Starting phenix.real_space_refine on Thu Jul 24 09:24:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i4f_35171/07_2025/8i4f_35171.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i4f_35171/07_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_35171/07_2025/8i4f_35171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i4f_35171/07_2025/8i4f_35171.map" model { file = "/net/cci-nas-00/data/ceres_data/8i4f_35171/07_2025/8i4f_35171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i4f_35171/07_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-5711/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: 4.64, per 1000 atoms: 0.80 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: 2.21 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 0.76 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: 2.89 Time building geometry restraints manager: 2.41 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: 42.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:4.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.710 ------------------------------------------------------------------------------- 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 5984 Z= 0.086 Angle : 0.451 5.640 8149 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 Details of bonding type rmsd hydrogen bonds : bond 0.18493 ( 125) hydrogen bonds : angle 6.95181 ( 333) SS BOND : bond 0.00152 ( 10) SS BOND : angle 0.65693 ( 20) covalent geometry : bond 0.00178 ( 5974) covalent geometry : angle 0.45040 ( 8129) *********************** 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 : 0.683 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: 0.2610 time to fit residues: 68.9160 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 : 0.905 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.141657 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 5984 Z= 0.162 Angle : 0.594 6.993 8149 Z= 0.311 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 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 125) hydrogen bonds : angle 5.26851 ( 333) SS BOND : bond 0.00299 ( 10) SS BOND : angle 1.03590 ( 20) covalent geometry : bond 0.00375 ( 5974) covalent geometry : angle 0.59220 ( 8129) *********************** 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 : 0.624 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: 0.8494 (mm) cc_final: 0.8237 (mt) REVERT: A 184 MET cc_start: 0.6363 (tmt) cc_final: 0.6117 (tmt) REVERT: A 212 SER cc_start: 0.7541 (t) cc_final: 0.7003 (m) REVERT: A 251 LEU cc_start: 0.7728 (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: 0.7544 (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: 0.8552 (mp) cc_final: 0.8058 (mp) REVERT: C 29 PHE cc_start: 0.7739 (m-10) cc_final: 0.7525 (m-10) REVERT: C 69 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7444 (p) outliers start: 37 outliers final: 20 residues processed: 195 average time/residue: 0.2067 time to fit residues: 51.5412 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 : 0.628 ------------------------------------------------------------------------------- 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: 0.6980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 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: 1.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3990 r_free = 0.3990 target = 0.150819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133892 restraints weight = 9462.155| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.44 r_work: 0.3626 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 5984 Z= 0.258 Angle : 0.716 13.976 8149 Z= 0.370 Chirality : 0.048 0.237 894 Planarity : 0.005 0.044 1051 Dihedral : 7.840 91.588 833 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.98 % Favored : 90.88 % Rotamer: Outliers : 6.69 % Allowed : 16.80 % 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: -3.52 (0.27), residues: 724 helix: -3.65 (0.74), residues: 28 sheet: -0.80 (0.41), residues: 160 loop : -3.02 (0.22), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 360 HIS 0.005 0.001 HIS A 214 PHE 0.034 0.003 PHE A 569 TYR 0.028 0.003 TYR A 430 ARG 0.005 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 125) hydrogen bonds : angle 5.62532 ( 333) SS BOND : bond 0.00532 ( 10) SS BOND : angle 2.20621 ( 20) covalent geometry : bond 0.00591 ( 5974) covalent geometry : angle 0.70896 ( 8129) *********************** 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 227 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7354 (mpp80) REVERT: A 60 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7682 (tm-30) REVERT: A 72 TRP cc_start: 0.8618 (t60) cc_final: 0.8341 (t60) REVERT: A 108 ILE cc_start: 0.7665 (mt) cc_final: 0.7448 (mt) REVERT: A 136 ILE cc_start: 0.8437 (mm) cc_final: 0.8126 (mt) REVERT: A 240 ILE cc_start: 0.6083 (OUTLIER) cc_final: 0.5804 (pt) REVERT: A 241 ASN cc_start: 0.5589 (OUTLIER) cc_final: 0.5040 (p0) REVERT: A 320 TYR cc_start: 0.7833 (m-80) cc_final: 0.7608 (m-10) REVERT: A 349 PHE cc_start: 0.8083 (m-80) cc_final: 0.7870 (m-80) REVERT: A 361 ASN cc_start: 0.8580 (p0) cc_final: 0.8365 (p0) REVERT: A 437 THR cc_start: 0.8083 (p) cc_final: 0.7881 (t) REVERT: A 443 TRP cc_start: 0.8416 (p90) cc_final: 0.7413 (p90) REVERT: A 444 ASN cc_start: 0.8449 (t0) cc_final: 0.7673 (t0) REVERT: A 446 ASN cc_start: 0.7379 (p0) cc_final: 0.7086 (p0) REVERT: A 477 THR cc_start: 0.8957 (p) cc_final: 0.8720 (t) REVERT: A 500 GLN cc_start: 0.5732 (tp40) cc_final: 0.5525 (tp40) REVERT: A 538 THR cc_start: 0.7815 (p) cc_final: 0.6715 (m) REVERT: A 544 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8366 (ttmm) REVERT: A 651 GLN cc_start: 0.7726 (tp-100) cc_final: 0.7133 (tp-100) REVERT: A 665 ASN cc_start: 0.8100 (t0) cc_final: 0.7535 (t0) REVERT: C 29 PHE cc_start: 0.7937 (m-10) cc_final: 0.7722 (m-10) REVERT: C 69 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7576 (p) REVERT: C 71 SER cc_start: 0.8330 (m) cc_final: 0.7968 (p) REVERT: C 81 LEU cc_start: 0.8021 (tp) cc_final: 0.7673 (tp) outliers start: 43 outliers final: 32 residues processed: 209 average time/residue: 0.1814 time to fit residues: 48.8045 Evaluate side-chains 202 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 475 ILE 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 572 PHE 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 21 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 LYS 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: 0.7980 chunk 46 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 65 optimal weight: 0.0370 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 ASN A 549 ASN A 682 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.155341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138266 restraints weight = 9690.455| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.58 r_work: 0.3700 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5984 Z= 0.119 Angle : 0.646 17.583 8149 Z= 0.321 Chirality : 0.046 0.246 894 Planarity : 0.004 0.043 1051 Dihedral : 7.276 89.380 832 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.13 % Allowed : 21.62 % Favored : 73.25 % 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: -3.27 (0.28), residues: 724 helix: -3.17 (0.87), residues: 28 sheet: -0.84 (0.38), residues: 191 loop : -2.87 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 36 HIS 0.004 0.001 HIS A 214 PHE 0.019 0.001 PHE A 282 TYR 0.024 0.001 TYR A 502 ARG 0.006 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.02977 ( 125) hydrogen bonds : angle 5.30223 ( 333) SS BOND : bond 0.00478 ( 10) SS BOND : angle 2.10781 ( 20) covalent geometry : bond 0.00286 ( 5974) covalent geometry : angle 0.63790 ( 8129) *********************** 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 200 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 72 TRP cc_start: 0.8534 (t60) cc_final: 0.8242 (t60) REVERT: A 108 ILE cc_start: 0.7674 (mt) cc_final: 0.7440 (mt) REVERT: A 136 ILE cc_start: 0.8493 (mm) cc_final: 0.8185 (mt) REVERT: A 331 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7330 (tt0) REVERT: A 378 PHE cc_start: 0.6296 (t80) cc_final: 0.5881 (t80) REVERT: A 432 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8499 (mp) REVERT: A 474 ASP cc_start: 0.8341 (t0) cc_final: 0.7992 (t70) REVERT: A 538 THR cc_start: 0.7483 (p) cc_final: 0.6056 (m) REVERT: A 544 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8263 (ttmm) REVERT: A 651 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7299 (tp-100) REVERT: A 665 ASN cc_start: 0.8006 (t0) cc_final: 0.7441 (t0) REVERT: C 29 PHE cc_start: 0.7939 (m-10) cc_final: 0.7732 (m-10) REVERT: C 69 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7416 (p) REVERT: C 71 SER cc_start: 0.8158 (m) cc_final: 0.7831 (p) REVERT: C 83 MET cc_start: 0.6159 (ptp) cc_final: 0.5828 (ptp) REVERT: C 105 TYR cc_start: 0.8726 (m-80) cc_final: 0.8417 (m-80) outliers start: 33 outliers final: 25 residues processed: 185 average time/residue: 0.1766 time to fit residues: 42.5744 Evaluate side-chains 187 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 34 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.154011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136886 restraints weight = 9285.918| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 3.40 r_work: 0.3690 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5984 Z= 0.172 Angle : 0.717 19.943 8149 Z= 0.359 Chirality : 0.047 0.245 894 Planarity : 0.005 0.099 1051 Dihedral : 7.346 91.054 830 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 6.07 % Allowed : 22.40 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.29), residues: 724 helix: -3.75 (0.72), residues: 34 sheet: -0.59 (0.41), residues: 161 loop : -2.64 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 360 HIS 0.003 0.001 HIS A 214 PHE 0.018 0.002 PHE A 63 TYR 0.022 0.002 TYR A 502 ARG 0.007 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 125) hydrogen bonds : angle 5.48148 ( 333) SS BOND : bond 0.00701 ( 10) SS BOND : angle 2.80104 ( 20) covalent geometry : bond 0.00406 ( 5974) covalent geometry : angle 0.70430 ( 8129) *********************** 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 199 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 136 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8119 (mt) REVERT: A 345 PHE cc_start: 0.7978 (m-80) cc_final: 0.7486 (m-80) REVERT: A 378 PHE cc_start: 0.6410 (t80) cc_final: 0.6141 (t80) REVERT: A 429 ASN cc_start: 0.7603 (m-40) cc_final: 0.7297 (m110) REVERT: A 443 TRP cc_start: 0.8430 (p90) cc_final: 0.7769 (p90) REVERT: A 474 ASP cc_start: 0.8293 (t0) cc_final: 0.7933 (t70) REVERT: A 538 THR cc_start: 0.7587 (p) cc_final: 0.6352 (m) REVERT: A 544 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8282 (ttmm) REVERT: A 651 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7382 (tp-100) REVERT: A 665 ASN cc_start: 0.8117 (t0) cc_final: 0.7562 (t0) REVERT: A 670 ASP cc_start: 0.7705 (t70) cc_final: 0.7394 (t0) REVERT: C 36 TRP cc_start: 0.7940 (m100) cc_final: 0.7719 (m100) REVERT: C 81 LEU cc_start: 0.7717 (tp) cc_final: 0.7442 (tp) REVERT: C 83 MET cc_start: 0.6192 (ptp) cc_final: 0.5965 (ptp) outliers start: 39 outliers final: 28 residues processed: 183 average time/residue: 0.1697 time to fit residues: 40.8684 Evaluate side-chains 187 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 136 ILE 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 447 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 496 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 572 PHE 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 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: 0.5980 chunk 66 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.137201 restraints weight = 9375.403| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.37 r_work: 0.3686 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5984 Z= 0.155 Angle : 0.686 20.697 8149 Z= 0.340 Chirality : 0.046 0.182 894 Planarity : 0.005 0.066 1051 Dihedral : 7.138 90.710 827 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 6.22 % Allowed : 23.02 % Favored : 70.76 % 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: -2.89 (0.29), residues: 724 helix: -3.28 (0.93), residues: 28 sheet: -0.38 (0.42), residues: 157 loop : -2.55 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 360 HIS 0.003 0.001 HIS A 214 PHE 0.025 0.002 PHE A 63 TYR 0.022 0.002 TYR A 502 ARG 0.005 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 125) hydrogen bonds : angle 5.49381 ( 333) SS BOND : bond 0.00590 ( 10) SS BOND : angle 2.44619 ( 20) covalent geometry : bond 0.00375 ( 5974) covalent geometry : angle 0.67571 ( 8129) *********************** 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 198 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 136 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8165 (mt) REVERT: A 241 ASN cc_start: 0.5691 (OUTLIER) cc_final: 0.5257 (p0) REVERT: A 345 PHE cc_start: 0.7860 (m-80) cc_final: 0.7382 (m-80) REVERT: A 354 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.8152 (t80) REVERT: A 369 VAL cc_start: 0.8394 (t) cc_final: 0.8098 (p) REVERT: A 421 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7250 (mt0) REVERT: A 429 ASN cc_start: 0.7567 (m-40) cc_final: 0.7253 (m110) REVERT: A 443 TRP cc_start: 0.8429 (p90) cc_final: 0.7702 (p90) REVERT: A 474 ASP cc_start: 0.8283 (t0) cc_final: 0.8005 (t70) REVERT: A 538 THR cc_start: 0.7558 (p) cc_final: 0.6265 (m) REVERT: A 544 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8257 (ttmm) REVERT: A 651 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7375 (tp-100) REVERT: A 665 ASN cc_start: 0.8125 (t0) cc_final: 0.7577 (t0) REVERT: A 670 ASP cc_start: 0.7741 (t70) cc_final: 0.7312 (t0) REVERT: C 36 TRP cc_start: 0.7903 (m100) cc_final: 0.7486 (m100) REVERT: C 69 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7413 (p) REVERT: C 81 LEU cc_start: 0.7791 (tp) cc_final: 0.7492 (tp) REVERT: C 83 MET cc_start: 0.6251 (ptp) cc_final: 0.5969 (ptp) outliers start: 40 outliers final: 30 residues processed: 180 average time/residue: 0.1771 time to fit residues: 41.8528 Evaluate side-chains 186 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 204 ILE 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 352 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 406 SER 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 496 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 572 PHE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 590 GLU 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 76 LYS 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: 0.6980 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 37 optimal weight: 0.3980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 A 682 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.154874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.138120 restraints weight = 9431.763| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.38 r_work: 0.3698 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5984 Z= 0.140 Angle : 0.691 21.451 8149 Z= 0.342 Chirality : 0.046 0.154 894 Planarity : 0.005 0.043 1051 Dihedral : 7.120 90.117 827 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 6.22 % Allowed : 24.42 % Favored : 69.36 % 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: -2.72 (0.30), residues: 724 helix: -3.11 (0.94), residues: 28 sheet: -0.22 (0.41), residues: 173 loop : -2.50 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 360 HIS 0.003 0.001 HIS A 214 PHE 0.030 0.002 PHE A 63 TYR 0.021 0.001 TYR A 502 ARG 0.007 0.000 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.02977 ( 125) hydrogen bonds : angle 5.43564 ( 333) SS BOND : bond 0.00572 ( 10) SS BOND : angle 2.66865 ( 20) covalent geometry : bond 0.00337 ( 5974) covalent geometry : angle 0.67901 ( 8129) *********************** 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 191 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 136 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8151 (mt) REVERT: A 241 ASN cc_start: 0.5661 (OUTLIER) cc_final: 0.5225 (p0) REVERT: A 345 PHE cc_start: 0.7909 (m-80) cc_final: 0.7432 (m-80) REVERT: A 354 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.8097 (t80) REVERT: A 421 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7288 (mt0) REVERT: A 429 ASN cc_start: 0.7632 (m-40) cc_final: 0.7328 (m110) REVERT: A 443 TRP cc_start: 0.8421 (p90) cc_final: 0.7703 (p90) REVERT: A 474 ASP cc_start: 0.8324 (t0) cc_final: 0.8044 (t70) REVERT: A 538 THR cc_start: 0.7557 (p) cc_final: 0.6230 (m) REVERT: A 544 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8230 (ttmm) REVERT: A 588 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.8033 (p) REVERT: A 651 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7361 (tp-100) REVERT: A 665 ASN cc_start: 0.8157 (t0) cc_final: 0.7631 (t0) REVERT: A 670 ASP cc_start: 0.7724 (t70) cc_final: 0.7219 (t70) REVERT: C 36 TRP cc_start: 0.7876 (m100) cc_final: 0.7492 (m100) REVERT: C 69 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7414 (p) REVERT: C 81 LEU cc_start: 0.7826 (tp) cc_final: 0.7547 (tp) REVERT: C 83 MET cc_start: 0.6297 (ptp) cc_final: 0.6000 (ptp) outliers start: 40 outliers final: 27 residues processed: 173 average time/residue: 0.1756 time to fit residues: 39.5594 Evaluate side-chains 180 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 204 ILE 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 349 PHE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 387 TYR 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 496 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 572 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.0020 chunk 20 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 424 ASN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.154234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138379 restraints weight = 9277.676| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.17 r_work: 0.3706 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5984 Z= 0.150 Angle : 0.707 21.637 8149 Z= 0.352 Chirality : 0.046 0.166 894 Planarity : 0.005 0.042 1051 Dihedral : 7.040 89.885 825 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 6.38 % Allowed : 25.82 % 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: -2.69 (0.30), residues: 724 helix: -3.06 (0.94), residues: 28 sheet: -0.22 (0.41), residues: 173 loop : -2.47 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 640 HIS 0.008 0.001 HIS A 74 PHE 0.023 0.002 PHE A 63 TYR 0.021 0.002 TYR A 502 ARG 0.007 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 125) hydrogen bonds : angle 5.44558 ( 333) SS BOND : bond 0.00611 ( 10) SS BOND : angle 2.54329 ( 20) covalent geometry : bond 0.00359 ( 5974) covalent geometry : angle 0.69685 ( 8129) *********************** 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 196 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7426 (tm-30) REVERT: A 136 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7846 (tt) REVERT: A 241 ASN cc_start: 0.5630 (OUTLIER) cc_final: 0.5191 (p0) REVERT: A 421 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7302 (mt0) REVERT: A 429 ASN cc_start: 0.7628 (m-40) cc_final: 0.7205 (m110) REVERT: A 443 TRP cc_start: 0.8438 (p90) cc_final: 0.7696 (p90) REVERT: A 474 ASP cc_start: 0.8280 (t0) cc_final: 0.8030 (t70) REVERT: A 538 THR cc_start: 0.7612 (p) cc_final: 0.6585 (m) REVERT: A 544 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8245 (ttmm) REVERT: A 588 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8061 (p) REVERT: A 651 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7360 (tp-100) REVERT: A 665 ASN cc_start: 0.8139 (t0) cc_final: 0.7631 (t0) REVERT: A 670 ASP cc_start: 0.7653 (t70) cc_final: 0.7162 (t70) REVERT: C 36 TRP cc_start: 0.7852 (m100) cc_final: 0.7494 (m100) REVERT: C 69 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7383 (p) REVERT: C 81 LEU cc_start: 0.7871 (tp) cc_final: 0.7588 (tp) REVERT: C 83 MET cc_start: 0.6198 (ptp) cc_final: 0.5912 (ptp) outliers start: 41 outliers final: 32 residues processed: 176 average time/residue: 0.1782 time to fit residues: 40.9799 Evaluate side-chains 185 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 175 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 204 ILE 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 361 ASN Chi-restraints excluded: chain A residue 387 TYR 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 496 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 572 PHE 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 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 71 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 0.0020 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 614 GLN A 664 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 = 0.4033 r_free = 0.4033 target = 0.154460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137298 restraints weight = 9446.616| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.40 r_work: 0.3683 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5984 Z= 0.147 Angle : 0.702 20.987 8149 Z= 0.348 Chirality : 0.046 0.151 894 Planarity : 0.004 0.042 1051 Dihedral : 7.038 89.590 825 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 6.22 % Allowed : 26.44 % Favored : 67.34 % 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: -2.65 (0.30), residues: 724 helix: -3.04 (0.95), residues: 28 sheet: -0.03 (0.41), residues: 166 loop : -2.48 (0.25), residues: 530 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 0.022 0.002 PHE A 63 TYR 0.021 0.001 TYR A 502 ARG 0.008 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 125) hydrogen bonds : angle 5.52876 ( 333) SS BOND : bond 0.00571 ( 10) SS BOND : angle 2.33477 ( 20) covalent geometry : bond 0.00350 ( 5974) covalent geometry : angle 0.69281 ( 8129) *********************** 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 195 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 136 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7748 (tt) REVERT: A 241 ASN cc_start: 0.5631 (OUTLIER) cc_final: 0.5163 (p0) REVERT: A 378 PHE cc_start: 0.6195 (t80) cc_final: 0.5372 (t80) REVERT: A 421 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7357 (mt0) REVERT: A 429 ASN cc_start: 0.7668 (m-40) cc_final: 0.7224 (m110) REVERT: A 443 TRP cc_start: 0.8494 (p90) cc_final: 0.7727 (p90) REVERT: A 474 ASP cc_start: 0.8344 (t0) cc_final: 0.7980 (t70) REVERT: A 531 VAL cc_start: 0.8026 (m) cc_final: 0.7809 (p) REVERT: A 538 THR cc_start: 0.7694 (p) cc_final: 0.6761 (m) REVERT: A 544 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8229 (ttmm) REVERT: A 588 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7986 (p) REVERT: A 651 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7307 (tp-100) REVERT: A 665 ASN cc_start: 0.8222 (t0) cc_final: 0.7636 (t0) REVERT: A 670 ASP cc_start: 0.7637 (t70) cc_final: 0.7055 (t70) REVERT: C 36 TRP cc_start: 0.7861 (m100) cc_final: 0.7472 (m100) REVERT: C 69 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7366 (p) REVERT: C 81 LEU cc_start: 0.7865 (tp) cc_final: 0.7576 (tp) REVERT: C 83 MET cc_start: 0.6381 (ptp) cc_final: 0.6075 (ptp) outliers start: 40 outliers final: 32 residues processed: 175 average time/residue: 0.1749 time to fit residues: 39.9928 Evaluate side-chains 188 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 175 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 204 ILE 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 361 ASN Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 409 ILE 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 496 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 572 PHE 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 71 SER 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: 1.9990 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4006 r_free = 0.4006 target = 0.151987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134596 restraints weight = 9352.173| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.46 r_work: 0.3644 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5984 Z= 0.198 Angle : 0.737 22.132 8149 Z= 0.366 Chirality : 0.047 0.170 894 Planarity : 0.005 0.048 1051 Dihedral : 7.231 89.634 825 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 5.91 % Allowed : 27.06 % Favored : 67.03 % 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: -2.66 (0.30), residues: 724 helix: -3.07 (0.95), residues: 28 sheet: -0.18 (0.42), residues: 160 loop : -2.41 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 640 HIS 0.003 0.001 HIS A 214 PHE 0.022 0.002 PHE A 63 TYR 0.021 0.002 TYR A 502 ARG 0.008 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 125) hydrogen bonds : angle 5.68099 ( 333) SS BOND : bond 0.00606 ( 10) SS BOND : angle 2.50139 ( 20) covalent geometry : bond 0.00461 ( 5974) covalent geometry : angle 0.72694 ( 8129) ********************** 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 198 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 136 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7788 (tt) REVERT: A 225 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7851 (mm110) REVERT: A 241 ASN cc_start: 0.5677 (OUTLIER) cc_final: 0.5205 (p0) REVERT: A 421 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7369 (mt0) REVERT: A 429 ASN cc_start: 0.7804 (m-40) cc_final: 0.7552 (m-40) REVERT: A 443 TRP cc_start: 0.8462 (p90) cc_final: 0.7868 (p90) REVERT: A 473 ARG cc_start: 0.8370 (mtp-110) cc_final: 0.8103 (mtm110) REVERT: A 474 ASP cc_start: 0.8372 (t0) cc_final: 0.8006 (t70) REVERT: A 544 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8291 (ttmm) REVERT: A 588 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8050 (p) REVERT: A 665 ASN cc_start: 0.8247 (t0) cc_final: 0.7644 (t0) REVERT: A 670 ASP cc_start: 0.7686 (t70) cc_final: 0.7090 (t70) REVERT: C 36 TRP cc_start: 0.7882 (m100) cc_final: 0.7588 (m100) REVERT: C 69 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7521 (p) REVERT: C 81 LEU cc_start: 0.7929 (tp) cc_final: 0.7636 (tp) REVERT: C 83 MET cc_start: 0.6422 (ptp) cc_final: 0.6137 (ptp) outliers start: 38 outliers final: 32 residues processed: 178 average time/residue: 0.2196 time to fit residues: 50.7562 Evaluate side-chains 192 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 175 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 204 ILE 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 349 PHE Chi-restraints excluded: chain A residue 387 TYR 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 496 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 572 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 GLU 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 71 SER 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: 0.9980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 328 GLN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137637 restraints weight = 9490.073| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 3.51 r_work: 0.3689 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5984 Z= 0.133 Angle : 0.696 20.308 8149 Z= 0.345 Chirality : 0.046 0.151 894 Planarity : 0.004 0.041 1051 Dihedral : 7.069 89.154 825 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.60 % Allowed : 27.68 % Favored : 66.72 % 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: -2.54 (0.30), residues: 724 helix: -3.11 (0.92), residues: 28 sheet: -0.03 (0.41), residues: 166 loop : -2.36 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 640 HIS 0.003 0.001 HIS A 214 PHE 0.028 0.002 PHE A 63 TYR 0.020 0.001 TYR A 502 ARG 0.008 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 125) hydrogen bonds : angle 5.52295 ( 333) SS BOND : bond 0.00512 ( 10) SS BOND : angle 2.04059 ( 20) covalent geometry : bond 0.00318 ( 5974) covalent geometry : angle 0.68938 ( 8129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3266.06 seconds wall clock time: 57 minutes 55.50 seconds (3475.50 seconds total)