Starting phenix.real_space_refine on Thu Nov 14 07:04:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hez_34705/11_2024/8hez_34705.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hez_34705/11_2024/8hez_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hez_34705/11_2024/8hez_34705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hez_34705/11_2024/8hez_34705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hez_34705/11_2024/8hez_34705.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hez_34705/11_2024/8hez_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-5513/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: 3.14, per 1000 atoms: 0.66 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: 1.25 Conformation dependent library (CDL) restraints added in 600.5 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: 0.47 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: 1.33 Time building geometry restraints manager: 1.43 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- 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 0.070 4863 Z= 0.996 Angle : 2.204 10.580 6634 Z= 1.652 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 *********************** 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 : 0.475 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: 1.3113 time to fit residues: 125.1100 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 : 0.459 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 4863 Z= 0.259 Angle : 0.705 16.582 6634 Z= 0.352 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 *********************** 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 : 0.468 Fit side-chains REVERT: A 44 MET cc_start: 0.6237 (mtm) cc_final: 0.5907 (mpp) REVERT: A 62 MET cc_start: 0.8910 (mmp) cc_final: 0.8463 (mmm) REVERT: A 103 LEU cc_start: 0.7443 (tt) cc_final: 0.7006 (mp) REVERT: A 136 ARG cc_start: 0.7549 (mtt180) cc_final: 0.6972 (mtp180) REVERT: A 167 GLN cc_start: 0.7590 (tt0) cc_final: 0.7255 (tt0) REVERT: A 206 PHE cc_start: 0.7688 (t80) cc_final: 0.6897 (t80) REVERT: A 300 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7438 (mpt180) REVERT: A 305 LYS cc_start: 0.7982 (tttp) cc_final: 0.7736 (tttt) REVERT: A 306 SER cc_start: 0.7884 (t) cc_final: 0.7355 (p) REVERT: A 333 MET cc_start: 0.8757 (mtp) cc_final: 0.8310 (mtm) REVERT: A 342 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: A 382 MET cc_start: 0.7624 (mmm) cc_final: 0.7336 (mmm) REVERT: A 482 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 495 MET cc_start: 0.7379 (mtp) cc_final: 0.6938 (mtt) REVERT: A 513 GLN cc_start: 0.6376 (mm110) cc_final: 0.5057 (mp10) REVERT: A 548 THR cc_start: 0.7010 (m) cc_final: 0.6545 (p) REVERT: A 558 ARG cc_start: 0.6243 (ptt180) cc_final: 0.5716 (ptp90) REVERT: A 567 LYS cc_start: 0.2564 (OUTLIER) cc_final: 0.1869 (mmtm) REVERT: A 651 ARG cc_start: 0.6690 (ttm110) cc_final: 0.5952 (ttm110) outliers start: 17 outliers final: 4 residues processed: 85 average time/residue: 1.0518 time to fit residues: 93.5432 Evaluate side-chains 68 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 567 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4863 Z= 0.179 Angle : 0.613 14.094 6634 Z= 0.303 Chirality : 0.041 0.148 774 Planarity : 0.005 0.043 810 Dihedral : 6.611 58.792 723 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 1.39 (0.34), residues: 605 helix: 1.64 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -1.29 (0.49), residues: 151 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 0.011 0.001 PHE A 453 TYR 0.015 0.001 TYR A 256 ARG 0.001 0.000 ARG A 499 *********************** 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 83 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.497 Fit side-chains REVERT: A 62 MET cc_start: 0.8882 (mmp) cc_final: 0.8398 (mmm) REVERT: A 99 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 103 LEU cc_start: 0.7500 (tt) cc_final: 0.7239 (mp) REVERT: A 136 ARG cc_start: 0.7521 (mtt180) cc_final: 0.6970 (mtp180) REVERT: A 151 ILE cc_start: 0.7853 (mt) cc_final: 0.7605 (mp) REVERT: A 167 GLN cc_start: 0.7725 (tt0) cc_final: 0.7338 (tt0) REVERT: A 206 PHE cc_start: 0.7737 (t80) cc_final: 0.6922 (t80) REVERT: A 305 LYS cc_start: 0.7902 (tttp) cc_final: 0.7623 (tttt) REVERT: A 308 THR cc_start: 0.8001 (t) cc_final: 0.7744 (m) REVERT: A 333 MET cc_start: 0.8729 (mtp) cc_final: 0.8283 (mtm) REVERT: A 342 GLU cc_start: 0.8045 (mp0) cc_final: 0.7810 (mp0) REVERT: A 382 MET cc_start: 0.7645 (mmm) cc_final: 0.7381 (mmm) REVERT: A 421 GLU cc_start: 0.8380 (tt0) cc_final: 0.8123 (tt0) REVERT: A 482 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 495 MET cc_start: 0.7515 (mtp) cc_final: 0.6987 (mtt) REVERT: A 513 GLN cc_start: 0.6307 (mm110) cc_final: 0.5192 (mp10) REVERT: A 548 THR cc_start: 0.6930 (m) cc_final: 0.6534 (p) REVERT: A 558 ARG cc_start: 0.6306 (ptt180) cc_final: 0.5699 (ptp90) REVERT: A 567 LYS cc_start: 0.2679 (OUTLIER) cc_final: 0.1786 (mmtm) REVERT: A 651 ARG cc_start: 0.6551 (ttm110) cc_final: 0.5750 (ttm170) REVERT: B 31 MET cc_start: 0.6113 (mmt) cc_final: 0.5301 (ptp) outliers start: 16 outliers final: 5 residues processed: 78 average time/residue: 1.1064 time to fit residues: 90.1203 Evaluate side-chains 68 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain A residue 567 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4863 Z= 0.225 Angle : 0.619 12.216 6634 Z= 0.307 Chirality : 0.042 0.154 774 Planarity : 0.005 0.048 810 Dihedral : 5.645 37.537 719 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.42 % Allowed : 10.89 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.34), residues: 605 helix: 1.68 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -1.18 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 PHE 0.011 0.001 PHE A 453 TYR 0.014 0.002 TYR A 128 ARG 0.002 0.000 ARG A 300 *********************** 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: 12 poor density : 65 time to evaluate : 0.513 Fit side-chains REVERT: A 62 MET cc_start: 0.8897 (mmp) cc_final: 0.8383 (mmm) REVERT: A 99 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8245 (mm-30) REVERT: A 136 ARG cc_start: 0.7554 (mtt180) cc_final: 0.6952 (mtp180) REVERT: A 167 GLN cc_start: 0.7719 (tt0) cc_final: 0.7333 (tt0) REVERT: A 206 PHE cc_start: 0.7772 (t80) cc_final: 0.6982 (t80) REVERT: A 305 LYS cc_start: 0.7891 (tttp) cc_final: 0.7624 (tttt) REVERT: A 333 MET cc_start: 0.8711 (mtp) cc_final: 0.8317 (mtm) REVERT: A 342 GLU cc_start: 0.7999 (mp0) cc_final: 0.7560 (mp0) REVERT: A 382 MET cc_start: 0.7599 (mmm) cc_final: 0.7296 (mmm) REVERT: A 482 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 495 MET cc_start: 0.7484 (mtp) cc_final: 0.6917 (mtt) REVERT: A 513 GLN cc_start: 0.6345 (mm110) cc_final: 0.5270 (mp10) REVERT: A 548 THR cc_start: 0.6909 (m) cc_final: 0.6511 (p) REVERT: A 558 ARG cc_start: 0.6388 (ptt180) cc_final: 0.5854 (ptp90) REVERT: A 567 LYS cc_start: 0.2780 (OUTLIER) cc_final: 0.1847 (mttm) REVERT: A 651 ARG cc_start: 0.6661 (ttm110) cc_final: 0.5960 (ttm110) REVERT: B 31 MET cc_start: 0.6104 (mmt) cc_final: 0.5256 (ptp) outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 1.0869 time to fit residues: 83.0915 Evaluate side-chains 64 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 567 LYS 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 43 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4863 Z= 0.171 Angle : 0.580 10.877 6634 Z= 0.286 Chirality : 0.040 0.146 774 Planarity : 0.005 0.050 810 Dihedral : 5.359 36.851 719 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.42 % Allowed : 12.10 % Favored : 85.48 % 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: 1.85 (0.35), residues: 605 helix: 1.90 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -0.90 (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 0.008 0.001 PHE A 534 TYR 0.014 0.001 TYR A 256 ARG 0.002 0.000 ARG A 267 *********************** 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 : 0.504 Fit side-chains REVERT: A 62 MET cc_start: 0.8895 (mmp) cc_final: 0.8426 (mmm) REVERT: A 103 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7300 (mt) REVERT: A 136 ARG cc_start: 0.7458 (mtt180) cc_final: 0.6862 (mtp180) REVERT: A 151 ILE cc_start: 0.7827 (mt) cc_final: 0.7576 (mp) REVERT: A 167 GLN cc_start: 0.7726 (tt0) cc_final: 0.7266 (tt0) REVERT: A 174 ILE cc_start: 0.7778 (pt) cc_final: 0.7533 (mp) REVERT: A 206 PHE cc_start: 0.7743 (t80) cc_final: 0.7031 (t80) REVERT: A 261 ASP cc_start: 0.8578 (p0) cc_final: 0.8336 (p0) REVERT: A 305 LYS cc_start: 0.7867 (tttp) cc_final: 0.7662 (tttt) REVERT: A 333 MET cc_start: 0.8695 (mtp) cc_final: 0.8296 (mtm) REVERT: A 342 GLU cc_start: 0.8030 (mp0) cc_final: 0.7794 (mp0) REVERT: A 382 MET cc_start: 0.7606 (mmm) cc_final: 0.7326 (mmm) REVERT: A 482 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 495 MET cc_start: 0.7460 (mtp) cc_final: 0.6897 (mtt) REVERT: A 513 GLN cc_start: 0.6437 (mm110) cc_final: 0.5412 (mp10) REVERT: A 548 THR cc_start: 0.6789 (m) cc_final: 0.6399 (p) REVERT: A 557 HIS cc_start: 0.6066 (OUTLIER) cc_final: 0.5742 (m-70) REVERT: A 558 ARG cc_start: 0.6311 (ptt180) cc_final: 0.5822 (ptp90) REVERT: A 651 ARG cc_start: 0.6579 (ttm110) cc_final: 0.5846 (ttm110) REVERT: B 31 MET cc_start: 0.6060 (mmt) cc_final: 0.5210 (ptp) outliers start: 12 outliers final: 4 residues processed: 70 average time/residue: 1.0982 time to fit residues: 80.4190 Evaluate side-chains 64 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain A residue 158 ASP 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 14 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 0.0170 chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4863 Z= 0.164 Angle : 0.579 10.112 6634 Z= 0.284 Chirality : 0.040 0.145 774 Planarity : 0.005 0.051 810 Dihedral : 4.900 36.481 715 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.22 % Allowed : 12.50 % Favored : 85.28 % 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: 2.03 (0.35), residues: 605 helix: 2.02 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -0.79 (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 0.008 0.001 PHE A 534 TYR 0.013 0.001 TYR A 256 ARG 0.010 0.000 ARG A 414 *********************** 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 75 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.523 Fit side-chains REVERT: A 62 MET cc_start: 0.8906 (mmp) cc_final: 0.8486 (mmm) REVERT: A 136 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6866 (mtp180) REVERT: A 206 PHE cc_start: 0.7718 (t80) cc_final: 0.7065 (t80) REVERT: A 231 ASP cc_start: 0.7299 (p0) cc_final: 0.6729 (m-30) REVERT: A 261 ASP cc_start: 0.8668 (p0) cc_final: 0.8461 (p0) REVERT: A 305 LYS cc_start: 0.7899 (tttp) cc_final: 0.7577 (ttpt) REVERT: A 333 MET cc_start: 0.8691 (mtp) cc_final: 0.8300 (mtm) REVERT: A 342 GLU cc_start: 0.8046 (mp0) cc_final: 0.7802 (mp0) REVERT: A 382 MET cc_start: 0.7599 (mmm) cc_final: 0.7292 (mmm) REVERT: A 495 MET cc_start: 0.7309 (mtp) cc_final: 0.6764 (mtt) REVERT: A 513 GLN cc_start: 0.6296 (mm110) cc_final: 0.5231 (mp10) REVERT: A 548 THR cc_start: 0.6795 (m) cc_final: 0.6402 (p) REVERT: A 557 HIS cc_start: 0.5909 (OUTLIER) cc_final: 0.5625 (m-70) REVERT: A 558 ARG cc_start: 0.6299 (ptt180) cc_final: 0.5764 (ptp90) REVERT: A 651 ARG cc_start: 0.6653 (ttm110) cc_final: 0.5932 (ttm110) REVERT: B 31 MET cc_start: 0.6048 (mmt) cc_final: 0.5200 (ptp) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 1.0059 time to fit residues: 75.0633 Evaluate side-chains 66 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 0.0270 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4863 Z= 0.160 Angle : 0.573 9.238 6634 Z= 0.282 Chirality : 0.040 0.145 774 Planarity : 0.005 0.050 810 Dihedral : 4.814 36.249 715 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.41 % Allowed : 14.52 % Favored : 84.07 % 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 (0.35), residues: 605 helix: 2.12 (0.24), residues: 455 sheet: None (None), residues: 0 loop : -0.73 (0.52), residues: 150 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 0.008 0.001 PHE A 534 TYR 0.010 0.001 TYR A 256 ARG 0.008 0.000 ARG A 414 *********************** 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 74 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.565 Fit side-chains REVERT: A 62 MET cc_start: 0.8933 (mmp) cc_final: 0.8422 (mmm) REVERT: A 136 ARG cc_start: 0.7357 (mtt180) cc_final: 0.6815 (mtp180) REVERT: A 151 ILE cc_start: 0.7811 (mt) cc_final: 0.7505 (mp) REVERT: A 206 PHE cc_start: 0.7723 (t80) cc_final: 0.7138 (t80) REVERT: A 231 ASP cc_start: 0.7392 (p0) cc_final: 0.6846 (m-30) REVERT: A 305 LYS cc_start: 0.7881 (tttp) cc_final: 0.7563 (ttpt) REVERT: A 333 MET cc_start: 0.8641 (mtp) cc_final: 0.8241 (mtm) REVERT: A 342 GLU cc_start: 0.8050 (mp0) cc_final: 0.7773 (mp0) REVERT: A 382 MET cc_start: 0.7595 (mmm) cc_final: 0.7276 (mmm) REVERT: A 495 MET cc_start: 0.7287 (mtp) cc_final: 0.6754 (mtt) REVERT: A 513 GLN cc_start: 0.6215 (mm110) cc_final: 0.5221 (mt0) REVERT: A 548 THR cc_start: 0.6832 (m) cc_final: 0.6440 (p) REVERT: A 558 ARG cc_start: 0.6355 (ptt180) cc_final: 0.5888 (ptp90) REVERT: A 651 ARG cc_start: 0.6613 (ttm110) cc_final: 0.5839 (ttm110) REVERT: B 31 MET cc_start: 0.6032 (mmt) cc_final: 0.5166 (ptp) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 1.0699 time to fit residues: 80.8687 Evaluate side-chains 61 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 539 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.0040 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4863 Z= 0.263 Angle : 0.636 9.153 6634 Z= 0.316 Chirality : 0.043 0.158 774 Planarity : 0.005 0.049 810 Dihedral : 5.321 37.693 715 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.61 % Allowed : 15.52 % 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: 1.92 (0.34), residues: 605 helix: 1.89 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.59 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 429 HIS 0.004 0.001 HIS A 80 PHE 0.013 0.002 PHE A 534 TYR 0.017 0.002 TYR A 128 ARG 0.007 0.000 ARG A 414 *********************** 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 62 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.531 Fit side-chains REVERT: A 62 MET cc_start: 0.8930 (mmp) cc_final: 0.8480 (mmm) REVERT: A 136 ARG cc_start: 0.7535 (mtt180) cc_final: 0.6893 (mtp180) REVERT: A 206 PHE cc_start: 0.7787 (t80) cc_final: 0.7076 (t80) REVERT: A 333 MET cc_start: 0.8691 (mtp) cc_final: 0.8270 (mtm) REVERT: A 382 MET cc_start: 0.7583 (mmm) cc_final: 0.7332 (mmm) REVERT: A 495 MET cc_start: 0.7470 (mtp) cc_final: 0.6878 (mtt) REVERT: A 513 GLN cc_start: 0.6196 (mm110) cc_final: 0.5154 (mp10) REVERT: A 548 THR cc_start: 0.6836 (m) cc_final: 0.6442 (p) REVERT: A 558 ARG cc_start: 0.6381 (ptt180) cc_final: 0.5810 (ptp90) REVERT: A 651 ARG cc_start: 0.6746 (ttm110) cc_final: 0.6003 (ttm110) REVERT: B 31 MET cc_start: 0.6093 (mmt) cc_final: 0.5222 (ptp) outliers start: 8 outliers final: 7 residues processed: 59 average time/residue: 1.0262 time to fit residues: 63.6216 Evaluate side-chains 61 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 252 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4863 Z= 0.186 Angle : 0.592 9.293 6634 Z= 0.293 Chirality : 0.041 0.148 774 Planarity : 0.005 0.050 810 Dihedral : 5.024 37.085 715 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.41 % Allowed : 15.73 % 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: 2.08 (0.35), residues: 605 helix: 2.01 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.53 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 PHE 0.010 0.001 PHE A 534 TYR 0.012 0.001 TYR A 256 ARG 0.007 0.000 ARG A 414 *********************** 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 64 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.469 Fit side-chains REVERT: A 62 MET cc_start: 0.8942 (mmp) cc_final: 0.8452 (mmm) REVERT: A 136 ARG cc_start: 0.7521 (mtt180) cc_final: 0.6916 (mtp180) REVERT: A 206 PHE cc_start: 0.7787 (t80) cc_final: 0.7100 (t80) REVERT: A 333 MET cc_start: 0.8695 (mtp) cc_final: 0.8316 (mtm) REVERT: A 382 MET cc_start: 0.7586 (mmm) cc_final: 0.7263 (mmm) REVERT: A 495 MET cc_start: 0.7494 (mtp) cc_final: 0.6928 (mtt) REVERT: A 513 GLN cc_start: 0.6208 (mm110) cc_final: 0.5165 (mp10) REVERT: A 548 THR cc_start: 0.6825 (m) cc_final: 0.6438 (p) REVERT: A 557 HIS cc_start: 0.6052 (m-70) cc_final: 0.5782 (m-70) REVERT: A 558 ARG cc_start: 0.6227 (ptt180) cc_final: 0.5755 (ptp90) REVERT: A 651 ARG cc_start: 0.6742 (ttm110) cc_final: 0.5994 (ttm110) REVERT: B 31 MET cc_start: 0.6065 (mmt) cc_final: 0.5195 (ptp) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 0.9995 time to fit residues: 64.2688 Evaluate side-chains 60 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 391 MET Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4863 Z= 0.166 Angle : 0.573 8.987 6634 Z= 0.282 Chirality : 0.040 0.145 774 Planarity : 0.005 0.050 810 Dihedral : 4.879 36.969 715 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.21 % Allowed : 15.52 % 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: 2.29 (0.35), residues: 605 helix: 2.16 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.43 (0.53), 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 0.009 0.001 PHE A 534 TYR 0.012 0.001 TYR A 256 ARG 0.007 0.000 ARG A 414 ********************** 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 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.613 Fit side-chains REVERT: A 62 MET cc_start: 0.8929 (mmp) cc_final: 0.8385 (mmm) REVERT: A 136 ARG cc_start: 0.7465 (mtt180) cc_final: 0.6874 (mtp180) REVERT: A 206 PHE cc_start: 0.7762 (t80) cc_final: 0.7114 (t80) REVERT: A 333 MET cc_start: 0.8677 (mtp) cc_final: 0.8330 (mtm) REVERT: A 382 MET cc_start: 0.7597 (mmm) cc_final: 0.7284 (mmm) REVERT: A 495 MET cc_start: 0.7305 (mtp) cc_final: 0.6764 (mtt) REVERT: A 513 GLN cc_start: 0.6230 (mm110) cc_final: 0.5205 (mt0) REVERT: A 548 THR cc_start: 0.6817 (m) cc_final: 0.6435 (p) REVERT: A 558 ARG cc_start: 0.6223 (ptt180) cc_final: 0.5744 (ptp90) REVERT: A 651 ARG cc_start: 0.6633 (ttm110) cc_final: 0.5897 (ttm110) REVERT: B 31 MET cc_start: 0.6165 (mmt) cc_final: 0.5298 (ptp) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 1.0028 time to fit residues: 64.3369 Evaluate side-chains 59 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 391 MET Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.126058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.098316 restraints weight = 4898.810| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.48 r_work: 0.2836 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4863 Z= 0.173 Angle : 0.577 8.881 6634 Z= 0.284 Chirality : 0.040 0.147 774 Planarity : 0.005 0.049 810 Dihedral : 4.861 36.855 715 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.41 % Allowed : 15.52 % 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: 2.31 (0.35), residues: 605 helix: 2.17 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.43 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 PHE 0.009 0.001 PHE A 534 TYR 0.010 0.001 TYR A 188 ARG 0.007 0.000 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.49 seconds wall clock time: 34 minutes 54.06 seconds (2094.06 seconds total)