Starting phenix.real_space_refine on Wed Jan 17 19:14:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4f_35171/01_2024/8i4f_35171.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4f_35171/01_2024/8i4f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4f_35171/01_2024/8i4f_35171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4f_35171/01_2024/8i4f_35171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4f_35171/01_2024/8i4f_35171.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4f_35171/01_2024/8i4f_35171.pdb" } 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 Residue "A ARG 86": "NH1" <-> "NH2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 3.69, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 1.99 Conformation dependent library (CDL) restraints added in 940.1 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: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.751A pdb=" N GLU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.921A pdb=" N TYR A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 377' Processing helix chain 'A' and resid 626 through 631 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 removed outlier: 7.811A pdb=" N ASN A 69 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR A 276 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 200 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 236 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 210 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL A 234 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER A 212 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 63 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.623A pdb=" N GLY A 115 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 125 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 128 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 135 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.623A pdb=" N GLY A 115 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 125 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS A 139 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 321 removed outlier: 3.543A pdb=" N THR A 606 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 619 " --> pdb=" O CYS A 656 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.804A pdb=" N GLU A 331 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASN A 549 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE A 333 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 363 through 365 removed outlier: 3.605A pdb=" N LYS A 385 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 442 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA A 383 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 460 through 461 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 662 removed outlier: 6.155A pdb=" N GLU A 661 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 682 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 671 through 674 removed outlier: 6.734A pdb=" N ILE A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 6 through 7 removed outlier: 3.554A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET C 83 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.830A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 333 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 2.20 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: 100.90 - 107.51: 209 107.51 - 114.12: 3261 114.12 - 120.73: 2293 120.73 - 127.34: 2316 127.34 - 133.96: 50 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 2.440 nonbonded pdb=" O GLU A 668 " pdb=" OH TYR A 702 " model vdw 2.284 2.440 nonbonded pdb=" O VAL A 138 " pdb=" OG1 THR A 174 " model vdw 2.314 2.440 nonbonded pdb=" OG1 THR A 116 " pdb=" O ASN A 241 " model vdw 2.315 2.440 nonbonded pdb=" OG1 THR A 400 " pdb=" O GLU A 523 " model vdw 2.323 2.440 ... (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 ========== 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: 0.800 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: 3.630 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.320 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5974 Z= 0.114 Angle : 0.450 5.640 8129 Z= 0.250 Chirality : 0.041 0.130 894 Planarity : 0.004 0.049 1051 Dihedral : 9.629 88.256 2112 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.44 % Allowed : 7.62 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.25), residues: 724 helix: -4.59 (0.40), residues: 33 sheet: -1.27 (0.38), residues: 171 loop : -3.60 (0.21), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 640 HIS 0.001 0.000 HIS A 57 PHE 0.010 0.001 PHE A 407 TYR 0.005 0.001 TYR A 376 ARG 0.002 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 0.579 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: 0.1863 time to fit residues: 48.9317 Evaluate side-chains 165 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 0.7980 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 180 GLN A 218 ASN A 416 GLN A 421 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5974 Z= 0.200 Angle : 0.566 6.890 8129 Z= 0.294 Chirality : 0.044 0.170 894 Planarity : 0.005 0.043 1051 Dihedral : 6.984 88.650 835 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.91 % Allowed : 14.31 % Favored : 79.78 % 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: -3.79 (0.26), residues: 724 helix: -4.27 (0.54), residues: 34 sheet: -1.04 (0.37), residues: 181 loop : -3.21 (0.22), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 36 HIS 0.003 0.001 HIS A 214 PHE 0.033 0.002 PHE A 378 TYR 0.033 0.002 TYR A 502 ARG 0.004 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7095 (p) REVERT: A 42 ARG cc_start: 0.6757 (mtt-85) cc_final: 0.6505 (mtt-85) REVERT: A 60 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7236 (tm-30) REVERT: A 136 ILE cc_start: 0.8430 (mm) cc_final: 0.8177 (mt) REVERT: A 212 SER cc_start: 0.7499 (t) cc_final: 0.7007 (m) REVERT: A 251 LEU cc_start: 0.7669 (tp) cc_final: 0.7416 (tp) REVERT: A 378 PHE cc_start: 0.5781 (t80) cc_final: 0.5338 (t80) REVERT: A 429 ASN cc_start: 0.7091 (m110) cc_final: 0.6764 (m110) REVERT: A 443 TRP cc_start: 0.8196 (p90) cc_final: 0.7452 (p90) REVERT: A 471 PHE cc_start: 0.8007 (m-10) cc_final: 0.7402 (m-10) REVERT: A 477 THR cc_start: 0.8697 (p) cc_final: 0.8420 (t) REVERT: A 544 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7985 (ttmm) REVERT: A 651 GLN cc_start: 0.7517 (tp-100) cc_final: 0.7037 (tp-100) REVERT: A 665 ASN cc_start: 0.7493 (t0) cc_final: 0.7090 (t0) REVERT: A 706 LEU cc_start: 0.8407 (mp) cc_final: 0.7857 (mp) REVERT: C 69 THR cc_start: 0.7448 (OUTLIER) cc_final: 0.7214 (p) outliers start: 38 outliers final: 20 residues processed: 195 average time/residue: 0.1907 time to fit residues: 47.4209 Evaluate side-chains 181 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 612 SER 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 36 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 429 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5974 Z= 0.282 Angle : 0.644 14.291 8129 Z= 0.324 Chirality : 0.047 0.236 894 Planarity : 0.005 0.044 1051 Dihedral : 7.277 89.647 833 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 5.60 % Allowed : 17.26 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.27), residues: 724 helix: -3.98 (0.65), residues: 34 sheet: -0.82 (0.41), residues: 157 loop : -2.97 (0.22), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 360 HIS 0.004 0.001 HIS A 214 PHE 0.032 0.002 PHE A 569 TYR 0.028 0.002 TYR A 502 ARG 0.005 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 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: 0.8029 (OUTLIER) cc_final: 0.7322 (p) REVERT: A 60 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 72 TRP cc_start: 0.8509 (t60) cc_final: 0.8271 (t60) REVERT: A 136 ILE cc_start: 0.8365 (mm) cc_final: 0.8073 (mt) REVERT: A 212 SER cc_start: 0.7598 (t) cc_final: 0.7007 (m) REVERT: A 251 LEU cc_start: 0.7624 (tp) cc_final: 0.7394 (tp) REVERT: A 320 TYR cc_start: 0.7391 (m-80) cc_final: 0.7153 (m-10) REVERT: A 378 PHE cc_start: 0.5988 (t80) cc_final: 0.5307 (t80) REVERT: A 429 ASN cc_start: 0.7053 (m110) cc_final: 0.6673 (m110) REVERT: A 477 THR cc_start: 0.8820 (p) cc_final: 0.8582 (t) REVERT: A 544 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8087 (ttmm) REVERT: A 665 ASN cc_start: 0.7708 (t0) cc_final: 0.7192 (t0) REVERT: C 69 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7335 (p) REVERT: C 71 SER cc_start: 0.8054 (m) cc_final: 0.7676 (p) REVERT: C 81 LEU cc_start: 0.7644 (tp) cc_final: 0.7438 (tp) outliers start: 36 outliers final: 28 residues processed: 196 average time/residue: 0.1826 time to fit residues: 45.6969 Evaluate side-chains 192 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 128 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 387 TYR 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 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 599 PHE Chi-restraints excluded: chain A residue 612 SER 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 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 64 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 0.0670 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 361 ASN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN A 549 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5974 Z= 0.178 Angle : 0.612 16.979 8129 Z= 0.301 Chirality : 0.045 0.255 894 Planarity : 0.004 0.042 1051 Dihedral : 7.039 88.492 831 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.44 % Allowed : 19.75 % Favored : 74.81 % 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: -3.21 (0.28), residues: 724 helix: -3.62 (0.74), residues: 34 sheet: -0.63 (0.38), residues: 178 loop : -2.80 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 36 HIS 0.004 0.001 HIS A 214 PHE 0.017 0.001 PHE A 650 TYR 0.024 0.001 TYR A 502 ARG 0.006 0.001 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7105 (p) REVERT: A 60 GLN cc_start: 0.7656 (tm-30) cc_final: 0.7380 (tm-30) REVERT: A 72 TRP cc_start: 0.8403 (t60) cc_final: 0.7956 (t60) REVERT: A 109 ILE cc_start: 0.8576 (mt) cc_final: 0.8370 (mt) REVERT: A 136 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8115 (mt) REVERT: A 212 SER cc_start: 0.7463 (t) cc_final: 0.6974 (m) REVERT: A 251 LEU cc_start: 0.7631 (tp) cc_final: 0.7380 (tp) REVERT: A 326 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.7095 (mtt-85) REVERT: A 378 PHE cc_start: 0.5905 (t80) cc_final: 0.5147 (t80) REVERT: A 477 THR cc_start: 0.8809 (p) cc_final: 0.8582 (t) REVERT: A 523 GLU cc_start: 0.6084 (mt-10) cc_final: 0.5865 (mt-10) REVERT: A 532 CYS cc_start: 0.3822 (OUTLIER) cc_final: 0.3558 (m) REVERT: A 544 LYS cc_start: 0.8311 (ttmt) cc_final: 0.8025 (ttmm) REVERT: A 651 GLN cc_start: 0.7348 (tp-100) cc_final: 0.7036 (tp40) REVERT: A 665 ASN cc_start: 0.7704 (t0) cc_final: 0.7165 (t0) REVERT: C 69 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7219 (p) REVERT: C 71 SER cc_start: 0.8004 (m) cc_final: 0.7653 (p) outliers start: 35 outliers final: 27 residues processed: 181 average time/residue: 0.1939 time to fit residues: 44.7974 Evaluate side-chains 184 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 215 THR 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 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 448 LEU 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 532 CYS 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 612 SER 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 12 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.0170 chunk 17 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5974 Z= 0.233 Angle : 0.640 18.952 8129 Z= 0.314 Chirality : 0.045 0.185 894 Planarity : 0.004 0.040 1051 Dihedral : 7.165 88.856 831 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 5.60 % Allowed : 20.84 % Favored : 73.56 % 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: -3.05 (0.29), residues: 724 helix: -3.71 (0.73), residues: 34 sheet: -0.50 (0.39), residues: 178 loop : -2.69 (0.25), residues: 512 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 0.018 0.002 PHE A 63 TYR 0.022 0.002 TYR A 502 ARG 0.005 0.001 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 0.982 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: 0.7919 (OUTLIER) cc_final: 0.7150 (p) REVERT: A 60 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 136 ILE cc_start: 0.8385 (mm) cc_final: 0.8083 (mt) REVERT: A 212 SER cc_start: 0.7631 (t) cc_final: 0.7098 (m) REVERT: A 251 LEU cc_start: 0.7689 (tp) cc_final: 0.7435 (tp) REVERT: A 345 PHE cc_start: 0.7855 (m-80) cc_final: 0.7480 (m-80) REVERT: A 378 PHE cc_start: 0.5830 (t80) cc_final: 0.5077 (t80) REVERT: A 477 THR cc_start: 0.8856 (p) cc_final: 0.8647 (t) REVERT: A 523 GLU cc_start: 0.6302 (mt-10) cc_final: 0.6082 (mt-10) REVERT: A 544 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8007 (ttmm) REVERT: A 651 GLN cc_start: 0.7284 (tp-100) cc_final: 0.6451 (tp-100) REVERT: A 665 ASN cc_start: 0.7787 (t0) cc_final: 0.7258 (t0) REVERT: C 69 THR cc_start: 0.7516 (OUTLIER) cc_final: 0.7242 (p) REVERT: C 81 LEU cc_start: 0.7394 (tp) cc_final: 0.7130 (tp) outliers start: 36 outliers final: 28 residues processed: 182 average time/residue: 0.1842 time to fit residues: 42.7804 Evaluate side-chains 187 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 128 VAL 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 395 ASN Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 612 SER 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 12 VAL 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 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5974 Z= 0.256 Angle : 0.692 19.961 8129 Z= 0.343 Chirality : 0.047 0.225 894 Planarity : 0.004 0.038 1051 Dihedral : 7.350 88.709 831 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 6.53 % Allowed : 20.68 % 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: -3.01 (0.29), residues: 724 helix: -3.66 (0.75), residues: 34 sheet: -0.48 (0.39), residues: 178 loop : -2.65 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 36 HIS 0.003 0.001 HIS A 214 PHE 0.013 0.002 PHE A 282 TYR 0.023 0.002 TYR A 502 ARG 0.005 0.000 ARG A 326 *********************** 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 199 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7129 (p) REVERT: A 60 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 136 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8063 (mt) REVERT: A 251 LEU cc_start: 0.7734 (tp) cc_final: 0.7453 (tp) REVERT: A 345 PHE cc_start: 0.7910 (m-80) cc_final: 0.7568 (m-80) REVERT: A 354 PHE cc_start: 0.8258 (m-80) cc_final: 0.8014 (t80) REVERT: A 363 LYS cc_start: 0.8371 (tttm) cc_final: 0.8137 (tttm) REVERT: A 378 PHE cc_start: 0.5897 (t80) cc_final: 0.5670 (t80) REVERT: A 477 THR cc_start: 0.8897 (p) cc_final: 0.8684 (t) REVERT: A 523 GLU cc_start: 0.6338 (mt-10) cc_final: 0.6137 (mt-10) REVERT: A 544 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8031 (ttmm) REVERT: A 588 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7910 (p) REVERT: A 651 GLN cc_start: 0.7328 (tp-100) cc_final: 0.6486 (tp-100) REVERT: A 665 ASN cc_start: 0.7862 (t0) cc_final: 0.7322 (t0) REVERT: C 69 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7265 (p) REVERT: C 72 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8032 (tpp80) REVERT: C 81 LEU cc_start: 0.7604 (tp) cc_final: 0.7263 (tp) outliers start: 42 outliers final: 33 residues processed: 180 average time/residue: 0.1880 time to fit residues: 43.6330 Evaluate side-chains 190 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 448 LEU 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 588 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 612 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.0980 chunk 39 optimal weight: 0.0370 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 361 ASN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5974 Z= 0.206 Angle : 0.667 19.941 8129 Z= 0.328 Chirality : 0.045 0.174 894 Planarity : 0.004 0.038 1051 Dihedral : 7.204 88.773 830 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 6.22 % Allowed : 22.86 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.29), residues: 724 helix: -3.58 (0.77), residues: 34 sheet: -0.35 (0.39), residues: 178 loop : -2.61 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 640 HIS 0.004 0.001 HIS A 214 PHE 0.021 0.001 PHE A 63 TYR 0.023 0.002 TYR A 502 ARG 0.008 0.001 ARG A 653 *********************** 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 fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7055 (p) REVERT: A 60 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 72 TRP cc_start: 0.8441 (t60) cc_final: 0.7821 (t60) REVERT: A 136 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7750 (tt) REVERT: A 251 LEU cc_start: 0.7778 (tp) cc_final: 0.7478 (tp) REVERT: A 345 PHE cc_start: 0.7851 (m-80) cc_final: 0.7549 (m-80) REVERT: A 378 PHE cc_start: 0.5831 (t80) cc_final: 0.4998 (t80) REVERT: A 443 TRP cc_start: 0.8386 (p90) cc_final: 0.7614 (p90) REVERT: A 477 THR cc_start: 0.8904 (p) cc_final: 0.8690 (t) REVERT: A 538 THR cc_start: 0.7295 (p) cc_final: 0.5894 (m) REVERT: A 544 LYS cc_start: 0.8331 (ttmt) cc_final: 0.8011 (ttmm) REVERT: A 588 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7973 (p) REVERT: A 651 GLN cc_start: 0.7449 (tp-100) cc_final: 0.6746 (tp-100) REVERT: A 665 ASN cc_start: 0.7850 (t0) cc_final: 0.7315 (t0) REVERT: C 69 THR cc_start: 0.7542 (OUTLIER) cc_final: 0.7243 (p) REVERT: C 72 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8041 (tpp80) REVERT: C 81 LEU cc_start: 0.7612 (tp) cc_final: 0.7297 (tp) outliers start: 40 outliers final: 31 residues processed: 172 average time/residue: 0.1993 time to fit residues: 43.4984 Evaluate side-chains 183 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 GLU 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 352 THR 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 448 LEU 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 588 THR Chi-restraints excluded: chain A residue 612 SER 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 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 20 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 0.0570 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5974 Z= 0.231 Angle : 0.678 20.917 8129 Z= 0.332 Chirality : 0.046 0.160 894 Planarity : 0.004 0.037 1051 Dihedral : 7.223 88.458 826 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 6.53 % Allowed : 23.48 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.29), residues: 724 helix: -3.55 (0.79), residues: 34 sheet: -0.23 (0.40), residues: 173 loop : -2.49 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 640 HIS 0.003 0.001 HIS A 214 PHE 0.019 0.002 PHE A 63 TYR 0.023 0.002 TYR A 502 ARG 0.008 0.001 ARG A 473 *********************** 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 192 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 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 37 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.6998 (p) REVERT: A 60 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 136 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7752 (tt) REVERT: A 169 SER cc_start: 0.8499 (m) cc_final: 0.7621 (t) REVERT: A 251 LEU cc_start: 0.7725 (tp) cc_final: 0.7434 (tp) REVERT: A 345 PHE cc_start: 0.7871 (m-80) cc_final: 0.7578 (m-80) REVERT: A 378 PHE cc_start: 0.5888 (t80) cc_final: 0.5632 (t80) REVERT: A 421 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7173 (mt0) REVERT: A 443 TRP cc_start: 0.8302 (p90) cc_final: 0.7749 (p90) REVERT: A 477 THR cc_start: 0.8943 (p) cc_final: 0.8724 (t) REVERT: A 538 THR cc_start: 0.7374 (p) cc_final: 0.6051 (m) REVERT: A 544 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8032 (ttmm) REVERT: A 588 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7917 (p) REVERT: A 665 ASN cc_start: 0.7908 (t0) cc_final: 0.7347 (t0) REVERT: C 69 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.7323 (p) REVERT: C 72 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.8083 (ttm170) REVERT: C 81 LEU cc_start: 0.7664 (tp) cc_final: 0.7353 (tp) outliers start: 42 outliers final: 30 residues processed: 172 average time/residue: 0.1842 time to fit residues: 40.4580 Evaluate side-chains 182 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR 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 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU 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 576 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 612 SER 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 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 66 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 543 ASN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 5974 Z= 0.414 Angle : 0.775 22.553 8129 Z= 0.392 Chirality : 0.049 0.193 894 Planarity : 0.005 0.043 1051 Dihedral : 7.533 89.290 822 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 5.75 % Allowed : 24.57 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.29), residues: 724 helix: -3.53 (0.78), residues: 34 sheet: -0.14 (0.42), residues: 166 loop : -2.59 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 640 HIS 0.004 0.001 HIS A 512 PHE 0.022 0.003 PHE A 325 TYR 0.023 0.003 TYR A 502 ARG 0.009 0.001 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 165 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 108 ILE cc_start: 0.7613 (mt) cc_final: 0.7384 (mt) REVERT: A 136 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7704 (tt) REVERT: A 169 SER cc_start: 0.8586 (m) cc_final: 0.7806 (t) REVERT: A 225 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7908 (mm110) REVERT: A 251 LEU cc_start: 0.7780 (tp) cc_final: 0.7498 (tp) REVERT: A 378 PHE cc_start: 0.6065 (t80) cc_final: 0.5813 (t80) REVERT: A 421 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7198 (mt0) REVERT: A 443 TRP cc_start: 0.8373 (p90) cc_final: 0.7828 (p90) REVERT: A 467 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8126 (mtpp) REVERT: A 544 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8224 (ttmm) REVERT: A 588 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7866 (p) REVERT: A 651 GLN cc_start: 0.7655 (tp-100) cc_final: 0.6937 (tp40) REVERT: A 665 ASN cc_start: 0.8066 (t0) cc_final: 0.7494 (t0) REVERT: C 34 MET cc_start: 0.7525 (mtt) cc_final: 0.7311 (mtt) REVERT: C 69 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7306 (p) REVERT: C 72 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.8046 (tpp80) REVERT: C 81 LEU cc_start: 0.7748 (tp) cc_final: 0.7377 (tp) outliers start: 37 outliers final: 29 residues processed: 184 average time/residue: 0.1983 time to fit residues: 46.2582 Evaluate side-chains 194 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR 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 164 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 448 LEU 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 593 ASP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 0.0370 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5974 Z= 0.231 Angle : 0.702 21.264 8129 Z= 0.348 Chirality : 0.046 0.162 894 Planarity : 0.004 0.044 1051 Dihedral : 7.184 88.278 822 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 4.98 % Allowed : 26.91 % 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: -2.70 (0.29), residues: 724 helix: -3.42 (0.81), residues: 34 sheet: -0.05 (0.42), residues: 166 loop : -2.47 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 640 HIS 0.003 0.001 HIS A 214 PHE 0.014 0.002 PHE A 336 TYR 0.029 0.002 TYR A 430 ARG 0.008 0.001 ARG A 473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7130 (p) REVERT: A 60 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7351 (tm-30) REVERT: A 108 ILE cc_start: 0.7608 (mt) cc_final: 0.7394 (mt) REVERT: A 136 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7696 (tt) REVERT: A 169 SER cc_start: 0.8511 (m) cc_final: 0.7561 (t) REVERT: A 225 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7863 (mm110) REVERT: A 251 LEU cc_start: 0.7696 (tp) cc_final: 0.7415 (tp) REVERT: A 317 LYS cc_start: 0.7137 (ttpp) cc_final: 0.6869 (ttpp) REVERT: A 378 PHE cc_start: 0.5813 (t80) cc_final: 0.5551 (t80) REVERT: A 421 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7117 (mt0) REVERT: A 443 TRP cc_start: 0.8401 (p90) cc_final: 0.7827 (p90) REVERT: A 446 ASN cc_start: 0.6968 (p0) cc_final: 0.6768 (p0) REVERT: A 544 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8126 (ttmm) REVERT: A 588 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7912 (p) REVERT: A 665 ASN cc_start: 0.8027 (t0) cc_final: 0.7498 (t0) REVERT: C 69 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7179 (p) REVERT: C 81 LEU cc_start: 0.7701 (tp) cc_final: 0.7408 (tp) outliers start: 32 outliers final: 24 residues processed: 173 average time/residue: 0.1993 time to fit residues: 43.6837 Evaluate side-chains 178 residues out of total 643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR 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 164 PHE Chi-restraints excluded: chain A residue 176 GLU 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 381 PHE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 448 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 612 SER Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** 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 = 0.4019 r_free = 0.4019 target = 0.152748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135406 restraints weight = 9343.067| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 3.46 r_work: 0.3670 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5974 Z= 0.236 Angle : 0.702 20.973 8129 Z= 0.349 Chirality : 0.046 0.161 894 Planarity : 0.004 0.042 1051 Dihedral : 7.182 89.620 822 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % 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: -2.63 (0.30), residues: 724 helix: -3.42 (0.81), residues: 34 sheet: -0.05 (0.41), residues: 176 loop : -2.44 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 640 HIS 0.003 0.001 HIS A 214 PHE 0.014 0.002 PHE A 381 TYR 0.033 0.002 TYR A 430 ARG 0.008 0.001 ARG A 641 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.85 seconds wall clock time: 35 minutes 2.33 seconds (2102.33 seconds total)