Starting phenix.real_space_refine on Sun Apr 27 14:44:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mx3_48708/04_2025/9mx3_48708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mx3_48708/04_2025/9mx3_48708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mx3_48708/04_2025/9mx3_48708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mx3_48708/04_2025/9mx3_48708.map" model { file = "/net/cci-nas-00/data/ceres_data/9mx3_48708/04_2025/9mx3_48708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mx3_48708/04_2025/9mx3_48708.cif" } resolution = 3.0 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= -0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 24 5.16 5 C 3606 2.51 5 N 1039 2.21 5 O 1225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5929 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5204 Classifications: {'peptide': 641} Link IDs: {'PTRANS': 26, 'TRANS': 614} Chain: "C" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 360 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "B" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 338 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.46, per 1000 atoms: 0.75 Number of scatterers: 5929 At special positions: 0 Unit cell: (95.048, 93.304, 76.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 35 15.00 O 1225 8.00 N 1039 7.00 C 3606 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 - 3.00 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: 1.53 Conformation dependent library (CDL) restraints added in 729.7 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 3 sheets defined 54.6% alpha, 10.3% beta 13 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.844A pdb=" N LYS A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 49 through 52 removed outlier: 3.517A pdb=" N ILE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 69 through 84 removed outlier: 4.016A pdb=" N VAL A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.569A pdb=" N TRP A 100 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.611A pdb=" N MET A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N HIS A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 234 through 257 Processing helix chain 'A' and resid 262 through 283 Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 301 through 304 removed outlier: 4.237A pdb=" N SER A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 304' Processing helix chain 'A' and resid 307 through 336 removed outlier: 3.573A pdb=" N ARG A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.601A pdb=" N VAL A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 364 removed outlier: 4.009A pdb=" N SER A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.844A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 437 removed outlier: 3.622A pdb=" N GLU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 removed outlier: 4.264A pdb=" N ALA A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 Processing helix chain 'A' and resid 523 through 529 Processing helix chain 'A' and resid 541 through 545 removed outlier: 4.338A pdb=" N ASP A 544 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 545 " --> pdb=" O GLY A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 545' Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 613 through 633 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 91 removed outlier: 4.087A pdb=" N THR A 118 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR A 63 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET A 117 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 65 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG A 62 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 138 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 140 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 170 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 27 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 173 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 228 removed outlier: 5.767A pdb=" N LYS A 222 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE A 488 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 224 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL A 490 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL A 226 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 489 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY A 370 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ALA A 444 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 372 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 582 removed outlier: 3.517A pdb=" N LYS A 575 " --> pdb=" O ARG A 595 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 577 " --> pdb=" O THR A 593 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1811 1.34 - 1.46: 1032 1.46 - 1.58: 3152 1.58 - 1.70: 67 1.70 - 1.82: 36 Bond restraints: 6098 Sorted by residual: bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" CB PHE A 321 " pdb=" CG PHE A 321 " ideal model delta sigma weight residual 1.502 1.527 -0.025 2.30e-02 1.89e+03 1.19e+00 bond pdb=" CB GLU A 580 " pdb=" CG GLU A 580 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CB MET A 589 " pdb=" CG MET A 589 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.86e-01 bond pdb=" CB ASN A 423 " pdb=" CG ASN A 423 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.88e-01 ... (remaining 6093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 8300 2.83 - 5.66: 66 5.66 - 8.49: 3 8.49 - 11.31: 2 11.31 - 14.14: 1 Bond angle restraints: 8372 Sorted by residual: angle pdb=" CB MET A 589 " pdb=" CG MET A 589 " pdb=" SD MET A 589 " ideal model delta sigma weight residual 112.70 126.84 -14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" CA LEU A 310 " pdb=" CB LEU A 310 " pdb=" CG LEU A 310 " ideal model delta sigma weight residual 116.30 125.74 -9.44 3.50e+00 8.16e-02 7.28e+00 angle pdb=" CA LEU A 515 " pdb=" CB LEU A 515 " pdb=" CG LEU A 515 " ideal model delta sigma weight residual 116.30 125.71 -9.41 3.50e+00 8.16e-02 7.23e+00 angle pdb=" C MET A 422 " pdb=" N ASN A 423 " pdb=" CA ASN A 423 " ideal model delta sigma weight residual 121.54 126.46 -4.92 1.91e+00 2.74e-01 6.62e+00 angle pdb=" CA GLU A 580 " pdb=" CB GLU A 580 " pdb=" CG GLU A 580 " ideal model delta sigma weight residual 114.10 119.19 -5.09 2.00e+00 2.50e-01 6.49e+00 ... (remaining 8367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.55: 3367 19.55 - 39.09: 327 39.09 - 58.64: 95 58.64 - 78.19: 32 78.19 - 97.74: 4 Dihedral angle restraints: 3825 sinusoidal: 1928 harmonic: 1897 Sorted by residual: dihedral pdb=" C2' ADP A 701 " pdb=" C1' ADP A 701 " pdb=" N9 ADP A 701 " pdb=" C4 ADP A 701 " ideal model delta sinusoidal sigma weight residual 91.55 -175.50 -92.95 1 2.00e+01 2.50e-03 2.52e+01 dihedral pdb=" O2A ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PA ADP A 701 " pdb=" PB ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 31.07 -91.07 1 2.00e+01 2.50e-03 2.44e+01 dihedral pdb=" O4' A B 22 " pdb=" C1' A B 22 " pdb=" N9 A B 22 " pdb=" C4 A B 22 " ideal model delta sinusoidal sigma weight residual 70.00 7.73 62.27 1 2.00e+01 2.50e-03 1.28e+01 ... (remaining 3822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 605 0.028 - 0.057: 215 0.057 - 0.085: 95 0.085 - 0.114: 39 0.114 - 0.142: 14 Chirality restraints: 968 Sorted by residual: chirality pdb=" C1' A B 22 " pdb=" O4' A B 22 " pdb=" C2' A B 22 " pdb=" N9 A B 22 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CG LEU A 331 " pdb=" CB LEU A 331 " pdb=" CD1 LEU A 331 " pdb=" CD2 LEU A 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ASN A 423 " pdb=" N ASN A 423 " pdb=" C ASN A 423 " pdb=" CB ASN A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 965 not shown) Planarity restraints: 955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 580 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" CD GLU A 580 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU A 580 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 580 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 344 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 345 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C C 7 " -0.017 2.00e-02 2.50e+03 1.00e-02 2.26e+00 pdb=" N1 C C 7 " 0.024 2.00e-02 2.50e+03 pdb=" C2 C C 7 " -0.000 2.00e-02 2.50e+03 pdb=" O2 C C 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C C 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C C 7 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C C 7 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C C 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C C 7 " -0.000 2.00e-02 2.50e+03 ... (remaining 952 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 712 2.75 - 3.29: 5744 3.29 - 3.82: 9579 3.82 - 4.36: 10809 4.36 - 4.90: 17997 Nonbonded interactions: 44841 Sorted by model distance: nonbonded pdb=" O2' C C 7 " pdb=" O5' C C 8 " model vdw 2.208 3.040 nonbonded pdb=" OG SER A 391 " pdb=" O PHE A 398 " model vdw 2.279 3.040 nonbonded pdb=" O ASP A 526 " pdb=" OG SER A 529 " model vdw 2.283 3.040 nonbonded pdb=" O LYS A 355 " pdb=" OG SER A 359 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 108 " model vdw 2.311 3.040 ... (remaining 44836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.880 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.740 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.003 0.032 6098 Z= 0.155 Angle : 0.634 14.143 8372 Z= 0.307 Chirality : 0.040 0.142 968 Planarity : 0.004 0.041 955 Dihedral : 17.065 97.737 2585 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.68 % Allowed : 17.98 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.34), residues: 639 helix: 2.63 (0.30), residues: 306 sheet: 0.58 (0.48), residues: 96 loop : -0.81 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.003 0.001 HIS A 409 PHE 0.011 0.001 PHE A 498 TYR 0.010 0.001 TYR A 160 ARG 0.007 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.17529 ( 288) hydrogen bonds : angle 4.92955 ( 813) covalent geometry : bond 0.00341 ( 6098) covalent geometry : angle 0.63358 ( 8372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8021 (ptm) REVERT: A 375 GLU cc_start: 0.8216 (tt0) cc_final: 0.7575 (tm-30) REVERT: A 632 MET cc_start: 0.8629 (ttm) cc_final: 0.7875 (tmm) outliers start: 10 outliers final: 3 residues processed: 30 average time/residue: 1.1979 time to fit residues: 38.4114 Evaluate side-chains 25 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.0030 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.108641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.077140 restraints weight = 15326.813| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.13 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6098 Z= 0.118 Angle : 0.570 7.090 8372 Z= 0.282 Chirality : 0.039 0.138 968 Planarity : 0.004 0.042 955 Dihedral : 15.731 97.797 1205 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.87 % Allowed : 14.96 % Favored : 81.18 % 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: 1.87 (0.34), residues: 639 helix: 2.81 (0.29), residues: 309 sheet: 0.79 (0.48), residues: 105 loop : -0.86 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 105 HIS 0.003 0.001 HIS A 145 PHE 0.009 0.001 PHE A 405 TYR 0.009 0.001 TYR A 160 ARG 0.004 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.05354 ( 288) hydrogen bonds : angle 4.07821 ( 813) covalent geometry : bond 0.00246 ( 6098) covalent geometry : angle 0.57049 ( 8372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 24 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8581 (tm-30) outliers start: 23 outliers final: 8 residues processed: 41 average time/residue: 1.0145 time to fit residues: 44.5906 Evaluate side-chains 28 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 550 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 0.0370 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.108395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.076954 restraints weight = 15510.424| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 4.17 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6098 Z= 0.116 Angle : 0.560 8.950 8372 Z= 0.272 Chirality : 0.039 0.139 968 Planarity : 0.003 0.040 955 Dihedral : 15.610 97.538 1199 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.36 % Allowed : 15.80 % Favored : 80.84 % 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: 1.84 (0.34), residues: 639 helix: 2.67 (0.29), residues: 315 sheet: 0.94 (0.48), residues: 105 loop : -0.89 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 105 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 321 TYR 0.009 0.001 TYR A 160 ARG 0.003 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.05392 ( 288) hydrogen bonds : angle 3.91121 ( 813) covalent geometry : bond 0.00246 ( 6098) covalent geometry : angle 0.56011 ( 8372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 27 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8584 (tm-30) REVERT: A 539 MET cc_start: 0.9327 (mmm) cc_final: 0.8300 (mtm) outliers start: 20 outliers final: 8 residues processed: 41 average time/residue: 1.0876 time to fit residues: 47.5527 Evaluate side-chains 30 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.108667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.077479 restraints weight = 15300.674| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.10 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6098 Z= 0.112 Angle : 0.555 10.478 8372 Z= 0.270 Chirality : 0.039 0.140 968 Planarity : 0.003 0.040 955 Dihedral : 15.526 97.660 1199 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.37 % Allowed : 15.63 % Favored : 80.00 % 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: 1.86 (0.34), residues: 639 helix: 2.68 (0.29), residues: 315 sheet: 0.99 (0.48), residues: 105 loop : -0.88 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 105 HIS 0.002 0.001 HIS A 83 PHE 0.008 0.001 PHE A 498 TYR 0.008 0.001 TYR A 160 ARG 0.003 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.05204 ( 288) hydrogen bonds : angle 3.77474 ( 813) covalent geometry : bond 0.00239 ( 6098) covalent geometry : angle 0.55545 ( 8372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 24 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9114 (mm) REVERT: A 202 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7294 (mmm-85) REVERT: A 356 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8556 (tm-30) REVERT: A 375 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: A 539 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8420 (mtm) outliers start: 26 outliers final: 8 residues processed: 44 average time/residue: 1.0426 time to fit residues: 49.0065 Evaluate side-chains 33 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.108813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.077298 restraints weight = 15266.171| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 4.14 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6098 Z= 0.119 Angle : 0.570 10.515 8372 Z= 0.277 Chirality : 0.038 0.141 968 Planarity : 0.003 0.040 955 Dihedral : 15.481 97.650 1198 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.53 % Allowed : 17.48 % Favored : 78.99 % 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: 1.89 (0.34), residues: 639 helix: 2.70 (0.29), residues: 315 sheet: 1.04 (0.48), residues: 105 loop : -0.88 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 105 HIS 0.002 0.001 HIS A 128 PHE 0.009 0.001 PHE A 321 TYR 0.008 0.001 TYR A 160 ARG 0.003 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.05347 ( 288) hydrogen bonds : angle 3.79923 ( 813) covalent geometry : bond 0.00257 ( 6098) covalent geometry : angle 0.56980 ( 8372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 21 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9102 (mm) REVERT: A 202 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7333 (mmm-85) REVERT: A 356 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8554 (tm-30) REVERT: A 375 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: A 539 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8415 (mtm) outliers start: 21 outliers final: 11 residues processed: 37 average time/residue: 1.1180 time to fit residues: 44.3445 Evaluate side-chains 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.106839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.074783 restraints weight = 15236.044| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 4.13 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6098 Z= 0.181 Angle : 0.621 12.354 8372 Z= 0.303 Chirality : 0.040 0.144 968 Planarity : 0.004 0.039 955 Dihedral : 15.509 97.545 1198 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.87 % Allowed : 17.48 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.34), residues: 639 helix: 2.78 (0.29), residues: 309 sheet: 0.79 (0.47), residues: 107 loop : -1.04 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.004 0.001 HIS A 146 PHE 0.015 0.002 PHE A 498 TYR 0.015 0.001 TYR A 160 ARG 0.002 0.000 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.06113 ( 288) hydrogen bonds : angle 3.98154 ( 813) covalent geometry : bond 0.00413 ( 6098) covalent geometry : angle 0.62098 ( 8372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 21 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9146 (mm) REVERT: A 202 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6893 (mmm-85) REVERT: A 356 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8692 (tm-30) REVERT: A 375 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: A 539 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8494 (mtm) REVERT: A 632 MET cc_start: 0.7863 (tmm) cc_final: 0.7577 (tmm) outliers start: 23 outliers final: 9 residues processed: 38 average time/residue: 1.2392 time to fit residues: 50.4626 Evaluate side-chains 34 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 20 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.0010 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.109617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.078063 restraints weight = 15148.771| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 4.13 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6098 Z= 0.102 Angle : 0.582 13.065 8372 Z= 0.275 Chirality : 0.039 0.138 968 Planarity : 0.004 0.041 955 Dihedral : 15.330 97.152 1198 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.86 % Allowed : 18.99 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.34), residues: 639 helix: 2.77 (0.29), residues: 315 sheet: 1.01 (0.48), residues: 104 loop : -0.94 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 105 HIS 0.002 0.001 HIS A 83 PHE 0.008 0.001 PHE A 321 TYR 0.008 0.001 TYR A 486 ARG 0.010 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 288) hydrogen bonds : angle 3.56555 ( 813) covalent geometry : bond 0.00212 ( 6098) covalent geometry : angle 0.58223 ( 8372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 23 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9130 (mm) REVERT: A 202 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7306 (mmm-85) REVERT: A 356 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8557 (tm-30) REVERT: A 539 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8361 (mtm) REVERT: A 632 MET cc_start: 0.7685 (tmm) cc_final: 0.7415 (tmm) outliers start: 17 outliers final: 10 residues processed: 35 average time/residue: 1.3169 time to fit residues: 49.4637 Evaluate side-chains 33 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 20 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.109574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.078121 restraints weight = 14976.611| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 4.16 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6098 Z= 0.102 Angle : 0.572 12.257 8372 Z= 0.271 Chirality : 0.038 0.137 968 Planarity : 0.004 0.040 955 Dihedral : 15.324 98.131 1198 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.86 % Allowed : 19.33 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.34), residues: 639 helix: 2.92 (0.30), residues: 309 sheet: 1.04 (0.48), residues: 105 loop : -0.65 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 105 HIS 0.002 0.001 HIS A 83 PHE 0.016 0.001 PHE A 321 TYR 0.008 0.001 TYR A 14 ARG 0.007 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 288) hydrogen bonds : angle 3.47326 ( 813) covalent geometry : bond 0.00216 ( 6098) covalent geometry : angle 0.57177 ( 8372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9089 (mm) REVERT: A 202 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7284 (mmm-85) REVERT: A 356 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8555 (tm-30) REVERT: A 539 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8431 (mtm) REVERT: A 632 MET cc_start: 0.7654 (tmm) cc_final: 0.7366 (tmm) outliers start: 17 outliers final: 9 residues processed: 37 average time/residue: 1.1107 time to fit residues: 44.0412 Evaluate side-chains 34 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.108212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.076581 restraints weight = 15131.616| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 4.16 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6098 Z= 0.128 Angle : 0.592 12.394 8372 Z= 0.282 Chirality : 0.039 0.147 968 Planarity : 0.004 0.040 955 Dihedral : 15.347 98.187 1198 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.19 % Allowed : 19.16 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.34), residues: 639 helix: 2.85 (0.30), residues: 309 sheet: 0.99 (0.48), residues: 107 loop : -0.74 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 105 HIS 0.003 0.001 HIS A 128 PHE 0.010 0.001 PHE A 498 TYR 0.011 0.001 TYR A 160 ARG 0.008 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.05209 ( 288) hydrogen bonds : angle 3.63899 ( 813) covalent geometry : bond 0.00287 ( 6098) covalent geometry : angle 0.59185 ( 8372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 22 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9099 (mm) REVERT: A 202 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7272 (mmm-85) REVERT: A 356 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8578 (tm-30) REVERT: A 539 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8459 (mtm) REVERT: A 632 MET cc_start: 0.7727 (tmm) cc_final: 0.7419 (tmm) outliers start: 19 outliers final: 13 residues processed: 36 average time/residue: 1.5012 time to fit residues: 57.3513 Evaluate side-chains 37 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 20 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.108650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.077100 restraints weight = 15033.007| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 4.16 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6098 Z= 0.116 Angle : 0.591 13.038 8372 Z= 0.280 Chirality : 0.039 0.139 968 Planarity : 0.004 0.050 955 Dihedral : 15.333 98.004 1198 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.36 % Allowed : 18.49 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.34), residues: 639 helix: 2.87 (0.30), residues: 309 sheet: 1.00 (0.48), residues: 107 loop : -0.70 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 105 HIS 0.002 0.001 HIS A 83 PHE 0.009 0.001 PHE A 498 TYR 0.009 0.001 TYR A 160 ARG 0.013 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.05057 ( 288) hydrogen bonds : angle 3.58687 ( 813) covalent geometry : bond 0.00253 ( 6098) covalent geometry : angle 0.59067 ( 8372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 20 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9099 (mm) REVERT: A 202 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7256 (mmm-85) REVERT: A 320 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9171 (pp) REVERT: A 356 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: A 539 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8432 (mtm) REVERT: A 632 MET cc_start: 0.7720 (tmm) cc_final: 0.7421 (tmm) outliers start: 20 outliers final: 13 residues processed: 35 average time/residue: 1.1336 time to fit residues: 42.6118 Evaluate side-chains 38 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 20 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 40 optimal weight: 0.0020 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 0.0170 chunk 23 optimal weight: 0.6980 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.110888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.079588 restraints weight = 15252.223| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.20 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6098 Z= 0.094 Angle : 0.568 12.870 8372 Z= 0.268 Chirality : 0.038 0.138 968 Planarity : 0.004 0.054 955 Dihedral : 15.276 97.790 1198 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.86 % Allowed : 19.33 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.34), residues: 639 helix: 2.89 (0.30), residues: 309 sheet: 1.14 (0.48), residues: 104 loop : -0.60 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 100 HIS 0.002 0.001 HIS A 145 PHE 0.009 0.001 PHE A 321 TYR 0.008 0.001 TYR A 14 ARG 0.012 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 288) hydrogen bonds : angle 3.32985 ( 813) covalent geometry : bond 0.00196 ( 6098) covalent geometry : angle 0.56817 ( 8372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.87 seconds wall clock time: 60 minutes 41.15 seconds (3641.15 seconds total)