.149A pdb=" N GLY A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 224 removed outlier: 3.630A pdb=" N VAL A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.575A pdb=" N PHE A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.659A pdb=" N TYR A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 293 Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.403A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.551A pdb=" N THR A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'A' and resid 377 through 409 removed outlier: 3.851A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 420 through 446 removed outlier: 3.609A pdb=" N VAL A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.819A pdb=" N ASP A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 481 through 507 Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 525 through 547 removed outlier: 3.586A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 672 Processing helix chain 'B' and resid 29 through 55 347 hydrogen bonds defined for protein. 1041 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: 1.27 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 703 1.31 - 1.44: 1405 1.44 - 1.58: 2697 1.58 - 1.71: 0 1.71 - 1.85: 58 Bond restraints: 4863 Sorted by residual: bond pdb=" C THR A 323 " pdb=" O THR A 323 " ideal model delta sigma weight residual 1.243 1.191 0.053 9.50e-03 1.11e+04 3.08e+01 bond pdb=" C PRO A 66 " pdb=" O PRO A 66 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.16e-02 7.43e+03 2.99e+01 bond pdb=" C TYR A 319 " pdb=" O TYR A 319 " ideal model delta sigma weight residual 1.236 1.293 -0.056 1.15e-02 7.56e+03 2.38e+01 bond pdb=" CA SER A 335 " pdb=" CB SER A 335 " ideal model delta sigma weight residual 1.528 1.461 0.068 1.56e-02 4.11e+03 1.90e+01 bond pdb=" N ASP A 261 " pdb=" CA ASP A 261 " ideal model delta sigma weight residual 1.457 1.505 -0.047 1.10e-02 8.26e+03 1.85e+01 ... (remaining 4858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 4306 2.12 - 4.23: 2000 4.23 - 6.35: 297 6.35 - 8.46: 25 8.46 - 10.58: 6 Bond angle restraints: 6634 Sorted by residual: angle pdb=" CA THR A 119 " pdb=" CB THR A 119 " pdb=" OG1 THR A 119 " ideal model delta sigma weight residual 109.60 120.00 -10.40 1.50e+00 4.44e-01 4.81e+01 angle pdb=" C LEU A 521 " pdb=" N CYS A 522 " pdb=" CA CYS A 522 " ideal model delta sigma weight residual 120.60 130.85 -10.25 1.60e+00 3.91e-01 4.11e+01 angle pdb=" C ALA A 303 " pdb=" N GLY A 304 " pdb=" CA GLY A 304 " ideal model delta sigma weight residual 120.10 126.02 -5.92 9.50e-01 1.11e+00 3.89e+01 angle pdb=" N PRO A 465 " pdb=" CA PRO A 465 " pdb=" C PRO A 465 " ideal model delta sigma weight residual 110.70 117.68 -6.98 1.22e+00 6.72e-01 3.27e+01 angle pdb=" CA LEU A 107 " pdb=" C LEU A 107 " pdb=" O LEU A 107 " ideal model delta sigma weight residual 120.42 114.37 6.05 1.06e+00 8.90e-01 3.26e+01 ... (remaining 6629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.53: 2450 13.53 - 27.05: 262 27.05 - 40.57: 86 40.57 - 54.09: 21 54.09 - 67.62: 9 Dihedral angle restraints: 2828 sinusoidal: 1088 harmonic: 1740 Sorted by residual: dihedral pdb=" CA HIS A 557 " pdb=" C HIS A 557 " pdb=" N ARG A 558 " pdb=" CA ARG A 558 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LYS A 554 " pdb=" C LYS A 554 " pdb=" N HIS A 555 " pdb=" CA HIS A 555 " ideal model delta harmonic sigma weight residual 180.00 152.24 27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA GLY A 92 " pdb=" C GLY A 92 " pdb=" N LEU A 93 " pdb=" CA LEU A 93 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 2825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 502 0.080 - 0.160: 225 0.160 - 0.240: 43 0.240 - 0.320: 3 0.320 - 0.400: 1 Chirality restraints: 774 Sorted by residual: chirality pdb=" CB VAL A 95 " pdb=" CA VAL A 95 " pdb=" CG1 VAL A 95 " pdb=" CG2 VAL A 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB VAL A 560 " pdb=" CA VAL A 560 " pdb=" CG1 VAL A 560 " pdb=" CG2 VAL A 560 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB VAL A 106 " pdb=" CA VAL A 106 " pdb=" CG1 VAL A 106 " pdb=" CG2 VAL A 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 771 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 98 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C PHE A 98 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 98 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 99 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 128 " 0.025 2.00e-02 2.50e+03 1.41e-02 3.95e+00 pdb=" CG TYR A 128 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 128 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 128 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 128 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 128 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 128 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 128 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 300 " -0.034 9.50e-02 1.11e+02 2.18e-02 3.17e+00 pdb=" NE ARG A 300 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 300 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 300 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 300 " 0.009 2.00e-02 2.50e+03 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 85 2.70 - 3.25: 4721 3.25 - 3.80: 7967 3.80 - 4.35: 10735 4.35 - 4.90: 17400 Nonbonded interactions: 40908 Sorted by model distance: nonbonded pdb=" O ALA A 73 " pdb="NA NA A 803 " model vdw 2.144 2.470 nonbonded pdb=" O ILE A 76 " pdb="NA NA A 803 " model vdw 2.213 2.470 nonbonded pdb=" OH TYR A 128 " pdb=" O LEU A 559 " model vdw 2.349 3.040 nonbonded pdb=" O TYR A 199 " pdb=" OG1 THR A 202 " model vdw 2.351 3.040 nonbonded pdb=" O MET A 407 " pdb=" OG1 THR A 411 " model vdw 2.375 3.040 ... (remaining 40903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 0.015 0.077 4868 Z= 1.116 Angle : 2.211 10.580 6645 Z= 1.653 Chirality : 0.086 0.400 774 Planarity : 0.004 0.024 810 Dihedral : 13.748 67.617 1708 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer: Outliers : 2.82 % Allowed : 5.24 % Favored : 91.94 % Cbeta Deviations : 0.36 % 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: -2.33 (0.29), residues: 605 helix: -1.18 (0.21), residues: 435 sheet: None (None), residues: 0 loop : -2.14 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 289 HIS 0.004 0.001 HIS A 557 PHE 0.022 0.003 PHE A 534 TYR 0.028 0.004 TYR A 128 ARG 0.030 0.001 ARG A 300 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 1) link_NAG-ASN : angle 3.85076 ( 3) hydrogen bonds : bond 0.18337 ( 347) hydrogen bonds : angle 8.85252 ( 1041) SS BOND : bond 0.05396 ( 4) SS BOND : angle 5.02663 ( 8) covalent geometry : bond 0.01516 ( 4863) covalent geometry : angle 2.20430 ( 6634) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.469 Fit side-chains REVERT: A 44 MET cc_start: 0.6684 (mtm) cc_final: 0.6401 (mpp) REVERT: A 49 ARG cc_start: 0.6199 (mtp-110) cc_final: 0.5792 (mtp-110) REVERT: A 62 MET cc_start: 0.8721 (mmp) cc_final: 0.8256 (mmm) REVERT: A 125 MET cc_start: 0.8536 (mmp) cc_final: 0.8292 (mmp) REVERT: A 136 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7011 (mtt-85) REVERT: A 168 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7482 (mm-40) REVERT: A 244 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 333 MET cc_start: 0.8938 (mtp) cc_final: 0.8358 (mtm) REVERT: A 342 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 382 MET cc_start: 0.7981 (mmm) cc_final: 0.7739 (mmm) REVERT: A 420 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6381 (ttp80) REVERT: A 445 GLN cc_start: 0.7284 (mm110) cc_final: 0.7061 (mm110) REVERT: A 483 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7163 (mm-40) REVERT: A 495 MET cc_start: 0.7536 (mtp) cc_final: 0.7104 (mtt) REVERT: A 513 GLN cc_start: 0.6490 (mm110) cc_final: 0.4947 (mp10) REVERT: A 548 THR cc_start: 0.7281 (m) cc_final: 0.6819 (p) REVERT: A 558 ARG cc_start: 0.6400 (ptt180) cc_final: 0.5862 (ptp90) REVERT: A 567 LYS cc_start: 0.2255 (OUTLIER) cc_final: 0.1624 (mttm) REVERT: A 651 ARG cc_start: 0.6584 (ttm110) cc_final: 0.5701 (tpp-160) outliers start: 14 outliers final: 1 residues processed: 92 average time/residue: 1.2547 time to fit residues: 119.7150 Evaluate side-chains 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 567 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 204 GLN A 295 GLN A 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.124832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.097407 restraints weight = 4867.024| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.42 r_work: 0.2753 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4868 Z= 0.175 Angle : 0.709 16.582 6645 Z= 0.353 Chirality : 0.045 0.158 774 Planarity : 0.005 0.041 810 Dihedral : 7.699 61.705 726 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.43 % Allowed : 7.86 % Favored : 88.71 % 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: 0.46 (0.33), residues: 605 helix: 0.97 (0.23), residues: 454 sheet: None (None), residues: 0 loop : -1.66 (0.46), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 65 HIS 0.004 0.001 HIS A 80 PHE 0.018 0.002 PHE A 453 TYR 0.016 0.002 TYR A 188 ARG 0.004 0.001 ARG A 267 Details of bonding type rmsd link_NAG-ASN : bond 0.00036 ( 1) link_NAG-ASN : angle 2.86253 ( 3) hydrogen bonds : bond 0.04931 ( 347) hydrogen bonds : angle 6.02309 ( 1041) SS BOND : bond 0.00546 ( 4) SS BOND : angle 1.26356 ( 8) covalent geometry : bond 0.00389 ( 4863) covalent geometry : angle 0.70517 ( 6634) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.501 Fit side-chains REVERT: A 62 MET cc_start: 0.9280 (mmp) cc_final: 0.8995 (mmm) REVERT: A 167 GLN cc_start: 0.8322 (tt0) cc_final: 0.7913 (tt0) REVERT: A 184 ILE cc_start: 0.8555 (mt) cc_final: 0.8322 (mm) REVERT: A 206 PHE cc_start: 0.8315 (t80) cc_final: 0.7653 (t80) REVERT: A 300 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8143 (mpt180) REVERT: A 333 MET cc_start: 0.9332 (mtp) cc_final: 0.9006 (mtm) REVERT: A 342 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8212 (mp0) REVERT: A 382 MET cc_start: 0.8583 (mmm) cc_final: 0.8337 (mmm) REVERT: A 407 MET cc_start: 0.8587 (mmm) cc_final: 0.8369 (mmt) REVERT: A 482 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 495 MET cc_start: 0.8292 (mtp) cc_final: 0.7944 (mtt) REVERT: A 513 GLN cc_start: 0.7130 (mm110) cc_final: 0.5505 (mp10) REVERT: A 651 ARG cc_start: 0.7286 (ttm110) cc_final: 0.6801 (ttm110) outliers start: 17 outliers final: 4 residues processed: 85 average time/residue: 1.0198 time to fit residues: 90.7105 Evaluate side-chains 65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.119076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.091217 restraints weight = 4920.210| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.47 r_work: 0.2742 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4868 Z= 0.150 Angle : 0.645 14.479 6645 Z= 0.320 Chirality : 0.042 0.154 774 Planarity : 0.005 0.045 810 Dihedral : 6.470 58.120 719 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.23 % Allowed : 9.27 % 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: 1.18 (0.34), residues: 605 helix: 1.46 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -1.25 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 PHE 0.013 0.001 PHE A 453 TYR 0.015 0.002 TYR A 256 ARG 0.003 0.000 ARG A 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 1) link_NAG-ASN : angle 2.15856 ( 3) hydrogen bonds : bond 0.04473 ( 347) hydrogen bonds : angle 5.73007 ( 1041) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.75077 ( 8) covalent geometry : bond 0.00339 ( 4863) covalent geometry : angle 0.64292 ( 6634) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.507 Fit side-chains REVERT: A 62 MET cc_start: 0.9251 (mmp) cc_final: 0.8949 (mmm) REVERT: A 167 GLN cc_start: 0.8405 (tt0) cc_final: 0.7978 (tt0) REVERT: A 206 PHE cc_start: 0.8308 (t80) cc_final: 0.7703 (t80) REVERT: A 300 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8257 (mpt180) REVERT: A 333 MET cc_start: 0.9301 (mtp) cc_final: 0.9006 (mtm) REVERT: A 382 MET cc_start: 0.8523 (mmm) cc_final: 0.8263 (mmm) REVERT: A 495 MET cc_start: 0.8361 (mtp) cc_final: 0.7890 (mtt) REVERT: A 513 GLN cc_start: 0.6997 (mm110) cc_final: 0.5589 (mp10) REVERT: A 651 ARG cc_start: 0.7232 (ttm110) cc_final: 0.6759 (ttm170) outliers start: 16 outliers final: 4 residues processed: 66 average time/residue: 0.9167 time to fit residues: 63.7796 Evaluate side-chains 57 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.120830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.093176 restraints weight = 4945.788| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.47 r_work: 0.2776 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4868 Z= 0.132 Angle : 0.606 12.193 6645 Z= 0.300 Chirality : 0.041 0.150 774 Planarity : 0.005 0.048 810 Dihedral : 5.273 37.373 715 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.62 % Allowed : 11.09 % Favored : 86.29 % 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: 1.54 (0.34), residues: 605 helix: 1.68 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -1.03 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 PHE 0.010 0.001 PHE A 453 TYR 0.014 0.001 TYR A 256 ARG 0.002 0.000 ARG A 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 1) link_NAG-ASN : angle 1.96031 ( 3) hydrogen bonds : bond 0.04117 ( 347) hydrogen bonds : angle 5.54577 ( 1041) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.60019 ( 8) covalent geometry : bond 0.00288 ( 4863) covalent geometry : angle 0.60460 ( 6634) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.579 Fit side-chains REVERT: A 62 MET cc_start: 0.9235 (mmp) cc_final: 0.8902 (mmm) REVERT: A 167 GLN cc_start: 0.8360 (tt0) cc_final: 0.7868 (tt0) REVERT: A 206 PHE cc_start: 0.8356 (t80) cc_final: 0.7714 (t80) REVERT: A 231 ASP cc_start: 0.8097 (p0) cc_final: 0.7263 (m-30) REVERT: A 300 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8282 (mpt180) REVERT: A 333 MET cc_start: 0.9271 (mtp) cc_final: 0.8989 (mtm) REVERT: A 342 GLU cc_start: 0.8465 (mp0) cc_final: 0.7986 (mp0) REVERT: A 382 MET cc_start: 0.8491 (mmm) cc_final: 0.8230 (mmm) REVERT: A 482 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 495 MET cc_start: 0.8314 (mtp) cc_final: 0.7848 (mtt) REVERT: A 513 GLN cc_start: 0.7019 (mm110) cc_final: 0.5619 (mp10) REVERT: A 557 HIS cc_start: 0.6871 (OUTLIER) cc_final: 0.6322 (m-70) REVERT: A 651 ARG cc_start: 0.7146 (ttm110) cc_final: 0.6735 (ttm110) REVERT: B 31 MET cc_start: 0.7308 (mmt) cc_final: 0.6263 (ptp) outliers start: 13 outliers final: 4 residues processed: 70 average time/residue: 1.1413 time to fit residues: 83.4574 Evaluate side-chains 62 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.122186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.094591 restraints weight = 4974.270| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.45 r_work: 0.2785 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4868 Z= 0.128 Angle : 0.603 11.271 6645 Z= 0.298 Chirality : 0.041 0.150 774 Planarity : 0.005 0.050 810 Dihedral : 5.132 37.139 715 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.42 % Allowed : 12.70 % Favored : 84.88 % 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: 1.74 (0.34), residues: 605 helix: 1.81 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -0.92 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.005 0.001 HIS A 80 PHE 0.009 0.001 PHE A 534 TYR 0.012 0.001 TYR A 256 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 1) link_NAG-ASN : angle 1.81134 ( 3) hydrogen bonds : bond 0.04055 ( 347) hydrogen bonds : angle 5.46141 ( 1041) SS BOND : bond 0.00381 ( 4) SS BOND : angle 1.41537 ( 8) covalent geometry : bond 0.00283 ( 4863) covalent geometry : angle 0.60056 ( 6634) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.468 Fit side-chains REVERT: A 62 MET cc_start: 0.9239 (mmp) cc_final: 0.8962 (mmm) REVERT: A 167 GLN cc_start: 0.8231 (tt0) cc_final: 0.7856 (tt0) REVERT: A 206 PHE cc_start: 0.8378 (t80) cc_final: 0.7757 (t80) REVERT: A 231 ASP cc_start: 0.7926 (p0) cc_final: 0.7232 (m-30) REVERT: A 241 THR cc_start: 0.9040 (p) cc_final: 0.8807 (p) REVERT: A 300 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8286 (mpt180) REVERT: A 305 LYS cc_start: 0.8827 (tttt) cc_final: 0.8612 (ttpt) REVERT: A 333 MET cc_start: 0.9267 (mtp) cc_final: 0.8980 (mtm) REVERT: A 342 GLU cc_start: 0.8505 (mp0) cc_final: 0.8267 (mp0) REVERT: A 382 MET cc_start: 0.8479 (mmm) cc_final: 0.8214 (mmm) REVERT: A 482 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 495 MET cc_start: 0.8298 (mtp) cc_final: 0.7833 (mtt) REVERT: A 513 GLN cc_start: 0.7082 (mm110) cc_final: 0.5694 (mp10) REVERT: A 557 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.6111 (m-70) REVERT: A 651 ARG cc_start: 0.7143 (ttm110) cc_final: 0.6739 (ttm110) REVERT: B 31 MET cc_start: 0.7267 (mmt) cc_final: 0.6242 (ptp) outliers start: 12 outliers final: 4 residues processed: 69 average time/residue: 1.1640 time to fit residues: 84.0671 Evaluate side-chains 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.122857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.095297 restraints weight = 4939.920| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.48 r_work: 0.2802 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4868 Z= 0.120 Angle : 0.590 10.318 6645 Z= 0.289 Chirality : 0.041 0.147 774 Planarity : 0.005 0.050 810 Dihedral : 5.000 36.879 715 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.22 % Allowed : 13.31 % Favored : 84.48 % 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: 1.91 (0.35), residues: 605 helix: 1.93 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -0.82 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 PHE 0.009 0.001 PHE A 534 TYR 0.012 0.001 TYR A 256 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 1) link_NAG-ASN : angle 1.64157 ( 3) hydrogen bonds : bond 0.03911 ( 347) hydrogen bonds : angle 5.37953 ( 1041) SS BOND : bond 0.00244 ( 4) SS BOND : angle 1.01429 ( 8) covalent geometry : bond 0.00261 ( 4863) covalent geometry : angle 0.58851 ( 6634) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.502 Fit side-chains REVERT: A 62 MET cc_start: 0.9241 (mmp) cc_final: 0.8930 (mmm) REVERT: A 206 PHE cc_start: 0.8366 (t80) cc_final: 0.7802 (t80) REVERT: A 231 ASP cc_start: 0.7887 (p0) cc_final: 0.7246 (m-30) REVERT: A 241 THR cc_start: 0.9023 (p) cc_final: 0.8786 (p) REVERT: A 300 ARG cc_start: 0.8556 (mmt-90) cc_final: 0.8320 (mpt180) REVERT: A 333 MET cc_start: 0.9268 (mtp) cc_final: 0.8986 (mtm) REVERT: A 342 GLU cc_start: 0.8504 (mp0) cc_final: 0.8261 (mp0) REVERT: A 382 MET cc_start: 0.8487 (mmm) cc_final: 0.8225 (mmm) REVERT: A 482 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 495 MET cc_start: 0.8301 (mtp) cc_final: 0.7845 (mtt) REVERT: A 513 GLN cc_start: 0.7007 (mm110) cc_final: 0.5580 (mp10) REVERT: A 557 HIS cc_start: 0.6499 (OUTLIER) cc_final: 0.5930 (m-70) REVERT: A 651 ARG cc_start: 0.7144 (ttm110) cc_final: 0.6734 (ttm110) REVERT: B 31 MET cc_start: 0.7202 (mmt) cc_final: 0.6224 (ptp) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 1.5861 time to fit residues: 110.7730 Evaluate side-chains 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.119858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.092263 restraints weight = 4927.315| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.46 r_work: 0.2749 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4868 Z= 0.154 Angle : 0.624 9.800 6645 Z= 0.309 Chirality : 0.043 0.155 774 Planarity : 0.005 0.051 810 Dihedral : 5.189 37.384 715 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.42 % Allowed : 13.91 % Favored : 83.67 % 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: 1.80 (0.34), residues: 605 helix: 1.82 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.71 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 PHE 0.012 0.002 PHE A 534 TYR 0.015 0.002 TYR A 128 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 1.64934 ( 3) hydrogen bonds : bond 0.04388 ( 347) hydrogen bonds : angle 5.54716 ( 1041) SS BOND : bond 0.00336 ( 4) SS BOND : angle 1.02112 ( 8) covalent geometry : bond 0.00357 ( 4863) covalent geometry : angle 0.62276 ( 6634) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.506 Fit side-chains REVERT: A 62 MET cc_start: 0.9275 (mmp) cc_final: 0.8958 (mmm) REVERT: A 206 PHE cc_start: 0.8433 (t80) cc_final: 0.7807 (t80) REVERT: A 231 ASP cc_start: 0.7945 (p0) cc_final: 0.7256 (m-30) REVERT: A 241 THR cc_start: 0.9156 (p) cc_final: 0.8903 (p) REVERT: A 300 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8289 (mpt180) REVERT: A 333 MET cc_start: 0.9278 (mtp) cc_final: 0.8977 (mtm) REVERT: A 342 GLU cc_start: 0.8577 (mp0) cc_final: 0.8313 (mp0) REVERT: A 382 MET cc_start: 0.8524 (mmm) cc_final: 0.8230 (mmm) REVERT: A 482 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 495 MET cc_start: 0.8378 (mtp) cc_final: 0.7876 (mtt) REVERT: A 513 GLN cc_start: 0.6966 (mm110) cc_final: 0.5518 (mp10) REVERT: A 557 HIS cc_start: 0.6675 (OUTLIER) cc_final: 0.6106 (m-70) REVERT: A 651 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6859 (ttm110) REVERT: B 31 MET cc_start: 0.7289 (mmt) cc_final: 0.6278 (ptp) outliers start: 12 outliers final: 5 residues processed: 65 average time/residue: 1.0493 time to fit residues: 71.4324 Evaluate side-chains 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.119323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.091248 restraints weight = 4959.645| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.48 r_work: 0.2734 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4868 Z= 0.164 Angle : 0.638 9.867 6645 Z= 0.315 Chirality : 0.043 0.156 774 Planarity : 0.005 0.051 810 Dihedral : 5.437 37.339 715 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.22 % Allowed : 14.52 % Favored : 83.27 % 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: 1.73 (0.34), residues: 605 helix: 1.75 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.65 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 PHE 0.012 0.002 PHE A 534 TYR 0.016 0.002 TYR A 128 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd link_NAG-ASN : bond 0.01405 ( 1) link_NAG-ASN : angle 1.60788 ( 3) hydrogen bonds : bond 0.04472 ( 347) hydrogen bonds : angle 5.60151 ( 1041) SS BOND : bond 0.00360 ( 4) SS BOND : angle 0.98665 ( 8) covalent geometry : bond 0.00382 ( 4863) covalent geometry : angle 0.63698 ( 6634) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.477 Fit side-chains REVERT: A 62 MET cc_start: 0.9271 (mmp) cc_final: 0.8949 (mmm) REVERT: A 206 PHE cc_start: 0.8414 (t80) cc_final: 0.7757 (t80) REVERT: A 231 ASP cc_start: 0.7932 (p0) cc_final: 0.7259 (m-30) REVERT: A 241 THR cc_start: 0.9041 (p) cc_final: 0.8809 (p) REVERT: A 300 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8245 (mpt180) REVERT: A 333 MET cc_start: 0.9263 (mtp) cc_final: 0.8964 (mtm) REVERT: A 342 GLU cc_start: 0.8558 (mp0) cc_final: 0.8317 (mp0) REVERT: A 382 MET cc_start: 0.8512 (mmm) cc_final: 0.8220 (mmm) REVERT: A 482 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 495 MET cc_start: 0.8377 (mtp) cc_final: 0.7863 (mtt) REVERT: A 513 GLN cc_start: 0.6928 (mm110) cc_final: 0.5444 (mp10) REVERT: A 557 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6148 (m-70) REVERT: A 651 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6821 (ttm110) REVERT: B 31 MET cc_start: 0.7229 (mmt) cc_final: 0.6166 (mtm) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 1.0562 time to fit residues: 70.8046 Evaluate side-chains 67 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.122751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.094992 restraints weight = 4974.086| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.48 r_work: 0.2784 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4868 Z= 0.126 Angle : 0.593 9.486 6645 Z= 0.292 Chirality : 0.041 0.147 774 Planarity : 0.005 0.051 810 Dihedral : 5.074 36.523 715 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.42 % Allowed : 14.52 % Favored : 83.06 % 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: 2.02 (0.34), residues: 605 helix: 1.97 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.57 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 PHE 0.010 0.001 PHE A 534 TYR 0.011 0.001 TYR A 256 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd link_NAG-ASN : bond 0.01451 ( 1) link_NAG-ASN : angle 2.15416 ( 3) hydrogen bonds : bond 0.03995 ( 347) hydrogen bonds : angle 5.42743 ( 1041) SS BOND : bond 0.00246 ( 4) SS BOND : angle 0.76939 ( 8) covalent geometry : bond 0.00275 ( 4863) covalent geometry : angle 0.59120 ( 6634) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.512 Fit side-chains REVERT: A 62 MET cc_start: 0.9283 (mmp) cc_final: 0.8956 (mmm) REVERT: A 206 PHE cc_start: 0.8393 (t80) cc_final: 0.7822 (t80) REVERT: A 231 ASP cc_start: 0.7865 (p0) cc_final: 0.7284 (m-30) REVERT: A 300 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8303 (mpt180) REVERT: A 333 MET cc_start: 0.9262 (mtp) cc_final: 0.9029 (mtm) REVERT: A 342 GLU cc_start: 0.8550 (mp0) cc_final: 0.8289 (mp0) REVERT: A 382 MET cc_start: 0.8505 (mmm) cc_final: 0.8250 (mmm) REVERT: A 482 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 495 MET cc_start: 0.8312 (mtp) cc_final: 0.7840 (mtt) REVERT: A 513 GLN cc_start: 0.6960 (mm110) cc_final: 0.5555 (mt0) REVERT: A 557 HIS cc_start: 0.6516 (OUTLIER) cc_final: 0.5920 (m-70) REVERT: A 651 ARG cc_start: 0.7264 (ttm110) cc_final: 0.6844 (ttm110) REVERT: B 31 MET cc_start: 0.7231 (mmt) cc_final: 0.6247 (ptp) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 1.1067 time to fit residues: 74.1928 Evaluate side-chains 66 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.123831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.096230 restraints weight = 4961.710| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.47 r_work: 0.2807 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4868 Z= 0.120 Angle : 0.585 8.990 6645 Z= 0.288 Chirality : 0.041 0.146 774 Planarity : 0.005 0.051 810 Dihedral : 4.969 36.593 715 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.81 % Allowed : 15.32 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.35), residues: 605 helix: 2.05 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.51 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 PHE 0.009 0.001 PHE A 534 TYR 0.012 0.001 TYR A 256 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd link_NAG-ASN : bond 0.01097 ( 1) link_NAG-ASN : angle 2.06128 ( 3) hydrogen bonds : bond 0.03908 ( 347) hydrogen bonds : angle 5.36324 ( 1041) SS BOND : bond 0.00229 ( 4) SS BOND : angle 0.73694 ( 8) covalent geometry : bond 0.00258 ( 4863) covalent geometry : angle 0.58367 ( 6634) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.463 Fit side-chains REVERT: A 62 MET cc_start: 0.9265 (mmp) cc_final: 0.8978 (mmm) REVERT: A 206 PHE cc_start: 0.8332 (t80) cc_final: 0.7775 (t80) REVERT: A 231 ASP cc_start: 0.7844 (p0) cc_final: 0.7253 (m-30) REVERT: A 300 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8306 (mpt180) REVERT: A 333 MET cc_start: 0.9246 (mtp) cc_final: 0.9012 (mtm) REVERT: A 342 GLU cc_start: 0.8546 (mp0) cc_final: 0.8287 (mp0) REVERT: A 382 MET cc_start: 0.8464 (mmm) cc_final: 0.8199 (mmm) REVERT: A 482 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 495 MET cc_start: 0.8255 (mtp) cc_final: 0.7790 (mtt) REVERT: A 513 GLN cc_start: 0.6871 (mm110) cc_final: 0.5535 (mt0) REVERT: A 557 HIS cc_start: 0.6409 (OUTLIER) cc_final: 0.5910 (m-70) REVERT: A 651 ARG cc_start: 0.7190 (ttm110) cc_final: 0.6763 (ttm110) REVERT: B 31 MET cc_start: 0.7215 (mmt) cc_final: 0.6226 (ptp) outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 1.0309 time to fit residues: 69.1283 Evaluate side-chains 65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.123997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.096502 restraints weight = 5030.260| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.47 r_work: 0.2819 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4868 Z= 0.118 Angle : 0.581 8.895 6645 Z= 0.286 Chirality : 0.041 0.152 774 Planarity : 0.005 0.050 810 Dihedral : 4.893 36.585 715 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.41 % Allowed : 15.93 % Favored : 82.66 % 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 (0.35), residues: 605 helix: 2.10 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.45 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 65 HIS 0.005 0.001 HIS A 80 PHE 0.009 0.001 PHE A 534 TYR 0.011 0.001 TYR A 256 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd link_NAG-ASN : bond 0.01032 ( 1) link_NAG-ASN : angle 2.13753 ( 3) hydrogen bonds : bond 0.03881 ( 347) hydrogen bonds : angle 5.32803 ( 1041) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.68908 ( 8) covalent geometry : bond 0.00254 ( 4863) covalent geometry : angle 0.57928 ( 6634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3380.91 seconds wall clock time: 58 minutes 49.04 seconds (3529.04 seconds total)