Starting phenix.real_space_refine on Tue Feb 11 13:34:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i4f_35171/02_2025/8i4f_35171.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i4f_35171/02_2025/8i4f_35171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i4f_35171/02_2025/8i4f_35171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i4f_35171/02_2025/8i4f_35171.map" model { file = "/net/cci-nas-00/data/ceres_data/8i4f_35171/02_2025/8i4f_35171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i4f_35171/02_2025/8i4f_35171.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3733 2.51 5 N 964 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5824 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4902 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 34, 'TRANS': 584} Chain breaks: 5 Chain: "C" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Time building chain proxies: 4.07, per 1000 atoms: 0.70 Number of scatterers: 5824 At special positions: 0 Unit cell: (71.764, 86.676, 128.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1102 8.00 N 964 7.00 C 3733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 545 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 624 " - pdb=" SG CYS A 656 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 678 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 901.4 milliseconds 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1374 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 13 sheets defined 2.7% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.751A pdb=" N GLU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.921A pdb=" N TYR A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 377' Processing helix chain 'A' and resid 626 through 631 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 removed outlier: 7.811A pdb=" N ASN A 69 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR A 276 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 200 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 236 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 210 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL A 234 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER A 212 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 63 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.623A pdb=" N GLY A 115 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 125 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 128 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 135 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.623A pdb=" N GLY A 115 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 125 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS A 139 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 321 removed outlier: 3.543A pdb=" N THR A 606 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 619 " --> pdb=" O CYS A 656 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.804A pdb=" N GLU A 331 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASN A 549 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE A 333 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 363 through 365 removed outlier: 3.605A pdb=" N LYS A 385 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 442 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA A 383 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 460 through 461 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 662 removed outlier: 6.155A pdb=" N GLU A 661 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 682 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 671 through 674 removed outlier: 6.734A pdb=" N ILE A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 6 through 7 removed outlier: 3.554A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET C 83 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.830A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 333 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1856 1.34 - 1.46: 1532 1.46 - 1.58: 2557 1.58 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5974 Sorted by residual: bond pdb=" CB PRO A 147 " pdb=" CG PRO A 147 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.08e-01 bond pdb=" C ALA A 379 " pdb=" N PRO A 380 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 6.19e-01 bond pdb=" C VAL A 627 " pdb=" N PRO A 628 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 4.27e-01 bond pdb=" C ASP A 301 " pdb=" N PRO A 302 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.05e-01 bond pdb=" C PHE A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.02e-01 ... (remaining 5969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 7889 1.13 - 2.26: 187 2.26 - 3.38: 47 3.38 - 4.51: 3 4.51 - 5.64: 3 Bond angle restraints: 8129 Sorted by residual: angle pdb=" CA TYR A 502 " pdb=" CB TYR A 502 " pdb=" CG TYR A 502 " ideal model delta sigma weight residual 113.90 117.01 -3.11 1.80e+00 3.09e-01 2.99e+00 angle pdb=" C GLY A 573 " pdb=" N ARG A 574 " pdb=" CA ARG A 574 " ideal model delta sigma weight residual 121.54 124.84 -3.30 1.91e+00 2.74e-01 2.98e+00 angle pdb=" C ALA A 379 " pdb=" N PRO A 380 " pdb=" CA PRO A 380 " ideal model delta sigma weight residual 119.84 121.96 -2.12 1.25e+00 6.40e-01 2.88e+00 angle pdb=" N PRO A 380 " pdb=" CA PRO A 380 " pdb=" C PRO A 380 " ideal model delta sigma weight residual 112.47 115.73 -3.26 2.06e+00 2.36e-01 2.50e+00 angle pdb=" C SER A 647 " pdb=" N ASN A 648 " pdb=" CA ASN A 648 " ideal model delta sigma weight residual 122.82 125.03 -2.21 1.42e+00 4.96e-01 2.43e+00 ... (remaining 8124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3330 17.65 - 35.30: 160 35.30 - 52.95: 19 52.95 - 70.61: 5 70.61 - 88.26: 2 Dihedral angle restraints: 3516 sinusoidal: 1367 harmonic: 2149 Sorted by residual: dihedral pdb=" CB GLU A 668 " pdb=" CG GLU A 668 " pdb=" CD GLU A 668 " pdb=" OE1 GLU A 668 " ideal model delta sinusoidal sigma weight residual 0.00 -88.26 88.26 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" SG CYS A 139 " pdb=" CB CYS A 173 " pdb=" SG CYS A 173 " pdb=" CA CYS A 173 " ideal model delta sinusoidal sigma weight residual 79.00 26.43 52.57 1 2.00e+01 2.50e-03 9.41e+00 dihedral pdb=" N PHE A 282 " pdb=" CA PHE A 282 " pdb=" CB PHE A 282 " pdb=" CG PHE A 282 " ideal model delta sinusoidal sigma weight residual -60.00 -115.68 55.68 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 3513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 498 0.026 - 0.052: 238 0.052 - 0.078: 81 0.078 - 0.104: 54 0.104 - 0.130: 23 Chirality restraints: 894 Sorted by residual: chirality pdb=" CB ILE A 417 " pdb=" CA ILE A 417 " pdb=" CG1 ILE A 417 " pdb=" CG2 ILE A 417 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE A 127 " pdb=" N ILE A 127 " pdb=" C ILE A 127 " pdb=" CB ILE A 127 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 891 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 451 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 452 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 343 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 344 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 93 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.015 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 869 2.77 - 3.30: 5359 3.30 - 3.83: 9549 3.83 - 4.37: 10883 4.37 - 4.90: 18833 Nonbonded interactions: 45493 Sorted by model distance: nonbonded pdb=" OH TYR A 45 " pdb=" O LEU A 62 " model vdw 2.232 3.040 nonbonded pdb=" O GLU A 668 " pdb=" OH TYR A 702 " model vdw 2.284 3.040 nonbonded pdb=" O VAL A 138 " pdb=" OG1 THR A 174 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR A 116 " pdb=" O ASN A 241 " model vdw 2.315 3.040 nonbonded pdb=" OG1 THR A 400 " pdb=" O GLU A 523 " model vdw 2.323 3.040 ... (remaining 45488 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: 1.180 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.940 Find NCS groups from input model: 0.100 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 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 : 0.002 0.042 5974 Z= 0.114 Angle : 0.450 5.640 8129 Z= 0.250 Chirality : 0.041 0.130 894 Planarity : 0.004 0.049 1051 Dihedral : 9.629 88.256 2112 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.44 % Allowed : 7.62 % Favored : 86.94 % 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: -4.30 (0.25), residues: 724 helix: -4.59 (0.40), residues: 33 sheet: -1.27 (0.38), residues: 171 loop : -3.60 (0.21), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 640 HIS 0.001 0.000 HIS A 57 PHE 0.010 0.001 PHE A 407 TYR 0.005 0.001 TYR A 376 ARG 0.002 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7567 (p) REVERT: A 74 HIS cc_start: 0.5942 (m-70) cc_final: 0.5623 (m-70) REVERT: A 118 LEU cc_start: 0.7341 (mp) cc_final: 0.6985 (mp) REVERT: A 136 ILE cc_start: 0.8337 (mm) cc_final: 0.8080 (mt) REVERT: A 196 LEU cc_start: 0.8265 (tp) cc_final: 0.7889 (tp) REVERT: A 212 SER cc_start: 0.7213 (t) cc_final: 0.6871 (m) REVERT: A 251 LEU cc_start: 0.7681 (tp) cc_final: 0.7426 (tp) REVERT: A 349 PHE cc_start: 0.7400 (m-80) cc_final: 0.6648 (m-80) REVERT: A 399 PHE cc_start: 0.7868 (m-80) cc_final: 0.7657 (m-10) REVERT: A 432 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 443 TRP cc_start: 0.8199 (p90) cc_final: 0.7131 (p90) REVERT: A 477 THR cc_start: 0.8672 (p) cc_final: 0.8460 (t) REVERT: A 544 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7849 (ttmm) REVERT: A 585 ASP cc_start: 0.7531 (t70) cc_final: 0.6840 (t70) REVERT: A 651 GLN cc_start: 0.7513 (tp40) cc_final: 0.7163 (tp-100) outliers start: 35 outliers final: 11 residues processed: 207 average time/residue: 0.2264 time to fit residues: 60.0280 Evaluate side-chains 165 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 0.0070 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 218 ASN A 416 GLN A 421 GLN A 429 ASN A 481 GLN A 570 GLN A 614 GLN A 651 GLN A 664 ASN A 682 GLN C 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.159054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.141653 restraints weight = 9502.588| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.54 r_work: 0.3742 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5974 Z= 0.241 Angle : 0.592 6.993 8129 Z= 0.310 Chirality : 0.045 0.169 894 Planarity : 0.005 0.046 1051 Dihedral : 7.151 92.655 835 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 5.75 % Allowed : 14.15 % Favored : 80.09 % 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: -3.79 (0.26), residues: 724 helix: -4.22 (0.54), residues: 34 sheet: -1.06 (0.38), residues: 176 loop : -3.19 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 36 HIS 0.003 0.001 HIS A 74 PHE 0.033 0.002 PHE A 378 TYR 0.033 0.002 TYR A 502 ARG 0.005 0.001 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7295 (p) REVERT: A 42 ARG cc_start: 0.7522 (mtt-85) cc_final: 0.7119 (mtt-85) REVERT: A 60 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 136 ILE cc_start: 0.8495 (mm) cc_final: 0.8237 (mt) REVERT: A 184 MET cc_start: 0.6364 (tmt) cc_final: 0.6118 (tmt) REVERT: A 212 SER cc_start: 0.7541 (t) cc_final: 0.7003 (m) REVERT: A 251 LEU cc_start: 0.7727 (tp) cc_final: 0.7516 (tp) REVERT: A 357 VAL cc_start: 0.7928 (t) cc_final: 0.7550 (t) REVERT: A 443 TRP cc_start: 0.8321 (p90) cc_final: 0.7545 (p90) REVERT: A 477 THR cc_start: 0.8793 (p) cc_final: 0.8535 (t) REVERT: A 544 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8259 (ttmm) REVERT: A 665 ASN cc_start: 0.7953 (t0) cc_final: 0.7484 (t0) REVERT: A 706 LEU cc_start: 0.8551 (mp) cc_final: 0.8057 (mp) REVERT: C 29 PHE cc_start: 0.7739 (m-10) cc_final: 0.7525 (m-10) REVERT: C 69 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7444 (p) outliers start: 37 outliers final: 20 residues processed: 195 average time/residue: 0.1950 time to fit residues: 48.6475 Evaluate side-chains 180 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.149749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133632 restraints weight = 9463.257| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.23 r_work: 0.3651 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 5974 Z= 0.466 Angle : 0.755 13.643 8129 Z= 0.395 Chirality : 0.050 0.250 894 Planarity : 0.006 0.048 1051 Dihedral : 8.092 93.021 833 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.39 % Favored : 90.47 % Rotamer: Outliers : 7.15 % Allowed : 16.33 % Favored : 76.52 % 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: -3.69 (0.27), residues: 724 helix: -3.96 (0.60), residues: 34 sheet: -0.98 (0.42), residues: 156 loop : -3.07 (0.22), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 360 HIS 0.005 0.001 HIS A 214 PHE 0.037 0.003 PHE A 569 TYR 0.035 0.003 TYR A 430 ARG 0.006 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7628 (tm-30) REVERT: A 72 TRP cc_start: 0.8617 (t60) cc_final: 0.8359 (t60) REVERT: A 108 ILE cc_start: 0.7722 (mt) cc_final: 0.7505 (mt) REVERT: A 136 ILE cc_start: 0.8457 (mm) cc_final: 0.8138 (mt) REVERT: A 241 ASN cc_start: 0.5757 (OUTLIER) cc_final: 0.5337 (p0) REVERT: A 361 ASN cc_start: 0.8613 (p0) cc_final: 0.8367 (p0) REVERT: A 429 ASN cc_start: 0.7717 (m-40) cc_final: 0.7351 (m110) REVERT: A 443 TRP cc_start: 0.8384 (p90) cc_final: 0.7534 (p90) REVERT: A 444 ASN cc_start: 0.8508 (t0) cc_final: 0.7679 (t0) REVERT: A 446 ASN cc_start: 0.7352 (p0) cc_final: 0.7070 (p0) REVERT: A 477 THR cc_start: 0.8985 (p) cc_final: 0.8748 (t) REVERT: A 544 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8476 (ttmm) REVERT: A 594 ILE cc_start: 0.8348 (mt) cc_final: 0.8135 (mt) REVERT: C 69 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7619 (p) REVERT: C 71 SER cc_start: 0.8347 (m) cc_final: 0.8036 (p) REVERT: C 81 LEU cc_start: 0.8026 (tp) cc_final: 0.7650 (tp) outliers start: 46 outliers final: 32 residues processed: 216 average time/residue: 0.1834 time to fit residues: 50.9684 Evaluate side-chains 201 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 3 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 65 optimal weight: 0.0470 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN A 547 ASN A 549 ASN A 682 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.156597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139665 restraints weight = 9527.891| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.45 r_work: 0.3719 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5974 Z= 0.185 Angle : 0.650 17.348 8129 Z= 0.324 Chirality : 0.046 0.243 894 Planarity : 0.004 0.043 1051 Dihedral : 7.193 89.846 830 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.60 % Allowed : 21.46 % Favored : 72.94 % 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: -3.34 (0.28), residues: 724 helix: -3.34 (0.83), residues: 28 sheet: -0.89 (0.39), residues: 171 loop : -2.86 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 36 HIS 0.005 0.001 HIS A 214 PHE 0.018 0.001 PHE A 282 TYR 0.024 0.002 TYR A 502 ARG 0.006 0.001 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 72 TRP cc_start: 0.8525 (t60) cc_final: 0.8219 (t60) REVERT: A 108 ILE cc_start: 0.7806 (mt) cc_final: 0.7571 (mt) REVERT: A 136 ILE cc_start: 0.8443 (mm) cc_final: 0.8126 (mt) REVERT: A 331 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7392 (tt0) REVERT: A 345 PHE cc_start: 0.7859 (m-80) cc_final: 0.7248 (m-80) REVERT: A 378 PHE cc_start: 0.6257 (t80) cc_final: 0.5830 (t80) REVERT: A 432 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8490 (mp) REVERT: A 474 ASP cc_start: 0.8280 (t0) cc_final: 0.8010 (t70) REVERT: A 500 GLN cc_start: 0.5341 (tp-100) cc_final: 0.5125 (tp-100) REVERT: A 525 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.6182 (mt) REVERT: A 538 THR cc_start: 0.7453 (p) cc_final: 0.6033 (m) REVERT: A 544 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8287 (ttmm) REVERT: A 651 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7252 (tp40) REVERT: A 665 ASN cc_start: 0.8043 (t0) cc_final: 0.7515 (t0) REVERT: C 69 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7384 (p) REVERT: C 71 SER cc_start: 0.8170 (m) cc_final: 0.7802 (p) REVERT: C 81 LEU cc_start: 0.7827 (tp) cc_final: 0.7594 (tp) REVERT: C 105 TYR cc_start: 0.8732 (m-80) cc_final: 0.8445 (m-80) outliers start: 36 outliers final: 20 residues processed: 188 average time/residue: 0.1840 time to fit residues: 44.9421 Evaluate side-chains 184 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 3 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 23 optimal weight: 0.0980 chunk 58 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 614 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.154704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137619 restraints weight = 9294.041| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.38 r_work: 0.3696 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5974 Z= 0.244 Angle : 0.700 19.702 8129 Z= 0.349 Chirality : 0.047 0.230 894 Planarity : 0.006 0.108 1051 Dihedral : 7.188 90.372 828 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 5.29 % Allowed : 23.79 % Favored : 70.92 % 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: -3.10 (0.28), residues: 724 helix: -3.79 (0.70), residues: 34 sheet: -0.62 (0.42), residues: 150 loop : -2.59 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 640 HIS 0.003 0.001 HIS A 214 PHE 0.021 0.002 PHE A 63 TYR 0.023 0.002 TYR A 502 ARG 0.007 0.001 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7998 (tpp80) cc_final: 0.7754 (mtt90) REVERT: A 60 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 108 ILE cc_start: 0.7787 (mt) cc_final: 0.7561 (mt) REVERT: A 136 ILE cc_start: 0.8433 (mm) cc_final: 0.8125 (mt) REVERT: A 378 PHE cc_start: 0.6373 (t80) cc_final: 0.6099 (t80) REVERT: A 429 ASN cc_start: 0.7563 (m-40) cc_final: 0.7257 (m-40) REVERT: A 432 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 443 TRP cc_start: 0.8368 (p90) cc_final: 0.7812 (p90) REVERT: A 474 ASP cc_start: 0.8332 (t0) cc_final: 0.8045 (t70) REVERT: A 538 THR cc_start: 0.7572 (p) cc_final: 0.6419 (m) REVERT: A 544 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8314 (ttmm) REVERT: A 651 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7296 (tp40) REVERT: A 665 ASN cc_start: 0.8049 (t0) cc_final: 0.7522 (t0) REVERT: A 670 ASP cc_start: 0.7630 (t70) cc_final: 0.7348 (t0) REVERT: C 34 MET cc_start: 0.7672 (mmt) cc_final: 0.7307 (mmt) REVERT: C 71 SER cc_start: 0.8130 (m) cc_final: 0.7882 (p) REVERT: C 83 MET cc_start: 0.6295 (ptp) cc_final: 0.5998 (ptp) outliers start: 34 outliers final: 27 residues processed: 175 average time/residue: 0.1947 time to fit residues: 44.5163 Evaluate side-chains 184 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 63 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.154785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.138286 restraints weight = 9360.524| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 3.27 r_work: 0.3711 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5974 Z= 0.224 Angle : 0.670 20.711 8129 Z= 0.332 Chirality : 0.046 0.178 894 Planarity : 0.005 0.070 1051 Dihedral : 7.178 90.656 828 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 6.53 % Allowed : 23.64 % Favored : 69.83 % 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: -2.94 (0.29), residues: 724 helix: -3.61 (0.77), residues: 34 sheet: -0.48 (0.42), residues: 150 loop : -2.49 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 36 HIS 0.003 0.001 HIS A 214 PHE 0.025 0.002 PHE A 63 TYR 0.021 0.002 TYR A 502 ARG 0.005 0.000 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 136 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8150 (mt) REVERT: A 378 PHE cc_start: 0.6065 (t80) cc_final: 0.5248 (t80) REVERT: A 429 ASN cc_start: 0.7559 (m-40) cc_final: 0.7251 (m-40) REVERT: A 432 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 443 TRP cc_start: 0.8336 (p90) cc_final: 0.7777 (p90) REVERT: A 474 ASP cc_start: 0.8287 (t0) cc_final: 0.8046 (t70) REVERT: A 538 THR cc_start: 0.7526 (p) cc_final: 0.6122 (m) REVERT: A 544 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8273 (ttmm) REVERT: A 588 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.8047 (p) REVERT: A 651 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7290 (tp40) REVERT: A 665 ASN cc_start: 0.8093 (t0) cc_final: 0.7576 (t0) REVERT: A 670 ASP cc_start: 0.7667 (t70) cc_final: 0.7249 (t0) REVERT: C 69 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7342 (p) REVERT: C 83 MET cc_start: 0.6230 (ptp) cc_final: 0.5947 (ptp) outliers start: 42 outliers final: 24 residues processed: 175 average time/residue: 0.1795 time to fit residues: 40.8812 Evaluate side-chains 173 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.0070 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.156710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.139930 restraints weight = 9453.180| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.39 r_work: 0.3721 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5974 Z= 0.199 Angle : 0.671 20.853 8129 Z= 0.332 Chirality : 0.045 0.159 894 Planarity : 0.004 0.043 1051 Dihedral : 6.977 89.972 826 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.29 % Allowed : 24.42 % Favored : 70.30 % 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: -2.75 (0.29), residues: 724 helix: -3.14 (0.93), residues: 28 sheet: -0.38 (0.40), residues: 167 loop : -2.45 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 640 HIS 0.003 0.001 HIS A 214 PHE 0.030 0.002 PHE A 63 TYR 0.020 0.001 TYR A 502 ARG 0.007 0.001 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7564 (mpp80) cc_final: 0.7322 (mpt-90) REVERT: A 60 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 136 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8163 (mt) REVERT: A 241 ASN cc_start: 0.5634 (OUTLIER) cc_final: 0.5216 (p0) REVERT: A 378 PHE cc_start: 0.5944 (t80) cc_final: 0.5133 (t80) REVERT: A 429 ASN cc_start: 0.7623 (m-40) cc_final: 0.7304 (m-40) REVERT: A 432 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8446 (mp) REVERT: A 443 TRP cc_start: 0.8326 (p90) cc_final: 0.7790 (p90) REVERT: A 474 ASP cc_start: 0.8313 (t0) cc_final: 0.8057 (t70) REVERT: A 538 THR cc_start: 0.7521 (p) cc_final: 0.6385 (m) REVERT: A 544 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8280 (ttmm) REVERT: A 588 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8035 (p) REVERT: A 651 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7289 (tp40) REVERT: A 665 ASN cc_start: 0.8129 (t0) cc_final: 0.7623 (t0) REVERT: A 670 ASP cc_start: 0.7622 (t70) cc_final: 0.7154 (t0) REVERT: C 34 MET cc_start: 0.7699 (mmt) cc_final: 0.7219 (mmt) REVERT: C 69 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7265 (p) REVERT: C 81 LEU cc_start: 0.7728 (tp) cc_final: 0.7467 (tp) REVERT: C 83 MET cc_start: 0.6258 (ptp) cc_final: 0.5946 (ptp) outliers start: 34 outliers final: 24 residues processed: 171 average time/residue: 0.1984 time to fit residues: 43.7241 Evaluate side-chains 173 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.153016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137194 restraints weight = 9291.569| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.14 r_work: 0.3688 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5974 Z= 0.286 Angle : 0.721 22.699 8129 Z= 0.359 Chirality : 0.047 0.178 894 Planarity : 0.005 0.039 1051 Dihedral : 7.255 90.408 826 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 6.22 % Allowed : 24.57 % Favored : 69.21 % 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: -2.75 (0.29), residues: 724 helix: -3.10 (0.95), residues: 28 sheet: -0.42 (0.40), residues: 167 loop : -2.42 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 640 HIS 0.005 0.001 HIS A 74 PHE 0.033 0.002 PHE A 63 TYR 0.021 0.002 TYR A 502 ARG 0.008 0.001 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7402 (tm-30) REVERT: A 134 VAL cc_start: 0.6107 (OUTLIER) cc_final: 0.5811 (p) REVERT: A 136 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8139 (mt) REVERT: A 241 ASN cc_start: 0.5617 (OUTLIER) cc_final: 0.5170 (p0) REVERT: A 378 PHE cc_start: 0.6115 (t80) cc_final: 0.5866 (t80) REVERT: A 429 ASN cc_start: 0.7696 (m-40) cc_final: 0.7440 (m-40) REVERT: A 432 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 443 TRP cc_start: 0.8360 (p90) cc_final: 0.7853 (p90) REVERT: A 474 ASP cc_start: 0.8313 (t0) cc_final: 0.8023 (t70) REVERT: A 544 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8293 (ttmm) REVERT: A 651 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7062 (tp-100) REVERT: A 665 ASN cc_start: 0.8185 (t0) cc_final: 0.7641 (t0) REVERT: A 670 ASP cc_start: 0.7679 (t70) cc_final: 0.7182 (t70) REVERT: C 34 MET cc_start: 0.7803 (mmt) cc_final: 0.7222 (mmt) REVERT: C 69 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7474 (p) REVERT: C 81 LEU cc_start: 0.7927 (tp) cc_final: 0.7649 (tp) REVERT: C 83 MET cc_start: 0.6268 (ptp) cc_final: 0.5950 (ptp) outliers start: 40 outliers final: 28 residues processed: 176 average time/residue: 0.1918 time to fit residues: 43.5634 Evaluate side-chains 185 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.152035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133501 restraints weight = 9243.892| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.57 r_work: 0.3609 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5974 Z= 0.291 Angle : 0.723 21.944 8129 Z= 0.361 Chirality : 0.047 0.172 894 Planarity : 0.005 0.040 1051 Dihedral : 7.289 89.690 825 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 5.75 % Allowed : 26.28 % Favored : 67.96 % 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: -2.63 (0.29), residues: 724 helix: -2.51 (1.14), residues: 22 sheet: -0.20 (0.41), residues: 161 loop : -2.42 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 640 HIS 0.004 0.001 HIS A 74 PHE 0.040 0.002 PHE A 63 TYR 0.021 0.002 TYR A 502 ARG 0.008 0.001 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 134 VAL cc_start: 0.6130 (OUTLIER) cc_final: 0.5807 (p) REVERT: A 136 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 225 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7876 (mm-40) REVERT: A 241 ASN cc_start: 0.5654 (OUTLIER) cc_final: 0.5163 (p0) REVERT: A 335 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7746 (mmm160) REVERT: A 432 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 443 TRP cc_start: 0.8417 (p90) cc_final: 0.7852 (p90) REVERT: A 474 ASP cc_start: 0.8449 (t0) cc_final: 0.8022 (t0) REVERT: A 544 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8272 (ttmm) REVERT: A 588 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7931 (p) REVERT: A 651 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7317 (tp40) REVERT: A 665 ASN cc_start: 0.8303 (t0) cc_final: 0.7637 (t0) REVERT: A 670 ASP cc_start: 0.7685 (t70) cc_final: 0.7059 (t70) REVERT: C 69 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7424 (p) REVERT: C 81 LEU cc_start: 0.7894 (tp) cc_final: 0.7609 (tp) REVERT: C 83 MET cc_start: 0.6502 (ptp) cc_final: 0.6163 (ptp) outliers start: 37 outliers final: 24 residues processed: 175 average time/residue: 0.2031 time to fit residues: 44.7504 Evaluate side-chains 179 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.0270 chunk 64 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 361 ASN A 424 ASN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.153420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134983 restraints weight = 9417.924| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.57 r_work: 0.3644 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5974 Z= 0.248 Angle : 0.721 21.878 8129 Z= 0.359 Chirality : 0.046 0.157 894 Planarity : 0.005 0.040 1051 Dihedral : 7.245 89.469 825 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 4.82 % Allowed : 27.37 % Favored : 67.81 % 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: -2.57 (0.30), residues: 724 helix: -2.53 (1.12), residues: 22 sheet: -0.06 (0.42), residues: 160 loop : -2.40 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 640 HIS 0.003 0.001 HIS A 214 PHE 0.043 0.002 PHE A 63 TYR 0.027 0.002 TYR A 430 ARG 0.009 0.001 ARG A 473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 134 VAL cc_start: 0.6114 (OUTLIER) cc_final: 0.5789 (p) REVERT: A 225 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7853 (mm-40) REVERT: A 241 ASN cc_start: 0.5668 (OUTLIER) cc_final: 0.5180 (p0) REVERT: A 335 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7529 (tpt90) REVERT: A 429 ASN cc_start: 0.7537 (m-40) cc_final: 0.7272 (m110) REVERT: A 432 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 443 TRP cc_start: 0.8414 (p90) cc_final: 0.7861 (p90) REVERT: A 473 ARG cc_start: 0.8349 (mtm110) cc_final: 0.8101 (mtm110) REVERT: A 474 ASP cc_start: 0.8414 (t0) cc_final: 0.7928 (t70) REVERT: A 544 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8277 (ttmm) REVERT: A 588 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7932 (p) REVERT: A 651 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7098 (tp-100) REVERT: A 665 ASN cc_start: 0.8314 (t0) cc_final: 0.7666 (t0) REVERT: A 670 ASP cc_start: 0.7589 (t70) cc_final: 0.6943 (t70) REVERT: C 34 MET cc_start: 0.7802 (mmt) cc_final: 0.7190 (mmt) REVERT: C 69 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7410 (p) REVERT: C 81 LEU cc_start: 0.7823 (tp) cc_final: 0.7544 (tp) outliers start: 31 outliers final: 24 residues processed: 168 average time/residue: 0.2197 time to fit residues: 47.0075 Evaluate side-chains 178 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.0170 chunk 71 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.154996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136216 restraints weight = 9378.617| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.67 r_work: 0.3675 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5974 Z= 0.200 Angle : 0.716 20.790 8129 Z= 0.355 Chirality : 0.047 0.224 894 Planarity : 0.005 0.041 1051 Dihedral : 7.117 89.459 825 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.04 % Allowed : 28.46 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.29), residues: 724 helix: -3.07 (0.93), residues: 28 sheet: 0.14 (0.42), residues: 158 loop : -2.42 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 640 HIS 0.003 0.001 HIS A 214 PHE 0.043 0.002 PHE A 63 TYR 0.029 0.001 TYR A 430 ARG 0.008 0.001 ARG A 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2894.23 seconds wall clock time: 52 minutes 17.37 seconds (3137.37 seconds total)