Starting phenix.real_space_refine on Fri Nov 15 11:19:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgr_37515/11_2024/8wgr_37515_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgr_37515/11_2024/8wgr_37515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgr_37515/11_2024/8wgr_37515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgr_37515/11_2024/8wgr_37515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgr_37515/11_2024/8wgr_37515_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgr_37515/11_2024/8wgr_37515_trim.cif" } resolution = 2.75 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= 0.002 sd= 0.159 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 S 20 5.16 5 Cl 1 4.86 5 C 2981 2.51 5 N 683 2.21 5 O 773 1.98 5 H 4371 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 8830 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8754 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 1 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 76 Unusual residues: {' K': 1, ' CL': 1, 'DSM': 2} Classifications: {'undetermined': 4, 'water': 34} Link IDs: {None: 37} Time building chain proxies: 4.92, per 1000 atoms: 0.56 Number of scatterers: 8830 At special positions: 0 Unit cell: (70.3625, 70.3625, 99.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 Cl 1 17.00 S 20 16.00 O 773 8.00 N 683 7.00 C 2981 6.00 H 4371 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 808.9 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 1 sheets defined 84.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.719A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.611A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.774A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.619A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.158A pdb=" N ILE A 230 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.664A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.796A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.630A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.746A pdb=" N LYS A 303 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.689A pdb=" N ALA A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 4.000A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.617A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.581A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.800A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.521A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 599 through 604 removed outlier: 4.333A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.879A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 295 hydrogen bonds defined for protein. 852 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: 3.17 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4364 1.03 - 1.23: 19 1.23 - 1.42: 2021 1.42 - 1.62: 2505 1.62 - 1.81: 31 Bond restraints: 8940 Sorted by residual: bond pdb=" C ALA A 73 " pdb=" O ALA A 73 " ideal model delta sigma weight residual 1.235 1.161 0.075 1.26e-02 6.30e+03 3.50e+01 bond pdb=" C VAL A 74 " pdb=" O VAL A 74 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.19e-02 7.06e+03 3.18e+01 bond pdb=" C ASN A 78 " pdb=" O ASN A 78 " ideal model delta sigma weight residual 1.236 1.176 0.061 1.18e-02 7.18e+03 2.63e+01 bond pdb=" C ASP A 75 " pdb=" O ASP A 75 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.17e-02 7.31e+03 2.20e+01 bond pdb=" C ASP A 75 " pdb=" N LEU A 76 " ideal model delta sigma weight residual 1.335 1.277 0.058 1.34e-02 5.57e+03 1.88e+01 ... (remaining 8935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.06: 16083 7.06 - 14.12: 12 14.12 - 21.18: 0 21.18 - 28.24: 0 28.24 - 35.30: 3 Bond angle restraints: 16098 Sorted by residual: angle pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 73.70 35.30 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 110.00 76.58 33.42 3.00e+00 1.11e-01 1.24e+02 angle pdb=" CB TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 76.12 32.88 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " pdb=" CG ASP A 75 " ideal model delta sigma weight residual 112.60 119.52 -6.92 1.00e+00 1.00e+00 4.79e+01 angle pdb=" O GLY A 71 " pdb=" C GLY A 71 " pdb=" N PHE A 72 " ideal model delta sigma weight residual 122.24 115.98 6.26 1.06e+00 8.90e-01 3.49e+01 ... (remaining 16093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3745 17.77 - 35.55: 337 35.55 - 53.32: 103 53.32 - 71.10: 41 71.10 - 88.87: 7 Dihedral angle restraints: 4233 sinusoidal: 2150 harmonic: 2083 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -132.22 9.62 0 2.50e+00 1.60e-01 1.48e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 132.02 -9.22 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 663 0.083 - 0.165: 25 0.165 - 0.248: 1 0.248 - 0.331: 0 0.331 - 0.413: 1 Chirality restraints: 690 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB VAL A 74 " pdb=" CA VAL A 74 " pdb=" CG1 VAL A 74 " pdb=" CG2 VAL A 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 687 not shown) Planarity restraints: 1281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 78 " 0.029 2.00e-02 2.50e+03 3.78e-02 2.14e+01 pdb=" CG ASN A 78 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 78 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN A 78 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 78 " -0.057 2.00e-02 2.50e+03 pdb="HD22 ASN A 78 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ILE A 103 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 75 " -0.015 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" CG ASP A 75 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASP A 75 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP A 75 " -0.020 2.00e-02 2.50e+03 ... (remaining 1278 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.24: 839 2.24 - 2.96: 23151 2.96 - 3.69: 33227 3.69 - 4.41: 50817 4.41 - 5.14: 80780 Nonbonded interactions: 188814 Sorted by model distance: nonbonded pdb=" OE1 GLN A 612 " pdb=" H GLN A 612 " model vdw 1.509 2.450 nonbonded pdb=" OE1 GLU A 425 " pdb="HH22 ARG A 442 " model vdw 1.629 2.450 nonbonded pdb=" H HIS A 178 " pdb=" OD1 ASN A 181 " model vdw 1.631 2.450 nonbonded pdb=" O ILE A 561 " pdb=" HG SER A 564 " model vdw 1.676 2.450 nonbonded pdb=" O ALA A 476 " pdb=" HG SER A 480 " model vdw 1.681 2.450 ... (remaining 188809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 0.170 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.090 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 4569 Z= 0.282 Angle : 0.709 9.254 6231 Z= 0.368 Chirality : 0.041 0.413 690 Planarity : 0.005 0.050 754 Dihedral : 17.038 88.869 1537 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.69 % Rotamer: Outliers : 2.38 % Allowed : 22.08 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.38), residues: 544 helix: 1.68 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -0.10 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.003 0.001 HIS A 598 PHE 0.027 0.001 PHE A 72 TYR 0.014 0.001 TYR A 271 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7184 (mm) cc_final: 0.6769 (mt) REVERT: A 113 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7836 (mt-10) REVERT: A 174 THR cc_start: 0.8224 (m) cc_final: 0.7983 (p) REVERT: A 301 ARG cc_start: 0.7514 (tpt90) cc_final: 0.7312 (tpt90) REVERT: A 376 ILE cc_start: 0.8183 (tt) cc_final: 0.7397 (mp) REVERT: A 458 LEU cc_start: 0.7707 (tt) cc_final: 0.7494 (tt) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 1.2448 time to fit residues: 120.7839 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 493 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4569 Z= 0.292 Angle : 0.621 7.983 6231 Z= 0.317 Chirality : 0.043 0.439 690 Planarity : 0.005 0.040 754 Dihedral : 11.451 141.998 618 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.25 % Allowed : 20.13 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.37), residues: 544 helix: 1.37 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.27 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 614 HIS 0.005 0.001 HIS A 598 PHE 0.016 0.002 PHE A 316 TYR 0.020 0.002 TYR A 84 ARG 0.003 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7145 (mm) cc_final: 0.6714 (mt) REVERT: A 107 MET cc_start: 0.7676 (mtt) cc_final: 0.7467 (ttp) REVERT: A 376 ILE cc_start: 0.8265 (tt) cc_final: 0.7505 (mp) REVERT: A 439 LYS cc_start: 0.7747 (ttmt) cc_final: 0.7409 (ttmp) REVERT: A 440 ARG cc_start: 0.7263 (mtp85) cc_final: 0.7042 (ttm-80) REVERT: A 458 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7592 (tt) REVERT: A 528 PHE cc_start: 0.8099 (m-80) cc_final: 0.7879 (m-80) outliers start: 15 outliers final: 5 residues processed: 67 average time/residue: 1.3739 time to fit residues: 99.0485 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.0040 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4569 Z= 0.157 Angle : 0.531 8.847 6231 Z= 0.264 Chirality : 0.039 0.412 690 Planarity : 0.005 0.037 754 Dihedral : 10.957 139.621 611 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.16 % Allowed : 20.13 % Favored : 77.71 % 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: 1.52 (0.38), residues: 544 helix: 1.56 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.29 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.004 0.001 HIS A 598 PHE 0.009 0.001 PHE A 316 TYR 0.015 0.001 TYR A 84 ARG 0.004 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7208 (mm) cc_final: 0.6803 (mt) REVERT: A 376 ILE cc_start: 0.8254 (tt) cc_final: 0.7513 (mp) REVERT: A 439 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7445 (ttmp) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 1.4234 time to fit residues: 88.7739 Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4569 Z= 0.179 Angle : 0.538 9.025 6231 Z= 0.268 Chirality : 0.039 0.423 690 Planarity : 0.005 0.037 754 Dihedral : 10.895 138.406 611 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.38 % Allowed : 19.91 % Favored : 77.71 % 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: 1.60 (0.37), residues: 544 helix: 1.63 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.29 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.004 0.001 HIS A 598 PHE 0.012 0.001 PHE A 316 TYR 0.016 0.001 TYR A 84 ARG 0.005 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7178 (mm) cc_final: 0.6763 (mt) REVERT: A 301 ARG cc_start: 0.7475 (tpt90) cc_final: 0.6640 (ttt180) REVERT: A 376 ILE cc_start: 0.8263 (tt) cc_final: 0.7488 (mp) REVERT: A 436 GLN cc_start: 0.7550 (pt0) cc_final: 0.6961 (mm110) REVERT: A 439 LYS cc_start: 0.7755 (ttmt) cc_final: 0.6940 (ttpp) REVERT: A 440 ARG cc_start: 0.7591 (ttp-110) cc_final: 0.6750 (mtt90) REVERT: A 581 GLN cc_start: 0.7757 (tt0) cc_final: 0.7522 (mt0) outliers start: 11 outliers final: 3 residues processed: 62 average time/residue: 1.4554 time to fit residues: 96.4971 Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 350 ASN A 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4569 Z= 0.201 Angle : 0.551 8.868 6231 Z= 0.274 Chirality : 0.040 0.424 690 Planarity : 0.005 0.038 754 Dihedral : 10.887 138.147 611 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.81 % Allowed : 19.70 % Favored : 77.49 % 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: 1.55 (0.37), residues: 544 helix: 1.59 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.30 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.003 0.001 HIS A 598 PHE 0.013 0.001 PHE A 316 TYR 0.017 0.001 TYR A 84 ARG 0.004 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6768 (mt) REVERT: A 301 ARG cc_start: 0.7498 (tpt90) cc_final: 0.6669 (ttt180) REVERT: A 376 ILE cc_start: 0.8265 (tt) cc_final: 0.7483 (mp) REVERT: A 436 GLN cc_start: 0.7548 (pt0) cc_final: 0.6892 (mm110) REVERT: A 439 LYS cc_start: 0.7723 (ttmt) cc_final: 0.6893 (ttpp) REVERT: A 528 PHE cc_start: 0.8191 (m-80) cc_final: 0.7959 (m-80) REVERT: A 581 GLN cc_start: 0.7739 (tt0) cc_final: 0.7518 (mt0) outliers start: 13 outliers final: 3 residues processed: 61 average time/residue: 1.4135 time to fit residues: 92.6876 Evaluate side-chains 54 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 350 ASN A 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4569 Z= 0.196 Angle : 0.548 8.899 6231 Z= 0.272 Chirality : 0.040 0.423 690 Planarity : 0.005 0.039 754 Dihedral : 10.901 138.136 611 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.38 % Allowed : 19.91 % Favored : 77.71 % 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: 1.57 (0.37), residues: 544 helix: 1.61 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.33 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 80 HIS 0.003 0.001 HIS A 598 PHE 0.013 0.001 PHE A 316 TYR 0.017 0.001 TYR A 84 ARG 0.007 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7160 (mm) cc_final: 0.6727 (mt) REVERT: A 303 LYS cc_start: 0.8271 (ptmt) cc_final: 0.7387 (ptmm) REVERT: A 376 ILE cc_start: 0.8255 (tt) cc_final: 0.7478 (mp) REVERT: A 436 GLN cc_start: 0.7552 (pt0) cc_final: 0.6992 (mm110) REVERT: A 439 LYS cc_start: 0.7685 (ttmt) cc_final: 0.6871 (ttpp) REVERT: A 440 ARG cc_start: 0.7589 (ttp-110) cc_final: 0.6688 (mtt90) REVERT: A 528 PHE cc_start: 0.8180 (m-80) cc_final: 0.7941 (m-80) outliers start: 11 outliers final: 4 residues processed: 60 average time/residue: 1.4110 time to fit residues: 90.8025 Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 350 ASN A 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4569 Z= 0.186 Angle : 0.541 8.846 6231 Z= 0.269 Chirality : 0.040 0.423 690 Planarity : 0.005 0.040 754 Dihedral : 10.893 138.327 611 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.16 % Allowed : 20.35 % Favored : 77.49 % 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: 1.60 (0.38), residues: 544 helix: 1.64 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.33 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 80 HIS 0.003 0.001 HIS A 598 PHE 0.013 0.001 PHE A 316 TYR 0.016 0.001 TYR A 84 ARG 0.008 0.001 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6727 (mt) REVERT: A 301 ARG cc_start: 0.7495 (tpt90) cc_final: 0.6669 (ttt180) REVERT: A 303 LYS cc_start: 0.8268 (ptmt) cc_final: 0.7385 (ptmm) REVERT: A 376 ILE cc_start: 0.8255 (tt) cc_final: 0.7482 (mp) REVERT: A 436 GLN cc_start: 0.7584 (pt0) cc_final: 0.6958 (mm110) REVERT: A 439 LYS cc_start: 0.7680 (ttmt) cc_final: 0.7009 (ttpp) REVERT: A 487 MET cc_start: 0.8916 (mmm) cc_final: 0.8676 (mmp) REVERT: A 528 PHE cc_start: 0.8157 (m-80) cc_final: 0.7925 (m-80) outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 1.5933 time to fit residues: 97.0967 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 350 ASN A 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4569 Z= 0.164 Angle : 0.530 8.870 6231 Z= 0.263 Chirality : 0.039 0.420 690 Planarity : 0.005 0.042 754 Dihedral : 10.876 138.705 611 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 21.00 % Favored : 77.06 % 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: 1.69 (0.38), residues: 544 helix: 1.71 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.28 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.003 0.001 HIS A 598 PHE 0.012 0.001 PHE A 316 TYR 0.015 0.001 TYR A 84 ARG 0.008 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6730 (mt) REVERT: A 204 LYS cc_start: 0.5740 (mmmt) cc_final: 0.5494 (mmmt) REVERT: A 301 ARG cc_start: 0.7482 (tpt90) cc_final: 0.6648 (ttt180) REVERT: A 376 ILE cc_start: 0.8258 (tt) cc_final: 0.7494 (mp) REVERT: A 436 GLN cc_start: 0.7577 (pt0) cc_final: 0.6976 (mm110) REVERT: A 439 LYS cc_start: 0.7643 (ttmt) cc_final: 0.6791 (ttpp) REVERT: A 487 MET cc_start: 0.8937 (mmm) cc_final: 0.8677 (mmp) REVERT: A 543 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8096 (tt) outliers start: 9 outliers final: 3 residues processed: 58 average time/residue: 1.5385 time to fit residues: 95.4742 Evaluate side-chains 55 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4569 Z= 0.170 Angle : 0.540 8.859 6231 Z= 0.268 Chirality : 0.039 0.421 690 Planarity : 0.005 0.040 754 Dihedral : 10.828 138.747 610 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.08 % Allowed : 22.51 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.37), residues: 544 helix: 1.69 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.36 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.002 0.001 HIS A 598 PHE 0.011 0.001 PHE A 316 TYR 0.015 0.001 TYR A 84 ARG 0.008 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6714 (mt) REVERT: A 204 LYS cc_start: 0.5785 (mmmt) cc_final: 0.5503 (mmmt) REVERT: A 301 ARG cc_start: 0.7485 (tpt90) cc_final: 0.6646 (ttt180) REVERT: A 376 ILE cc_start: 0.8255 (tt) cc_final: 0.7499 (mp) REVERT: A 436 GLN cc_start: 0.7557 (pt0) cc_final: 0.6971 (mm110) REVERT: A 439 LYS cc_start: 0.7633 (ttmt) cc_final: 0.6777 (ttpp) REVERT: A 487 MET cc_start: 0.8929 (mmm) cc_final: 0.8680 (mmp) REVERT: A 612 GLN cc_start: 0.7129 (mp10) cc_final: 0.6888 (mm110) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 1.6083 time to fit residues: 93.3055 Evaluate side-chains 55 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4569 Z= 0.198 Angle : 0.554 8.836 6231 Z= 0.276 Chirality : 0.040 0.427 690 Planarity : 0.005 0.038 754 Dihedral : 10.834 138.222 610 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 22.29 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.37), residues: 544 helix: 1.65 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.36 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.002 0.001 HIS A 598 PHE 0.014 0.001 PHE A 316 TYR 0.017 0.001 TYR A 84 ARG 0.007 0.001 ARG A 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6715 (mt) REVERT: A 204 LYS cc_start: 0.5855 (mmmt) cc_final: 0.5567 (mmmt) REVERT: A 205 TYR cc_start: 0.4462 (OUTLIER) cc_final: 0.3746 (t80) REVERT: A 301 ARG cc_start: 0.7487 (tpt90) cc_final: 0.6651 (ttt180) REVERT: A 376 ILE cc_start: 0.8265 (tt) cc_final: 0.7497 (mp) REVERT: A 436 GLN cc_start: 0.7599 (pt0) cc_final: 0.7023 (mm110) REVERT: A 439 LYS cc_start: 0.7665 (ttmt) cc_final: 0.6807 (ttpp) REVERT: A 487 MET cc_start: 0.8916 (mmm) cc_final: 0.8666 (mmp) REVERT: A 528 PHE cc_start: 0.8090 (m-80) cc_final: 0.7846 (m-80) REVERT: A 612 GLN cc_start: 0.7135 (mp10) cc_final: 0.6861 (mm110) outliers start: 6 outliers final: 1 residues processed: 54 average time/residue: 1.5480 time to fit residues: 89.3963 Evaluate side-chains 55 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112521 restraints weight = 15298.004| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.76 r_work: 0.3347 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4569 Z= 0.179 Angle : 0.542 8.850 6231 Z= 0.270 Chirality : 0.039 0.424 690 Planarity : 0.005 0.039 754 Dihedral : 10.828 138.623 610 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.08 % Allowed : 22.29 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.37), residues: 544 helix: 1.70 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.33 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.002 0.001 HIS A 598 PHE 0.012 0.001 PHE A 316 TYR 0.015 0.001 TYR A 84 ARG 0.008 0.001 ARG A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3422.80 seconds wall clock time: 61 minutes 20.59 seconds (3680.59 seconds total)