Starting phenix.real_space_refine on Sat May 10 10:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mx3_48708/05_2025/9mx3_48708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mx3_48708/05_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_48708/05_2025/9mx3_48708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mx3_48708/05_2025/9mx3_48708.map" model { file = "/net/cci-nas-00/data/ceres_data/9mx3_48708/05_2025/9mx3_48708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mx3_48708/05_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-5687/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: 1.81 Conformation dependent library (CDL) restraints added in 813.0 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: 1.84 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: 2.08 Time building geometry restraints manager: 1.85 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- 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 : 0.726 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: 1.2492 time to fit residues: 39.9754 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 : 0.694 ------------------------------------------------------------------------------- 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 = 0.077142 restraints weight = 15326.825| |-----------------------------------------------------------------------------| 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 97.796 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 : 0.596 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: 0.9465 time to fit residues: 41.6217 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 : 0.614 ------------------------------------------------------------------------------- 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: 0.0770 chunk 6 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.110161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.078763 restraints weight = 15371.352| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.17 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1238 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= 0.097 Angle : 0.545 8.652 8372 Z= 0.263 Chirality : 0.038 0.140 968 Planarity : 0.003 0.041 955 Dihedral : 15.572 97.246 1199 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.36 % Allowed : 15.97 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.34), residues: 639 helix: 2.69 (0.29), residues: 315 sheet: 0.92 (0.50), residues: 98 loop : -0.72 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 105 HIS 0.002 0.001 HIS A 83 PHE 0.009 0.001 PHE A 321 TYR 0.007 0.001 TYR A 14 ARG 0.002 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04960 ( 288) hydrogen bonds : angle 3.76950 ( 813) covalent geometry : bond 0.00193 ( 6098) covalent geometry : angle 0.54539 ( 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 48 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 28 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9260 (pp) REVERT: A 356 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8595 (tm-30) REVERT: A 550 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7743 (mtm) outliers start: 20 outliers final: 5 residues processed: 40 average time/residue: 1.0399 time to fit residues: 44.5052 Evaluate side-chains 28 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 139 LEU 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 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.107235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.075235 restraints weight = 15514.405| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.18 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6098 Z= 0.159 Angle : 0.598 10.973 8372 Z= 0.291 Chirality : 0.039 0.143 968 Planarity : 0.004 0.039 955 Dihedral : 15.588 98.340 1198 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.37 % Allowed : 16.30 % Favored : 79.33 % 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: 2.01 (0.34), residues: 639 helix: 2.90 (0.29), residues: 303 sheet: 0.97 (0.48), residues: 107 loop : -0.71 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.003 0.001 HIS A 146 PHE 0.013 0.001 PHE A 498 TYR 0.014 0.001 TYR A 160 ARG 0.004 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.05806 ( 288) hydrogen bonds : angle 3.94682 ( 813) covalent geometry : bond 0.00358 ( 6098) covalent geometry : angle 0.59755 ( 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 47 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 21 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9108 (mm) REVERT: A 202 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7269 (mmm-85) REVERT: A 356 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8567 (tm-30) REVERT: A 375 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: A 539 MET cc_start: 0.9301 (mmm) cc_final: 0.8491 (mtm) outliers start: 26 outliers final: 12 residues processed: 42 average time/residue: 1.0276 time to fit residues: 46.1475 Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 20 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 204 VAL Chi-restraints excluded: chain A residue 296 ILE 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 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.109451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.078190 restraints weight = 15182.603| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 4.12 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1464 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= 0.105 Angle : 0.566 11.552 8372 Z= 0.273 Chirality : 0.038 0.140 968 Planarity : 0.003 0.041 955 Dihedral : 15.465 97.446 1198 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.70 % Allowed : 17.31 % 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: 1.95 (0.34), residues: 639 helix: 2.75 (0.29), residues: 315 sheet: 1.13 (0.48), residues: 104 loop : -0.87 (0.41), residues: 220 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 321 TYR 0.007 0.001 TYR A 14 ARG 0.003 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 288) hydrogen bonds : angle 3.73434 ( 813) covalent geometry : bond 0.00213 ( 6098) covalent geometry : angle 0.56550 ( 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 45 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 23 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9089 (mm) REVERT: A 202 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7320 (mmm-85) REVERT: A 356 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8568 (tm-30) REVERT: A 539 MET cc_start: 0.9316 (mmm) cc_final: 0.8423 (mtm) REVERT: A 632 MET cc_start: 0.7610 (tmm) cc_final: 0.7291 (tmm) outliers start: 22 outliers final: 10 residues processed: 40 average time/residue: 1.0015 time to fit residues: 42.8421 Evaluate side-chains 32 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 139 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 204 VAL 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 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: 2.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.107216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.075088 restraints weight = 15199.299| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.16 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6098 Z= 0.176 Angle : 0.614 12.112 8372 Z= 0.300 Chirality : 0.040 0.142 968 Planarity : 0.004 0.040 955 Dihedral : 15.507 97.914 1198 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.87 % Allowed : 18.15 % Favored : 77.98 % 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: 1.94 (0.34), residues: 639 helix: 2.90 (0.29), residues: 303 sheet: 0.85 (0.47), residues: 107 loop : -0.79 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.003 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.06002 ( 288) hydrogen bonds : angle 3.93995 ( 813) covalent geometry : bond 0.00402 ( 6098) covalent geometry : angle 0.61399 ( 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 43 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 20 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9128 (mm) REVERT: A 202 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.6871 (mmm-85) REVERT: A 356 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8591 (tm-30) REVERT: A 375 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: A 539 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8502 (mtm) outliers start: 23 outliers final: 10 residues processed: 37 average time/residue: 1.0383 time to fit residues: 41.3331 Evaluate side-chains 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 204 VAL 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: 1.9990 chunk 44 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.108461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.076740 restraints weight = 15140.059| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.13 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6098 Z= 0.120 Angle : 0.596 12.598 8372 Z= 0.281 Chirality : 0.039 0.139 968 Planarity : 0.003 0.040 955 Dihedral : 15.380 97.568 1198 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.70 % Allowed : 18.49 % 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: 1.94 (0.34), residues: 639 helix: 2.80 (0.30), residues: 309 sheet: 0.90 (0.48), residues: 107 loop : -0.77 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 105 HIS 0.003 0.001 HIS A 128 PHE 0.009 0.001 PHE A 498 TYR 0.009 0.001 TYR A 160 ARG 0.002 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.05255 ( 288) hydrogen bonds : angle 3.69816 ( 813) covalent geometry : bond 0.00263 ( 6098) covalent geometry : angle 0.59566 ( 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 45 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 23 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9132 (mm) REVERT: A 202 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7310 (mmm-85) REVERT: A 356 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8583 (tm-30) REVERT: A 539 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8408 (mtm) REVERT: A 632 MET cc_start: 0.7693 (tmm) cc_final: 0.7396 (tmm) outliers start: 22 outliers final: 13 residues processed: 39 average time/residue: 1.1615 time to fit residues: 48.1903 Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 19 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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 449 GLU 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: 0.9980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.0030 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.0050 overall best weight: 0.5004 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.110311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.078822 restraints weight = 15000.482| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 4.12 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.002 0.032 6098 Z= 0.100 Angle : 0.581 13.180 8372 Z= 0.274 Chirality : 0.038 0.138 968 Planarity : 0.004 0.041 955 Dihedral : 15.308 97.761 1198 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.52 % Allowed : 19.50 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.34), residues: 639 helix: 2.86 (0.29), residues: 315 sheet: 1.12 (0.49), residues: 104 loop : -0.89 (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 0.014 0.001 PHE A 321 TYR 0.007 0.001 TYR A 14 ARG 0.011 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 288) hydrogen bonds : angle 3.46566 ( 813) covalent geometry : bond 0.00210 ( 6098) covalent geometry : angle 0.58105 ( 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 39 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9118 (mm) REVERT: A 356 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: A 539 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8405 (mtm) outliers start: 15 outliers final: 8 residues processed: 34 average time/residue: 0.9636 time to fit residues: 35.3950 Evaluate side-chains 32 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 296 ILE Chi-restraints excluded: chain A residue 356 GLN 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=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: 1.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 0.0570 chunk 41 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 0.0040 chunk 8 optimal weight: 0.6980 overall best weight: 0.3710 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.110512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.079202 restraints weight = 14996.206| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 4.14 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1939 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= 0.098 Angle : 0.592 12.265 8372 Z= 0.282 Chirality : 0.039 0.141 968 Planarity : 0.003 0.041 955 Dihedral : 15.306 98.035 1198 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.52 % Allowed : 19.83 % 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: 1.97 (0.34), residues: 639 helix: 2.76 (0.29), residues: 315 sheet: 1.13 (0.48), residues: 104 loop : -0.83 (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 0.007 0.001 PHE A 321 TYR 0.007 0.001 TYR A 14 ARG 0.009 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 288) hydrogen bonds : angle 3.44980 ( 813) covalent geometry : bond 0.00202 ( 6098) covalent geometry : angle 0.59249 ( 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 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 21 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9044 (mm) REVERT: A 356 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8585 (tm-30) REVERT: A 539 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8429 (mtm) outliers start: 15 outliers final: 11 residues processed: 32 average time/residue: 0.9853 time to fit residues: 34.1634 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 : 0.612 ------------------------------------------------------------------------------- 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 139 LEU 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 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 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.109447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.078050 restraints weight = 15039.181| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 4.15 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6098 Z= 0.117 Angle : 0.601 12.875 8372 Z= 0.284 Chirality : 0.039 0.140 968 Planarity : 0.003 0.041 955 Dihedral : 15.321 98.370 1198 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.69 % Allowed : 19.83 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.34), residues: 639 helix: 2.84 (0.30), residues: 309 sheet: 1.03 (0.48), residues: 107 loop : -0.63 (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 128 PHE 0.008 0.001 PHE A 321 TYR 0.009 0.001 TYR A 160 ARG 0.011 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 288) hydrogen bonds : angle 3.52149 ( 813) covalent geometry : bond 0.00258 ( 6098) covalent geometry : angle 0.60116 ( 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 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9083 (mm) REVERT: A 320 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9175 (pp) REVERT: A 356 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: A 539 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.8442 (mtm) outliers start: 16 outliers final: 9 residues processed: 31 average time/residue: 0.9365 time to fit residues: 31.4689 Evaluate side-chains 32 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 139 LEU 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 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 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.110191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.078826 restraints weight = 15207.685| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.16 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2047 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= 0.100 Angle : 0.587 12.819 8372 Z= 0.278 Chirality : 0.038 0.139 968 Planarity : 0.004 0.042 955 Dihedral : 15.304 98.285 1198 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.52 % Allowed : 20.34 % Favored : 77.14 % 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: 2.09 (0.34), residues: 639 helix: 2.85 (0.30), residues: 309 sheet: 1.10 (0.48), residues: 105 loop : -0.62 (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 0.010 0.001 PHE A 321 TYR 0.007 0.001 TYR A 14 ARG 0.010 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 288) hydrogen bonds : angle 3.42573 ( 813) covalent geometry : bond 0.00212 ( 6098) covalent geometry : angle 0.58665 ( 8372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.00 seconds wall clock time: 51 minutes 28.50 seconds (3088.50 seconds total)