Starting phenix.real_space_refine on Sat May 10 09:24:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i4f_35171/05_2025/8i4f_35171.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i4f_35171/05_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_35171/05_2025/8i4f_35171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i4f_35171/05_2025/8i4f_35171.map" model { file = "/net/cci-nas-00/data/ceres_data/8i4f_35171/05_2025/8i4f_35171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i4f_35171/05_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-5687/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: 4.05, per 1000 atoms: 0.70 Number of scatterers: 5824 At special positions: 0 Unit cell: (71.764, 86.676, 128.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1102 8.00 N 964 7.00 C 3733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 545 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 624 " - pdb=" SG CYS A 656 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 678 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 957.6 milliseconds 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1374 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 13 sheets defined 2.7% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 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: 2.95 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1856 1.34 - 1.46: 1532 1.46 - 1.58: 2557 1.58 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5974 Sorted by residual: bond pdb=" CB PRO A 147 " pdb=" CG PRO A 147 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.08e-01 bond pdb=" C ALA A 379 " pdb=" N PRO A 380 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 6.19e-01 bond pdb=" C VAL A 627 " pdb=" N PRO A 628 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 4.27e-01 bond pdb=" C ASP A 301 " pdb=" N PRO A 302 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.05e-01 bond pdb=" C PHE A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.02e-01 ... (remaining 5969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 7889 1.13 - 2.26: 187 2.26 - 3.38: 47 3.38 - 4.51: 3 4.51 - 5.64: 3 Bond angle restraints: 8129 Sorted by residual: angle pdb=" CA TYR A 502 " pdb=" CB TYR A 502 " pdb=" CG TYR A 502 " ideal model delta sigma weight residual 113.90 117.01 -3.11 1.80e+00 3.09e-01 2.99e+00 angle pdb=" C GLY A 573 " pdb=" N ARG A 574 " pdb=" CA ARG A 574 " ideal model delta sigma weight residual 121.54 124.84 -3.30 1.91e+00 2.74e-01 2.98e+00 angle pdb=" C ALA A 379 " pdb=" N PRO A 380 " pdb=" CA PRO A 380 " ideal model delta sigma weight residual 119.84 121.96 -2.12 1.25e+00 6.40e-01 2.88e+00 angle pdb=" N PRO A 380 " pdb=" CA PRO A 380 " pdb=" C PRO A 380 " ideal model delta sigma weight residual 112.47 115.73 -3.26 2.06e+00 2.36e-01 2.50e+00 angle pdb=" C SER A 647 " pdb=" N ASN A 648 " pdb=" CA ASN A 648 " ideal model delta sigma weight residual 122.82 125.03 -2.21 1.42e+00 4.96e-01 2.43e+00 ... (remaining 8124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3330 17.65 - 35.30: 160 35.30 - 52.95: 19 52.95 - 70.61: 5 70.61 - 88.26: 2 Dihedral angle restraints: 3516 sinusoidal: 1367 harmonic: 2149 Sorted by residual: dihedral pdb=" CB GLU A 668 " pdb=" CG GLU A 668 " pdb=" CD GLU A 668 " pdb=" OE1 GLU A 668 " ideal model delta sinusoidal sigma weight residual 0.00 -88.26 88.26 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" SG CYS A 139 " pdb=" CB CYS A 173 " pdb=" SG CYS A 173 " pdb=" CA CYS A 173 " ideal model delta sinusoidal sigma weight residual 79.00 26.43 52.57 1 2.00e+01 2.50e-03 9.41e+00 dihedral pdb=" N PHE A 282 " pdb=" CA PHE A 282 " pdb=" CB PHE A 282 " pdb=" CG PHE A 282 " ideal model delta sinusoidal sigma weight residual -60.00 -115.68 55.68 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 3513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 498 0.026 - 0.052: 238 0.052 - 0.078: 81 0.078 - 0.104: 54 0.104 - 0.130: 23 Chirality restraints: 894 Sorted by residual: chirality pdb=" CB ILE A 417 " pdb=" CA ILE A 417 " pdb=" CG1 ILE A 417 " pdb=" CG2 ILE A 417 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE A 127 " pdb=" N ILE A 127 " pdb=" C ILE A 127 " pdb=" CB ILE A 127 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 891 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 451 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 452 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 343 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 344 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 93 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.015 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 869 2.77 - 3.30: 5359 3.30 - 3.83: 9549 3.83 - 4.37: 10883 4.37 - 4.90: 18833 Nonbonded interactions: 45493 Sorted by model distance: nonbonded pdb=" OH TYR A 45 " pdb=" O LEU A 62 " model vdw 2.232 3.040 nonbonded pdb=" O GLU A 668 " pdb=" OH TYR A 702 " model vdw 2.284 3.040 nonbonded pdb=" O VAL A 138 " pdb=" OG1 THR A 174 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR A 116 " pdb=" O ASN A 241 " model vdw 2.315 3.040 nonbonded pdb=" OG1 THR A 400 " pdb=" O GLU A 523 " model vdw 2.323 3.040 ... (remaining 45488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.400 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- 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 : 0.618 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: 0.1999 time to fit residues: 52.6436 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 : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 0.0070 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 218 ASN A 416 GLN A 421 GLN A 429 ASN A 481 GLN A 570 GLN A 614 GLN A 651 GLN A 664 ASN A 682 GLN C 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.159054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.141653 restraints weight = 9502.588| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.54 r_work: 0.3742 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 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 : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7295 (p) REVERT: A 42 ARG cc_start: 0.7522 (mtt-85) cc_final: 0.7119 (mtt-85) REVERT: A 60 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 136 ILE cc_start: 0.8495 (mm) cc_final: 0.8237 (mt) REVERT: A 184 MET cc_start: 0.6364 (tmt) cc_final: 0.6118 (tmt) REVERT: A 212 SER cc_start: 0.7541 (t) cc_final: 0.7003 (m) REVERT: A 251 LEU cc_start: 0.7727 (tp) cc_final: 0.7516 (tp) REVERT: A 357 VAL cc_start: 0.7928 (t) cc_final: 0.7550 (t) REVERT: A 443 TRP cc_start: 0.8321 (p90) cc_final: 0.7545 (p90) REVERT: A 477 THR cc_start: 0.8793 (p) cc_final: 0.8535 (t) REVERT: A 544 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8259 (ttmm) REVERT: A 665 ASN cc_start: 0.7953 (t0) cc_final: 0.7484 (t0) REVERT: A 706 LEU cc_start: 0.8551 (mp) cc_final: 0.8057 (mp) REVERT: C 29 PHE cc_start: 0.7739 (m-10) cc_final: 0.7525 (m-10) REVERT: C 69 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7444 (p) outliers start: 37 outliers final: 20 residues processed: 195 average time/residue: 0.1911 time to fit residues: 47.7179 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 : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.150147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133217 restraints weight = 9489.825| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.45 r_work: 0.3629 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 5984 Z= 0.256 Angle : 0.706 13.896 8149 Z= 0.365 Chirality : 0.048 0.246 894 Planarity : 0.005 0.045 1051 Dihedral : 7.760 91.340 833 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.98 % Favored : 90.88 % Rotamer: Outliers : 6.38 % Allowed : 17.57 % Favored : 76.05 % 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: -3.54 (0.27), residues: 724 helix: -3.69 (0.74), residues: 28 sheet: -0.82 (0.41), residues: 160 loop : -3.03 (0.22), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 360 HIS 0.005 0.001 HIS A 214 PHE 0.034 0.003 PHE A 569 TYR 0.027 0.003 TYR A 430 ARG 0.006 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 125) hydrogen bonds : angle 5.55675 ( 333) SS BOND : bond 0.00710 ( 10) SS BOND : angle 2.17182 ( 20) covalent geometry : bond 0.00587 ( 5974) covalent geometry : angle 0.69888 ( 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 225 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.642 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: 0.7571 (mtm-85) cc_final: 0.7327 (mpp80) REVERT: A 60 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 72 TRP cc_start: 0.8620 (t60) cc_final: 0.8350 (t60) REVERT: A 108 ILE cc_start: 0.7672 (mt) cc_final: 0.7456 (mt) REVERT: A 136 ILE cc_start: 0.8442 (mm) cc_final: 0.8137 (mt) REVERT: A 240 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5955 (pt) REVERT: A 320 TYR cc_start: 0.7825 (m-80) cc_final: 0.7608 (m-10) REVERT: A 349 PHE cc_start: 0.8065 (m-80) cc_final: 0.7842 (m-80) REVERT: A 361 ASN cc_start: 0.8565 (p0) cc_final: 0.8358 (p0) REVERT: A 443 TRP cc_start: 0.8409 (p90) cc_final: 0.7430 (p90) REVERT: A 444 ASN cc_start: 0.8444 (t0) cc_final: 0.7627 (t0) REVERT: A 446 ASN cc_start: 0.7358 (p0) cc_final: 0.7070 (p0) REVERT: A 477 THR cc_start: 0.8961 (p) cc_final: 0.8721 (t) REVERT: A 500 GLN cc_start: 0.5711 (tp40) cc_final: 0.5490 (tp40) REVERT: A 538 THR cc_start: 0.7757 (p) cc_final: 0.6687 (m) REVERT: A 544 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8371 (ttmm) REVERT: A 651 GLN cc_start: 0.7743 (tp-100) cc_final: 0.7183 (tp-100) REVERT: A 665 ASN cc_start: 0.8039 (t0) cc_final: 0.7446 (t0) REVERT: C 29 PHE cc_start: 0.7934 (m-10) cc_final: 0.7716 (m-10) REVERT: C 69 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7580 (p) REVERT: C 71 SER cc_start: 0.8280 (m) cc_final: 0.7921 (p) REVERT: C 81 LEU cc_start: 0.8000 (tp) cc_final: 0.7650 (tp) outliers start: 41 outliers final: 31 residues processed: 207 average time/residue: 0.1818 time to fit residues: 48.4023 Evaluate side-chains 201 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 240 ILE 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: 9.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 65 optimal weight: 0.0670 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 547 ASN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.154363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137234 restraints weight = 9692.398| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 3.59 r_work: 0.3686 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5984 Z= 0.128 Angle : 0.649 17.522 8149 Z= 0.322 Chirality : 0.046 0.256 894 Planarity : 0.004 0.044 1051 Dihedral : 7.284 89.490 832 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.98 % Allowed : 22.24 % Favored : 72.78 % 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: -3.29 (0.28), residues: 724 helix: -3.15 (0.88), residues: 28 sheet: -0.92 (0.39), residues: 175 loop : -2.81 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 36 HIS 0.004 0.001 HIS A 214 PHE 0.019 0.001 PHE A 282 TYR 0.024 0.002 TYR A 502 ARG 0.006 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 125) hydrogen bonds : angle 5.31764 ( 333) SS BOND : bond 0.00836 ( 10) SS BOND : angle 2.24541 ( 20) covalent geometry : bond 0.00310 ( 5974) covalent geometry : angle 0.63987 ( 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 197 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 72 TRP cc_start: 0.8538 (t60) cc_final: 0.8240 (t60) REVERT: A 108 ILE cc_start: 0.7712 (mt) cc_final: 0.7480 (mt) REVERT: A 136 ILE cc_start: 0.8452 (mm) cc_final: 0.8140 (mt) REVERT: A 241 ASN cc_start: 0.5585 (OUTLIER) cc_final: 0.5182 (p0) REVERT: A 331 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7327 (tt0) REVERT: A 345 PHE cc_start: 0.7888 (m-80) cc_final: 0.7673 (m-80) REVERT: A 378 PHE cc_start: 0.6303 (t80) cc_final: 0.5873 (t80) REVERT: A 432 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8509 (mp) REVERT: A 474 ASP cc_start: 0.8376 (t0) cc_final: 0.8011 (t70) REVERT: A 538 THR cc_start: 0.7541 (p) cc_final: 0.6185 (m) REVERT: A 544 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8258 (ttmm) REVERT: A 651 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7290 (tp-100) REVERT: A 665 ASN cc_start: 0.8010 (t0) cc_final: 0.7448 (t0) REVERT: C 29 PHE cc_start: 0.7915 (m-10) cc_final: 0.7700 (m-10) REVERT: C 69 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7430 (p) REVERT: C 71 SER cc_start: 0.8171 (m) cc_final: 0.7850 (p) REVERT: C 83 MET cc_start: 0.6199 (ptp) cc_final: 0.5869 (ptp) outliers start: 32 outliers final: 24 residues processed: 183 average time/residue: 0.1818 time to fit residues: 43.1941 Evaluate side-chains 186 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 241 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 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 572 PHE 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 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 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: 0.0060 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.154202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.137291 restraints weight = 9281.463| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.36 r_work: 0.3688 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4358 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= 0.170 Angle : 0.721 19.681 8149 Z= 0.360 Chirality : 0.047 0.244 894 Planarity : 0.004 0.044 1051 Dihedral : 7.329 90.863 830 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 5.91 % Allowed : 22.71 % Favored : 71.38 % 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: -3.13 (0.29), residues: 724 helix: -3.73 (0.73), residues: 34 sheet: -0.65 (0.40), residues: 161 loop : -2.65 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 640 HIS 0.003 0.001 HIS A 214 PHE 0.019 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 0.03371 ( 125) hydrogen bonds : angle 5.42359 ( 333) SS BOND : bond 0.01126 ( 10) SS BOND : angle 3.19835 ( 20) covalent geometry : bond 0.00399 ( 5974) covalent geometry : angle 0.70384 ( 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: 38 poor density : 161 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 136 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8117 (mt) REVERT: A 241 ASN cc_start: 0.5565 (OUTLIER) cc_final: 0.5157 (p0) REVERT: A 349 PHE cc_start: 0.8232 (m-80) cc_final: 0.7943 (m-80) REVERT: A 378 PHE cc_start: 0.6391 (t80) cc_final: 0.6112 (t80) REVERT: A 429 ASN cc_start: 0.7600 (m-40) cc_final: 0.7296 (m110) REVERT: A 443 TRP cc_start: 0.8446 (p90) cc_final: 0.7753 (p90) REVERT: A 474 ASP cc_start: 0.8299 (t0) cc_final: 0.8014 (t70) REVERT: A 538 THR cc_start: 0.7589 (p) cc_final: 0.6330 (m) REVERT: A 544 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8265 (ttmm) REVERT: A 651 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7359 (tp-100) REVERT: A 665 ASN cc_start: 0.8095 (t0) cc_final: 0.7575 (t0) REVERT: A 670 ASP cc_start: 0.7715 (t70) cc_final: 0.7367 (t0) REVERT: C 81 LEU cc_start: 0.7714 (tp) cc_final: 0.7456 (tp) REVERT: C 83 MET cc_start: 0.6159 (ptp) cc_final: 0.5936 (ptp) outliers start: 38 outliers final: 29 residues processed: 182 average time/residue: 0.1738 time to fit residues: 41.3960 Evaluate side-chains 185 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 241 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 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 576 ILE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 66 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.0170 chunk 9 optimal weight: 0.0030 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 overall best weight: 0.1686 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.158369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.141492 restraints weight = 9297.941| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.41 r_work: 0.3746 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5984 Z= 0.111 Angle : 0.653 19.499 8149 Z= 0.322 Chirality : 0.045 0.158 894 Planarity : 0.004 0.045 1051 Dihedral : 6.980 90.819 828 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 6.07 % Allowed : 23.17 % 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: -2.88 (0.29), residues: 724 helix: -3.57 (0.76), residues: 34 sheet: -0.31 (0.40), residues: 173 loop : -2.58 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 36 HIS 0.003 0.001 HIS A 214 PHE 0.022 0.001 PHE A 63 TYR 0.020 0.001 TYR A 502 ARG 0.005 0.000 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.02714 ( 125) hydrogen bonds : angle 5.33274 ( 333) SS BOND : bond 0.00544 ( 10) SS BOND : angle 2.07242 ( 20) covalent geometry : bond 0.00265 ( 5974) covalent geometry : angle 0.64556 ( 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 194 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 136 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8168 (mt) REVERT: A 241 ASN cc_start: 0.5544 (OUTLIER) cc_final: 0.5139 (p0) REVERT: A 378 PHE cc_start: 0.5993 (t80) cc_final: 0.5241 (t80) REVERT: A 421 GLN cc_start: 0.7389 (mm-40) cc_final: 0.7172 (mt0) REVERT: A 467 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8321 (mtpp) REVERT: A 474 ASP cc_start: 0.8318 (t0) cc_final: 0.8050 (t70) REVERT: A 538 THR cc_start: 0.7327 (p) cc_final: 0.5687 (m) REVERT: A 544 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8213 (ttmm) REVERT: A 651 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7372 (tp-100) REVERT: A 665 ASN cc_start: 0.8106 (t0) cc_final: 0.7617 (t0) REVERT: A 670 ASP cc_start: 0.7663 (t70) cc_final: 0.7237 (t0) REVERT: C 36 TRP cc_start: 0.7900 (m100) cc_final: 0.7571 (m100) REVERT: C 81 LEU cc_start: 0.7620 (tp) cc_final: 0.7353 (tp) REVERT: C 83 MET cc_start: 0.6168 (ptp) cc_final: 0.5923 (ptp) outliers start: 39 outliers final: 26 residues processed: 176 average time/residue: 0.1845 time to fit residues: 42.2240 Evaluate side-chains 175 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 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 352 THR 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 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 627 VAL Chi-restraints excluded: chain A residue 668 GLU 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 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 ASN A 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.152696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136039 restraints weight = 9471.685| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 3.36 r_work: 0.3668 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5984 Z= 0.190 Angle : 0.713 20.866 8149 Z= 0.357 Chirality : 0.047 0.181 894 Planarity : 0.006 0.125 1051 Dihedral : 7.259 90.106 828 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 6.07 % Allowed : 24.11 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.29), residues: 724 helix: -3.15 (0.94), residues: 28 sheet: -0.19 (0.40), residues: 166 loop : -2.48 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 360 HIS 0.003 0.001 HIS A 526 PHE 0.027 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 0.03406 ( 125) hydrogen bonds : angle 5.59237 ( 333) SS BOND : bond 0.00656 ( 10) SS BOND : angle 3.21452 ( 20) covalent geometry : bond 0.00449 ( 5974) covalent geometry : angle 0.69544 ( 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 200 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 136 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (mt) REVERT: A 173 CYS cc_start: 0.4681 (p) cc_final: 0.4434 (p) REVERT: A 241 ASN cc_start: 0.5681 (OUTLIER) cc_final: 0.5229 (p0) REVERT: A 369 VAL cc_start: 0.8234 (t) cc_final: 0.7956 (p) REVERT: A 421 GLN cc_start: 0.7449 (mm-40) cc_final: 0.7238 (mt0) REVERT: A 429 ASN cc_start: 0.7707 (m-40) cc_final: 0.7412 (m-40) REVERT: A 443 TRP cc_start: 0.8459 (p90) cc_final: 0.7700 (p90) REVERT: A 474 ASP cc_start: 0.8364 (t0) cc_final: 0.7968 (t70) REVERT: A 538 THR cc_start: 0.7737 (p) cc_final: 0.6764 (m) REVERT: A 544 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8318 (ttmm) REVERT: A 651 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7335 (tp-100) REVERT: A 665 ASN cc_start: 0.8178 (t0) cc_final: 0.7628 (t0) REVERT: A 670 ASP cc_start: 0.7760 (t70) cc_final: 0.7208 (t70) REVERT: C 34 MET cc_start: 0.7704 (mmt) cc_final: 0.7255 (mmt) REVERT: C 69 THR cc_start: 0.7786 (OUTLIER) cc_final: 0.7465 (p) REVERT: C 81 LEU cc_start: 0.7895 (tp) cc_final: 0.7602 (tp) REVERT: C 83 MET cc_start: 0.6292 (ptp) cc_final: 0.5991 (ptp) outliers start: 39 outliers final: 27 residues processed: 183 average time/residue: 0.1708 time to fit residues: 40.9658 Evaluate side-chains 187 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 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 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 593 ASP Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8340 ------------------------------------------------------------------------------- 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 424 ASN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 682 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.152257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135100 restraints weight = 9188.846| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.44 r_work: 0.3660 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5984 Z= 0.183 Angle : 0.741 22.277 8149 Z= 0.368 Chirality : 0.047 0.182 894 Planarity : 0.005 0.071 1051 Dihedral : 7.251 89.640 826 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 5.91 % Allowed : 25.35 % Favored : 68.74 % 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: -2.71 (0.29), residues: 724 helix: -3.07 (0.95), residues: 28 sheet: -0.29 (0.41), residues: 160 loop : -2.42 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 640 HIS 0.005 0.001 HIS A 74 PHE 0.030 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 0.03400 ( 125) hydrogen bonds : angle 5.61905 ( 333) SS BOND : bond 0.00754 ( 10) SS BOND : angle 3.45804 ( 20) covalent geometry : bond 0.00431 ( 5974) covalent geometry : angle 0.72212 ( 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 193 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8080 (tpp80) cc_final: 0.7813 (mtt180) REVERT: A 60 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7621 (tm-30) REVERT: A 136 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8089 (mt) REVERT: A 241 ASN cc_start: 0.5662 (OUTLIER) cc_final: 0.5183 (p0) REVERT: A 421 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7329 (mt0) REVERT: A 429 ASN cc_start: 0.7707 (m-40) cc_final: 0.7422 (m-40) REVERT: A 443 TRP cc_start: 0.8440 (p90) cc_final: 0.7772 (p90) REVERT: A 474 ASP cc_start: 0.8387 (t0) cc_final: 0.7874 (t70) REVERT: A 544 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8271 (ttmm) REVERT: A 588 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.8009 (p) REVERT: A 651 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7307 (tp-100) REVERT: A 665 ASN cc_start: 0.8245 (t0) cc_final: 0.7628 (t0) REVERT: A 670 ASP cc_start: 0.7622 (t70) cc_final: 0.7019 (t70) REVERT: C 69 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7453 (p) REVERT: C 81 LEU cc_start: 0.7910 (tp) cc_final: 0.7585 (tp) REVERT: C 83 MET cc_start: 0.6432 (ptp) cc_final: 0.6123 (ptp) outliers start: 38 outliers final: 29 residues processed: 177 average time/residue: 0.1778 time to fit residues: 41.2705 Evaluate side-chains 183 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 361 ASN Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 409 ILE 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 526 HIS 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 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: 1.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- 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** A 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.148082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129304 restraints weight = 9341.085| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.69 r_work: 0.3606 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5984 Z= 0.179 Angle : 0.745 22.084 8149 Z= 0.370 Chirality : 0.047 0.168 894 Planarity : 0.005 0.058 1051 Dihedral : 7.213 89.425 825 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 6.53 % Allowed : 25.35 % Favored : 68.12 % 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 (0.29), residues: 724 helix: -3.14 (0.93), residues: 28 sheet: -0.22 (0.42), residues: 160 loop : -2.42 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 640 HIS 0.003 0.001 HIS A 74 PHE 0.029 0.002 PHE A 63 TYR 0.022 0.002 TYR A 502 ARG 0.008 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 125) hydrogen bonds : angle 5.65361 ( 333) SS BOND : bond 0.00714 ( 10) SS BOND : angle 3.02371 ( 20) covalent geometry : bond 0.00423 ( 5974) covalent geometry : angle 0.73116 ( 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 194 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 136 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8100 (mt) REVERT: A 241 ASN cc_start: 0.5697 (OUTLIER) cc_final: 0.5218 (p0) REVERT: A 421 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7406 (mt0) REVERT: A 429 ASN cc_start: 0.7794 (m-40) cc_final: 0.7534 (m-40) REVERT: A 443 TRP cc_start: 0.8472 (p90) cc_final: 0.7805 (p90) REVERT: A 474 ASP cc_start: 0.8460 (t0) cc_final: 0.7996 (t70) REVERT: A 544 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8303 (ttmm) REVERT: A 588 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8019 (p) REVERT: A 665 ASN cc_start: 0.8379 (t0) cc_final: 0.7724 (t0) REVERT: A 670 ASP cc_start: 0.7699 (t70) cc_final: 0.7023 (t70) REVERT: C 34 MET cc_start: 0.7810 (mmt) cc_final: 0.7415 (mmt) REVERT: C 69 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7475 (p) REVERT: C 81 LEU cc_start: 0.7931 (tp) cc_final: 0.7607 (tp) REVERT: C 83 MET cc_start: 0.6506 (ptp) cc_final: 0.6196 (ptp) outliers start: 42 outliers final: 31 residues processed: 173 average time/residue: 0.1732 time to fit residues: 39.2914 Evaluate side-chains 184 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 387 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 526 HIS 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 74 ASN Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.151243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.132423 restraints weight = 9389.991| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.65 r_work: 0.3622 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5984 Z= 0.166 Angle : 0.727 20.167 8149 Z= 0.363 Chirality : 0.047 0.158 894 Planarity : 0.005 0.040 1051 Dihedral : 7.210 89.353 825 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.29 % Allowed : 26.28 % Favored : 68.43 % 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: -2.60 (0.30), residues: 724 helix: -3.17 (0.92), residues: 28 sheet: -0.20 (0.42), residues: 161 loop : -2.33 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 640 HIS 0.006 0.001 HIS A 74 PHE 0.029 0.002 PHE A 40 TYR 0.022 0.002 TYR A 502 ARG 0.008 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 125) hydrogen bonds : angle 5.61410 ( 333) SS BOND : bond 0.00694 ( 10) SS BOND : angle 2.86926 ( 20) covalent geometry : bond 0.00392 ( 5974) covalent geometry : angle 0.71411 ( 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 184 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 136 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8107 (mt) REVERT: A 241 ASN cc_start: 0.5677 (OUTLIER) cc_final: 0.5198 (p0) REVERT: A 421 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7390 (mt0) REVERT: A 429 ASN cc_start: 0.7784 (m-40) cc_final: 0.7539 (m-40) REVERT: A 443 TRP cc_start: 0.8481 (p90) cc_final: 0.7857 (p90) REVERT: A 474 ASP cc_start: 0.8437 (t0) cc_final: 0.7986 (t70) REVERT: A 544 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8295 (ttmm) REVERT: A 588 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (p) REVERT: A 651 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7716 (tp-100) REVERT: A 665 ASN cc_start: 0.8338 (t0) cc_final: 0.7697 (t0) REVERT: A 670 ASP cc_start: 0.7662 (t70) cc_final: 0.7006 (t70) REVERT: C 34 MET cc_start: 0.7806 (mmt) cc_final: 0.7379 (mmt) REVERT: C 69 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7437 (p) REVERT: C 81 LEU cc_start: 0.7907 (tp) cc_final: 0.7518 (tp) REVERT: C 83 MET cc_start: 0.6502 (ptp) cc_final: 0.6188 (ptp) outliers start: 34 outliers final: 27 residues processed: 168 average time/residue: 0.1809 time to fit residues: 39.5053 Evaluate side-chains 176 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 387 TYR Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 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 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: 4.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.149110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130048 restraints weight = 9428.937| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.76 r_work: 0.3576 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5984 Z= 0.162 Angle : 0.710 19.248 8149 Z= 0.354 Chirality : 0.047 0.156 894 Planarity : 0.005 0.048 1051 Dihedral : 7.184 89.390 825 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 5.29 % Allowed : 26.28 % Favored : 68.43 % 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: -2.58 (0.30), residues: 724 helix: -3.18 (0.92), residues: 28 sheet: -0.26 (0.41), residues: 170 loop : -2.32 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 36 HIS 0.003 0.001 HIS A 214 PHE 0.026 0.002 PHE A 40 TYR 0.021 0.002 TYR A 502 ARG 0.008 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 125) hydrogen bonds : angle 5.62183 ( 333) SS BOND : bond 0.00638 ( 10) SS BOND : angle 2.45688 ( 20) covalent geometry : bond 0.00383 ( 5974) covalent geometry : angle 0.70028 ( 8129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.19 seconds wall clock time: 52 minutes 27.45 seconds (3147.45 seconds total)