Starting phenix.real_space_refine on Mon Mar 11 04:12:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/03_2024/8hhl_34803.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/03_2024/8hhl_34803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/03_2024/8hhl_34803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/03_2024/8hhl_34803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/03_2024/8hhl_34803.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/03_2024/8hhl_34803.pdb" } resolution = 2.87 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 ------------------------------------------------------------------------------- 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= -0.012 sd= 0.253 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 Zn 1 6.06 5 P 111 5.49 5 Mg 3 5.21 5 S 19 5.16 5 C 3939 2.51 5 N 1321 2.21 5 O 1577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6971 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1066 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 28, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 43} Chain: "C" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 624 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 647 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4630 Classifications: {'peptide': 592} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 567} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6663 SG CYS A 552 87.861 24.922 31.530 1.00120.60 S ATOM 6796 SG CYS A 569 84.715 23.574 29.746 1.00120.99 S ATOM 6814 SG CYS A 572 86.921 21.084 31.118 1.00121.86 S Time building chain proxies: 4.54, per 1000 atoms: 0.65 Number of scatterers: 6971 At special positions: 0 Unit cell: (101.094, 89.474, 103.418, 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) Zn 1 29.99 S 19 16.00 P 111 15.00 Mg 3 11.99 O 1577 8.00 N 1321 7.00 C 3939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.07 Conformation dependent library (CDL) restraints added in 880.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 549 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 569 " Number of angles added : 3 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 58.1% alpha, 14.4% beta 40 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 18 through 52 Processing helix chain 'A' and resid 53 through 85 Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.558A pdb=" N THR A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 176 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.605A pdb=" N LEU A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 362 through 397 removed outlier: 4.195A pdb=" N GLU A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.230A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 434 through 479 removed outlier: 3.520A pdb=" N TRP A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 500 removed outlier: 4.495A pdb=" N MET A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 518 through 534 Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.570A pdb=" N LEU A 563 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 564' Processing helix chain 'A' and resid 579 through 591 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 6.076A pdb=" N ILE A 278 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG A 301 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 280 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA A 294 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 10 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY A 253 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE A 262 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG A 251 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 264 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG A 249 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 266 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR A 247 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 360 removed outlier: 4.813A pdb=" N THR A 327 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG A 321 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 329 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 485 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 318 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 567 through 568 300 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1580 1.33 - 1.45: 2077 1.45 - 1.57: 3432 1.57 - 1.69: 219 1.69 - 1.81: 31 Bond restraints: 7339 Sorted by residual: bond pdb=" C3' DG D -9 " pdb=" O3' DG D -9 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.24e+00 bond pdb=" C3' DT D -10 " pdb=" O3' DT D -10 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" C2' DG D 0 " pdb=" C1' DG D 0 " ideal model delta sigma weight residual 1.525 1.504 0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CA ASP A 560 " pdb=" CB ASP A 560 " ideal model delta sigma weight residual 1.532 1.547 -0.015 1.51e-02 4.39e+03 9.66e-01 bond pdb=" O4' DG D 0 " pdb=" C1' DG D 0 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.01e-01 ... (remaining 7334 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.77: 656 105.77 - 112.85: 4148 112.85 - 119.93: 2457 119.93 - 127.02: 2867 127.02 - 134.10: 342 Bond angle restraints: 10470 Sorted by residual: angle pdb=" C2' DG D 0 " pdb=" C1' DG D 0 " pdb=" N9 DG D 0 " ideal model delta sigma weight residual 113.50 117.07 -3.57 1.50e+00 4.44e-01 5.66e+00 angle pdb=" C ASP A 559 " pdb=" N ASP A 560 " pdb=" CA ASP A 560 " ideal model delta sigma weight residual 122.61 126.22 -3.61 1.56e+00 4.11e-01 5.36e+00 angle pdb=" C4' DG D 0 " pdb=" O4' DG D 0 " pdb=" C1' DG D 0 " ideal model delta sigma weight residual 109.70 106.45 3.25 1.50e+00 4.44e-01 4.70e+00 angle pdb=" CA ASP A 560 " pdb=" CB ASP A 560 " pdb=" CG ASP A 560 " ideal model delta sigma weight residual 112.60 114.65 -2.05 1.00e+00 1.00e+00 4.21e+00 angle pdb=" OP2 DT D -8 " pdb=" P DT D -8 " pdb=" O5' DT D -8 " ideal model delta sigma weight residual 108.00 102.09 5.91 3.00e+00 1.11e-01 3.88e+00 ... (remaining 10465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 3630 23.75 - 47.50: 449 47.50 - 71.25: 226 71.25 - 95.00: 19 95.00 - 118.75: 1 Dihedral angle restraints: 4325 sinusoidal: 2602 harmonic: 1723 Sorted by residual: dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual -106.00 -172.34 66.34 1 1.70e+01 3.46e-03 1.99e+01 dihedral pdb=" C4' DG D -9 " pdb=" C3' DG D -9 " pdb=" O3' DG D -9 " pdb=" P DT D -8 " ideal model delta sinusoidal sigma weight residual 220.00 101.25 118.75 1 3.50e+01 8.16e-04 1.16e+01 dihedral pdb=" CA ASP A 477 " pdb=" CB ASP A 477 " pdb=" CG ASP A 477 " pdb=" OD1 ASP A 477 " ideal model delta sinusoidal sigma weight residual -30.00 -86.97 56.97 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 4322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 889 0.033 - 0.066: 241 0.066 - 0.099: 58 0.099 - 0.133: 17 0.133 - 0.166: 5 Chirality restraints: 1210 Sorted by residual: chirality pdb=" C1' DG D 0 " pdb=" O4' DG D 0 " pdb=" C2' DG D 0 " pdb=" N9 DG D 0 " both_signs ideal model delta sigma weight residual False 2.42 2.25 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ASP A 560 " pdb=" N ASP A 560 " pdb=" C ASP A 560 " pdb=" CB ASP A 560 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1207 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG D 0 " 0.027 2.00e-02 2.50e+03 1.15e-02 3.97e+00 pdb=" N9 DG D 0 " -0.028 2.00e-02 2.50e+03 pdb=" C8 DG D 0 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG D 0 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG D 0 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG D 0 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG D 0 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG D 0 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG D 0 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG D 0 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG D 0 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG D 0 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 2 " 0.025 2.00e-02 2.50e+03 1.06e-02 3.34e+00 pdb=" N9 G B 2 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G B 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 2 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G B 2 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 2 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 2 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 2 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 2 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 452 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C GLN A 452 " -0.031 2.00e-02 2.50e+03 pdb=" O GLN A 452 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 453 " 0.010 2.00e-02 2.50e+03 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 215 2.68 - 3.24: 6117 3.24 - 3.79: 12497 3.79 - 4.35: 16282 4.35 - 4.90: 24625 Nonbonded interactions: 59736 Sorted by model distance: nonbonded pdb=" OD1 ASP A 579 " pdb="MG MG A 601 " model vdw 2.126 2.170 nonbonded pdb=" OP1 G B -22 " pdb="MG MG B 101 " model vdw 2.134 2.170 nonbonded pdb=" OP1 DG D 15 " pdb="MG MG A 601 " model vdw 2.143 2.170 nonbonded pdb=" OG SER A 334 " pdb=" O ALA A 336 " model vdw 2.154 2.440 nonbonded pdb=" NE2 HIS A 317 " pdb="MG MG A 601 " model vdw 2.198 2.250 ... (remaining 59731 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: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 27.180 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.062 7339 Z= 0.217 Angle : 0.499 5.911 10470 Z= 0.284 Chirality : 0.035 0.166 1210 Planarity : 0.004 0.042 951 Dihedral : 22.356 118.750 3205 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.29 % Allowed : 12.29 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.28 (0.35), residues: 590 helix: 2.63 (0.29), residues: 323 sheet: 1.62 (0.63), residues: 60 loop : -0.37 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 232 HIS 0.002 0.000 HIS A 12 PHE 0.006 0.001 PHE A 443 TYR 0.010 0.001 TYR A 42 ARG 0.002 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.568 Fit side-chains REVERT: A 63 MET cc_start: 0.8112 (ttt) cc_final: 0.7844 (ttp) REVERT: A 160 ASP cc_start: 0.7952 (m-30) cc_final: 0.7678 (m-30) REVERT: A 172 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7002 (mm-40) REVERT: A 199 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7586 (tt0) REVERT: A 264 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8790 (mt) REVERT: A 404 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7712 (p0) REVERT: A 416 LYS cc_start: 0.6723 (mttt) cc_final: 0.5308 (tttm) REVERT: A 458 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7644 (mmm-85) REVERT: A 575 MET cc_start: 0.8659 (mtp) cc_final: 0.8283 (mtt) outliers start: 11 outliers final: 2 residues processed: 82 average time/residue: 1.6837 time to fit residues: 143.5928 Evaluate side-chains 51 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 404 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 242 GLN A 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7339 Z= 0.270 Angle : 0.547 7.836 10470 Z= 0.303 Chirality : 0.037 0.172 1210 Planarity : 0.005 0.100 951 Dihedral : 23.857 117.910 2123 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.54 % Allowed : 17.08 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.77 (0.34), residues: 590 helix: 3.14 (0.28), residues: 324 sheet: 1.59 (0.59), residues: 62 loop : -0.31 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 232 HIS 0.003 0.001 HIS A 269 PHE 0.005 0.001 PHE A 155 TYR 0.009 0.001 TYR A 42 ARG 0.007 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.691 Fit side-chains REVERT: A 63 MET cc_start: 0.8147 (ttt) cc_final: 0.7858 (ttp) REVERT: A 89 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8050 (pp) REVERT: A 95 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8082 (tp40) REVERT: A 103 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7960 (mtm180) REVERT: A 160 ASP cc_start: 0.7807 (m-30) cc_final: 0.7556 (m-30) REVERT: A 172 GLN cc_start: 0.7235 (mm-40) cc_final: 0.7021 (mm-40) REVERT: A 258 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8014 (mm110) REVERT: A 416 LYS cc_start: 0.6784 (mttt) cc_final: 0.5331 (tttm) REVERT: A 458 ARG cc_start: 0.8393 (mmm160) cc_final: 0.7992 (mmm-85) REVERT: A 501 GLU cc_start: 0.8183 (tp30) cc_final: 0.7825 (tm-30) REVERT: A 575 MET cc_start: 0.8644 (mtp) cc_final: 0.8266 (mtt) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 1.8114 time to fit residues: 124.1416 Evaluate side-chains 57 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7339 Z= 0.255 Angle : 0.526 7.280 10470 Z= 0.292 Chirality : 0.037 0.168 1210 Planarity : 0.005 0.106 951 Dihedral : 23.823 116.321 2118 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.96 % Allowed : 18.96 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.90 (0.34), residues: 590 helix: 3.24 (0.27), residues: 324 sheet: 1.49 (0.59), residues: 62 loop : -0.18 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.003 0.001 HIS A 269 PHE 0.006 0.001 PHE A 155 TYR 0.009 0.001 TYR A 42 ARG 0.004 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 48 time to evaluate : 0.770 Fit side-chains REVERT: A 63 MET cc_start: 0.8136 (ttt) cc_final: 0.7851 (ttp) REVERT: A 103 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7978 (mtm180) REVERT: A 160 ASP cc_start: 0.7807 (m-30) cc_final: 0.7582 (m-30) REVERT: A 172 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7014 (mm-40) REVERT: A 351 ASP cc_start: 0.6093 (p0) cc_final: 0.5785 (p0) REVERT: A 367 ARG cc_start: 0.7663 (mtp85) cc_final: 0.7364 (ttp-110) REVERT: A 416 LYS cc_start: 0.6733 (mttt) cc_final: 0.5267 (tttm) REVERT: A 458 ARG cc_start: 0.8440 (mmm160) cc_final: 0.8013 (mmm-85) REVERT: A 498 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6403 (pm20) REVERT: A 501 GLU cc_start: 0.8123 (tp30) cc_final: 0.7851 (tm-30) REVERT: A 575 MET cc_start: 0.8648 (mtp) cc_final: 0.8271 (mtt) outliers start: 19 outliers final: 12 residues processed: 62 average time/residue: 1.7019 time to fit residues: 109.9575 Evaluate side-chains 56 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 0.0670 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7339 Z= 0.276 Angle : 0.544 7.132 10470 Z= 0.301 Chirality : 0.037 0.167 1210 Planarity : 0.004 0.054 951 Dihedral : 23.853 115.508 2118 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.96 % Allowed : 19.58 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.90 (0.34), residues: 590 helix: 3.23 (0.27), residues: 324 sheet: 1.45 (0.60), residues: 62 loop : -0.16 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.003 0.001 HIS A 269 PHE 0.006 0.001 PHE A 443 TYR 0.009 0.001 TYR A 42 ARG 0.003 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.8138 (ttt) cc_final: 0.7849 (ttp) REVERT: A 88 LYS cc_start: 0.8596 (pptt) cc_final: 0.8384 (tppt) REVERT: A 103 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7985 (mtm180) REVERT: A 160 ASP cc_start: 0.7811 (m-30) cc_final: 0.7593 (m-30) REVERT: A 172 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7052 (mm-40) REVERT: A 351 ASP cc_start: 0.6138 (p0) cc_final: 0.5808 (p0) REVERT: A 367 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7361 (ttp-110) REVERT: A 404 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7842 (p0) REVERT: A 416 LYS cc_start: 0.6691 (mttt) cc_final: 0.5193 (tttm) REVERT: A 458 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8016 (mmm-85) REVERT: A 501 GLU cc_start: 0.8076 (tp30) cc_final: 0.7865 (tm-30) REVERT: A 575 MET cc_start: 0.8630 (mtp) cc_final: 0.8260 (mtt) outliers start: 19 outliers final: 14 residues processed: 61 average time/residue: 1.7483 time to fit residues: 111.1328 Evaluate side-chains 57 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7339 Z= 0.183 Angle : 0.492 6.319 10470 Z= 0.277 Chirality : 0.034 0.152 1210 Planarity : 0.004 0.048 951 Dihedral : 23.779 112.784 2118 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.17 % Allowed : 18.96 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.18 (0.34), residues: 590 helix: 3.50 (0.27), residues: 324 sheet: 1.47 (0.59), residues: 62 loop : -0.07 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 232 HIS 0.002 0.000 HIS A 269 PHE 0.006 0.001 PHE A 155 TYR 0.007 0.001 TYR A 42 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 0.788 Fit side-chains REVERT: A 63 MET cc_start: 0.8116 (ttt) cc_final: 0.7761 (ttp) REVERT: A 103 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7972 (mtm180) REVERT: A 146 ARG cc_start: 0.8339 (mtp85) cc_final: 0.7587 (mtm-85) REVERT: A 160 ASP cc_start: 0.7861 (m-30) cc_final: 0.7641 (m-30) REVERT: A 172 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6975 (mm-40) REVERT: A 351 ASP cc_start: 0.6113 (p0) cc_final: 0.5828 (p0) REVERT: A 367 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7340 (ttp-110) REVERT: A 404 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7813 (p0) REVERT: A 413 LYS cc_start: 0.7829 (tttt) cc_final: 0.6785 (tptp) REVERT: A 416 LYS cc_start: 0.6660 (mttt) cc_final: 0.5208 (tttm) REVERT: A 458 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8025 (mmm-85) REVERT: A 498 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6241 (pm20) REVERT: A 575 MET cc_start: 0.8633 (mtp) cc_final: 0.8254 (mtt) outliers start: 20 outliers final: 10 residues processed: 62 average time/residue: 1.6675 time to fit residues: 107.7050 Evaluate side-chains 53 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7339 Z= 0.393 Angle : 0.605 7.580 10470 Z= 0.330 Chirality : 0.041 0.176 1210 Planarity : 0.005 0.045 951 Dihedral : 23.975 115.742 2118 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.17 % Allowed : 19.79 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.68 (0.34), residues: 590 helix: 3.04 (0.27), residues: 324 sheet: 1.39 (0.60), residues: 62 loop : -0.25 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 232 HIS 0.004 0.001 HIS A 269 PHE 0.007 0.002 PHE A 443 TYR 0.011 0.002 TYR A 42 ARG 0.004 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 42 time to evaluate : 0.661 Fit side-chains REVERT: A 63 MET cc_start: 0.8139 (ttt) cc_final: 0.7855 (ttp) REVERT: A 88 LYS cc_start: 0.8709 (tmmt) cc_final: 0.8361 (tppt) REVERT: A 103 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7867 (mtm180) REVERT: A 160 ASP cc_start: 0.7830 (m-30) cc_final: 0.7610 (m-30) REVERT: A 172 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7080 (mm-40) REVERT: A 351 ASP cc_start: 0.6338 (p0) cc_final: 0.6129 (p0) REVERT: A 367 ARG cc_start: 0.7701 (mtp85) cc_final: 0.7386 (ttp-110) REVERT: A 404 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7835 (p0) REVERT: A 416 LYS cc_start: 0.6754 (mttt) cc_final: 0.5228 (tttm) REVERT: A 458 ARG cc_start: 0.8493 (mmm160) cc_final: 0.7977 (mmm-85) REVERT: A 498 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: A 575 MET cc_start: 0.8635 (mtp) cc_final: 0.8293 (mtt) outliers start: 20 outliers final: 13 residues processed: 58 average time/residue: 1.6154 time to fit residues: 98.0734 Evaluate side-chains 55 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 30 optimal weight: 0.0020 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7339 Z= 0.200 Angle : 0.521 9.995 10470 Z= 0.288 Chirality : 0.035 0.151 1210 Planarity : 0.004 0.036 951 Dihedral : 23.859 113.387 2118 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.33 % Allowed : 21.46 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.06 (0.34), residues: 590 helix: 3.41 (0.27), residues: 324 sheet: 1.42 (0.60), residues: 62 loop : -0.15 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.002 0.000 HIS A 269 PHE 0.006 0.001 PHE A 155 TYR 0.008 0.001 TYR A 42 ARG 0.003 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.8109 (ttt) cc_final: 0.7770 (ttp) REVERT: A 103 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7859 (mtm180) REVERT: A 160 ASP cc_start: 0.7825 (m-30) cc_final: 0.7612 (m-30) REVERT: A 172 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6961 (mm-40) REVERT: A 351 ASP cc_start: 0.6140 (p0) cc_final: 0.5866 (p0) REVERT: A 367 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7367 (ttp-110) REVERT: A 404 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7826 (p0) REVERT: A 413 LYS cc_start: 0.7851 (tttt) cc_final: 0.6782 (tptp) REVERT: A 416 LYS cc_start: 0.6693 (mttt) cc_final: 0.5223 (tttm) REVERT: A 458 ARG cc_start: 0.8487 (mmm160) cc_final: 0.7970 (mmm-85) REVERT: A 498 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6180 (pm20) REVERT: A 575 MET cc_start: 0.8634 (mtp) cc_final: 0.8258 (mtt) outliers start: 16 outliers final: 11 residues processed: 56 average time/residue: 1.5491 time to fit residues: 90.8868 Evaluate side-chains 55 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7339 Z= 0.222 Angle : 0.525 9.727 10470 Z= 0.290 Chirality : 0.036 0.190 1210 Planarity : 0.004 0.034 951 Dihedral : 23.863 112.099 2118 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.33 % Allowed : 21.46 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.07 (0.34), residues: 590 helix: 3.40 (0.27), residues: 324 sheet: 1.45 (0.59), residues: 62 loop : -0.11 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.003 0.001 HIS A 426 PHE 0.006 0.001 PHE A 443 TYR 0.008 0.001 TYR A 42 ARG 0.003 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.8101 (ttt) cc_final: 0.7807 (ttp) REVERT: A 88 LYS cc_start: 0.8644 (tmmt) cc_final: 0.8315 (tppt) REVERT: A 103 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7863 (mtm180) REVERT: A 160 ASP cc_start: 0.7830 (m-30) cc_final: 0.7618 (m-30) REVERT: A 172 GLN cc_start: 0.7262 (mm-40) cc_final: 0.6971 (mm-40) REVERT: A 351 ASP cc_start: 0.6148 (p0) cc_final: 0.5874 (p0) REVERT: A 367 ARG cc_start: 0.7717 (mtp85) cc_final: 0.7363 (ttp-110) REVERT: A 404 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7830 (p0) REVERT: A 413 LYS cc_start: 0.7830 (tttt) cc_final: 0.6791 (tptp) REVERT: A 416 LYS cc_start: 0.6698 (mttt) cc_final: 0.5229 (tttm) REVERT: A 458 ARG cc_start: 0.8446 (mmm160) cc_final: 0.7963 (mmm-85) REVERT: A 498 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: A 575 MET cc_start: 0.8636 (mtp) cc_final: 0.8258 (mtt) outliers start: 16 outliers final: 12 residues processed: 56 average time/residue: 1.5932 time to fit residues: 93.4592 Evaluate side-chains 58 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7339 Z= 0.222 Angle : 0.535 9.692 10470 Z= 0.292 Chirality : 0.035 0.170 1210 Planarity : 0.004 0.034 951 Dihedral : 23.869 111.680 2118 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.33 % Allowed : 22.08 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.09 (0.34), residues: 590 helix: 3.41 (0.27), residues: 324 sheet: 1.48 (0.59), residues: 62 loop : -0.11 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.002 0.001 HIS A 183 PHE 0.006 0.001 PHE A 443 TYR 0.008 0.001 TYR A 42 ARG 0.004 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.669 Fit side-chains REVERT: A 63 MET cc_start: 0.8096 (ttt) cc_final: 0.7794 (ttp) REVERT: A 88 LYS cc_start: 0.8672 (tmmt) cc_final: 0.8339 (tppt) REVERT: A 103 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7863 (mtm180) REVERT: A 160 ASP cc_start: 0.7834 (m-30) cc_final: 0.7621 (m-30) REVERT: A 172 GLN cc_start: 0.7292 (mm-40) cc_final: 0.7002 (mm-40) REVERT: A 351 ASP cc_start: 0.6143 (p0) cc_final: 0.5870 (p0) REVERT: A 367 ARG cc_start: 0.7714 (mtp85) cc_final: 0.7360 (ttp-110) REVERT: A 404 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7831 (p0) REVERT: A 413 LYS cc_start: 0.7858 (tttt) cc_final: 0.6811 (tptp) REVERT: A 416 LYS cc_start: 0.6695 (mttt) cc_final: 0.5228 (tttm) REVERT: A 458 ARG cc_start: 0.8449 (mmm160) cc_final: 0.7971 (mmm-85) REVERT: A 498 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: A 575 MET cc_start: 0.8632 (mtp) cc_final: 0.8254 (mtt) outliers start: 16 outliers final: 12 residues processed: 54 average time/residue: 1.5369 time to fit residues: 87.0128 Evaluate side-chains 56 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 chunk 50 optimal weight: 0.0670 chunk 8 optimal weight: 10.0000 overall best weight: 3.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7339 Z= 0.257 Angle : 0.544 9.161 10470 Z= 0.299 Chirality : 0.036 0.162 1210 Planarity : 0.004 0.034 951 Dihedral : 23.902 112.429 2118 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.54 % Allowed : 22.29 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.99 (0.34), residues: 590 helix: 3.32 (0.27), residues: 324 sheet: 1.50 (0.59), residues: 62 loop : -0.14 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.003 0.001 HIS A 269 PHE 0.007 0.001 PHE A 443 TYR 0.009 0.001 TYR A 42 ARG 0.003 0.000 ARG A 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.660 Fit side-chains REVERT: A 63 MET cc_start: 0.8155 (ttt) cc_final: 0.7881 (ttp) REVERT: A 88 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8370 (tppt) REVERT: A 103 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7867 (mtm180) REVERT: A 160 ASP cc_start: 0.7839 (m-30) cc_final: 0.7623 (m-30) REVERT: A 172 GLN cc_start: 0.7327 (mm-40) cc_final: 0.7027 (mm-40) REVERT: A 351 ASP cc_start: 0.6099 (p0) cc_final: 0.5819 (p0) REVERT: A 367 ARG cc_start: 0.7734 (mtp85) cc_final: 0.7396 (ttp-110) REVERT: A 404 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7833 (p0) REVERT: A 413 LYS cc_start: 0.7857 (tttt) cc_final: 0.6810 (tptp) REVERT: A 416 LYS cc_start: 0.6716 (mttt) cc_final: 0.5234 (tttm) REVERT: A 458 ARG cc_start: 0.8288 (mmm160) cc_final: 0.7954 (mmm-85) REVERT: A 498 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: A 575 MET cc_start: 0.8637 (mtp) cc_final: 0.8266 (mtt) outliers start: 17 outliers final: 14 residues processed: 55 average time/residue: 1.5129 time to fit residues: 87.3505 Evaluate side-chains 59 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.137750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105498 restraints weight = 9345.030| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.37 r_work: 0.3278 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7339 Z= 0.276 Angle : 0.564 10.589 10470 Z= 0.306 Chirality : 0.037 0.163 1210 Planarity : 0.004 0.034 951 Dihedral : 23.846 113.082 2118 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.54 % Allowed : 22.29 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.94 (0.34), residues: 590 helix: 3.29 (0.27), residues: 324 sheet: 1.46 (0.59), residues: 62 loop : -0.18 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.003 0.001 HIS A 269 PHE 0.007 0.001 PHE A 443 TYR 0.009 0.001 TYR A 42 ARG 0.004 0.000 ARG A 499 =============================================================================== Job complete usr+sys time: 2364.28 seconds wall clock time: 42 minutes 41.60 seconds (2561.60 seconds total)