Starting phenix.real_space_refine on Sun Mar 17 09:51:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avb_15677/03_2024/8avb_15677.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avb_15677/03_2024/8avb_15677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avb_15677/03_2024/8avb_15677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avb_15677/03_2024/8avb_15677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avb_15677/03_2024/8avb_15677.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avb_15677/03_2024/8avb_15677.pdb" } resolution = 4.43 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6823 atoms to isotropic. 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 51 5.16 5 C 6790 2.51 5 N 1778 2.21 5 O 1972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 61": "OD1" <-> "OD2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 563": "OE1" <-> "OE2" Residue "B PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10591 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "F" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Time building chain proxies: 6.17, per 1000 atoms: 0.58 Number of scatterers: 10591 At special positions: 0 Unit cell: (99.66, 137.41, 175.16, 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 51 16.00 O 1972 8.00 N 1778 7.00 C 6790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 410 " distance=2.04 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.04 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 410 " distance=2.03 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 416 " distance=2.02 Simple disulfide: pdb=" SG CYS F 434 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 471 " - pdb=" SG CYS F 526 " distance=2.03 Simple disulfide: pdb=" SG CYS F 486 " - pdb=" SG CYS F 496 " distance=2.03 Simple disulfide: pdb=" SG CYS F 602 " - pdb=" SG CYS F 672 " distance=2.02 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: 3.85 Conformation dependent library (CDL) restraints added in 2.7 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2538 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 29 sheets defined 10.0% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 23 through 44 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.564A pdb=" N GLN A 49 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 removed outlier: 3.853A pdb=" N SER A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.677A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.855A pdb=" N VAL B 533 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.942A pdb=" N LYS B 735 " --> pdb=" O PRO B 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.821A pdb=" N VAL F 533 " --> pdb=" O ASP F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 731 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246 removed outlier: 5.590A pdb=" N GLY B 241 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 257 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286 Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 340 Processing sheet with id=AA6, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA7, first strand: chain 'B' and resid 432 through 436 removed outlier: 3.694A pdb=" N VAL B 487 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.578A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.578A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545 removed outlier: 6.016A pdb=" N ASN B 540 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU B 557 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AB3, first strand: chain 'B' and resid 643 through 648 Processing sheet with id=AB4, first strand: chain 'B' and resid 687 through 694 removed outlier: 6.094A pdb=" N TYR B 677 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 739 through 745 Processing sheet with id=AB6, first strand: chain 'B' and resid 782 through 787 Processing sheet with id=AB7, first strand: chain 'F' and resid 240 through 246 removed outlier: 5.214A pdb=" N GLY F 241 " --> pdb=" O ASP F 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 279 through 286 Processing sheet with id=AB9, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AC1, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AC2, first strand: chain 'F' and resid 337 through 339 removed outlier: 6.596A pdb=" N ILE F 338 " --> pdb=" O TYR F 424 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 433 through 436 Processing sheet with id=AC4, first strand: chain 'F' and resid 482 through 484 removed outlier: 4.031A pdb=" N LEU F 462 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 482 through 484 removed outlier: 4.031A pdb=" N LEU F 462 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 539 through 545 removed outlier: 3.816A pdb=" N VAL F 541 " --> pdb=" O SER F 555 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER F 555 " --> pdb=" O VAL F 541 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA F 543 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS F 553 " --> pdb=" O ALA F 543 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 582 through 586 Processing sheet with id=AC8, first strand: chain 'F' and resid 643 through 648 Processing sheet with id=AC9, first strand: chain 'F' and resid 690 through 694 removed outlier: 5.576A pdb=" N TYR F 677 " --> pdb=" O VAL F 693 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 739 through 746 Processing sheet with id=AD2, first strand: chain 'F' and resid 782 through 787 removed outlier: 3.839A pdb=" N TYR F 767 " --> pdb=" O VAL F 812 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1140 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: 4.23 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1808 1.32 - 1.46: 3328 1.46 - 1.59: 5659 1.59 - 1.72: 1 1.72 - 1.85: 72 Bond restraints: 10868 Sorted by residual: bond pdb=" CG PRO F 801 " pdb=" CD PRO F 801 " ideal model delta sigma weight residual 1.503 1.191 0.312 3.40e-02 8.65e+02 8.41e+01 bond pdb=" N PRO F 801 " pdb=" CD PRO F 801 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" CB PRO F 801 " pdb=" CG PRO F 801 " ideal model delta sigma weight residual 1.492 1.680 -0.188 5.00e-02 4.00e+02 1.41e+01 bond pdb=" CB ASN A 103 " pdb=" CG ASN A 103 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.66e+00 bond pdb=" N PRO F 801 " pdb=" CA PRO F 801 " ideal model delta sigma weight residual 1.472 1.446 0.025 1.34e-02 5.57e+03 3.61e+00 ... (remaining 10863 not shown) Histogram of bond angle deviations from ideal: 86.46 - 96.20: 2 96.20 - 105.93: 311 105.93 - 115.67: 6996 115.67 - 125.41: 7240 125.41 - 135.14: 266 Bond angle restraints: 14815 Sorted by residual: angle pdb=" N PRO F 801 " pdb=" CD PRO F 801 " pdb=" CG PRO F 801 " ideal model delta sigma weight residual 103.20 86.46 16.74 1.50e+00 4.44e-01 1.25e+02 angle pdb=" CA PRO F 801 " pdb=" N PRO F 801 " pdb=" CD PRO F 801 " ideal model delta sigma weight residual 112.00 97.20 14.80 1.40e+00 5.10e-01 1.12e+02 angle pdb=" CB ARG A 41 " pdb=" CG ARG A 41 " pdb=" CD ARG A 41 " ideal model delta sigma weight residual 111.30 135.14 -23.84 2.30e+00 1.89e-01 1.07e+02 angle pdb=" CA PRO F 801 " pdb=" CB PRO F 801 " pdb=" CG PRO F 801 " ideal model delta sigma weight residual 104.50 93.66 10.84 1.90e+00 2.77e-01 3.26e+01 angle pdb=" N SER A 46 " pdb=" CA SER A 46 " pdb=" C SER A 46 " ideal model delta sigma weight residual 110.80 121.38 -10.58 2.13e+00 2.20e-01 2.47e+01 ... (remaining 14810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6133 17.93 - 35.87: 350 35.87 - 53.80: 57 53.80 - 71.73: 7 71.73 - 89.66: 6 Dihedral angle restraints: 6553 sinusoidal: 2639 harmonic: 3914 Sorted by residual: dihedral pdb=" CB CYS F 411 " pdb=" SG CYS F 411 " pdb=" SG CYS F 416 " pdb=" CB CYS F 416 " ideal model delta sinusoidal sigma weight residual 93.00 42.00 51.00 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA PHE B 502 " pdb=" C PHE B 502 " pdb=" N LEU B 503 " pdb=" CA LEU B 503 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 49.96 43.04 1 1.00e+01 1.00e-02 2.58e+01 ... (remaining 6550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1444 0.075 - 0.149: 223 0.149 - 0.224: 8 0.224 - 0.298: 1 0.298 - 0.373: 1 Chirality restraints: 1677 Sorted by residual: chirality pdb=" CA GLN A 96 " pdb=" N GLN A 96 " pdb=" C GLN A 96 " pdb=" CB GLN A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE F 753 " pdb=" CA ILE F 753 " pdb=" CG1 ILE F 753 " pdb=" CG2 ILE F 753 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA PRO A 90 " pdb=" N PRO A 90 " pdb=" C PRO A 90 " pdb=" CB PRO A 90 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 1674 not shown) Planarity restraints: 1863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 800 " -0.106 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO F 801 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO F 801 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO F 801 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 558 " 0.050 5.00e-02 4.00e+02 7.71e-02 9.51e+00 pdb=" N PRO B 559 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 559 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 559 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 24 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C ILE A 24 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE A 24 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN A 25 " -0.018 2.00e-02 2.50e+03 ... (remaining 1860 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 320 2.69 - 3.25: 10270 3.25 - 3.80: 17396 3.80 - 4.35: 22860 4.35 - 4.90: 36161 Nonbonded interactions: 87007 Sorted by model distance: nonbonded pdb=" OD1 ASN A 103 " pdb=" OG SER B 505 " model vdw 2.142 2.440 nonbonded pdb=" OG1 THR F 397 " pdb=" O VAL F 425 " model vdw 2.142 2.440 nonbonded pdb=" NE2 GLN A 96 " pdb=" N ILE B 501 " model vdw 2.178 3.200 nonbonded pdb=" NE1 TRP B 644 " pdb=" OE2 GLU B 771 " model vdw 2.182 2.520 nonbonded pdb=" NH1 ARG F 368 " pdb=" OD2 ASP F 406 " model vdw 2.206 2.520 ... (remaining 87002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' } 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 group one per residue 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 2.750 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 31.180 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 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 : 0.005 0.312 10868 Z= 0.275 Angle : 0.810 23.843 14815 Z= 0.456 Chirality : 0.050 0.373 1677 Planarity : 0.006 0.146 1863 Dihedral : 11.641 89.664 3976 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.40 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.50 % 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: -0.47 (0.23), residues: 1318 helix: -0.94 (0.42), residues: 107 sheet: -0.07 (0.21), residues: 574 loop : -0.27 (0.27), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 366 HIS 0.013 0.001 HIS F 418 PHE 0.016 0.001 PHE B 334 TYR 0.033 0.002 TYR A 140 ARG 0.024 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8697 (m-10) cc_final: 0.8208 (m-10) REVERT: A 149 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7247 (mtp180) REVERT: A 155 GLN cc_start: 0.8374 (tp-100) cc_final: 0.7905 (tp-100) REVERT: B 509 MET cc_start: 0.8881 (pmm) cc_final: 0.8623 (pmm) REVERT: B 638 MET cc_start: 0.9329 (mmp) cc_final: 0.9112 (mmm) REVERT: F 397 THR cc_start: 0.6489 (p) cc_final: 0.6239 (p) REVERT: F 403 PHE cc_start: 0.7248 (m-10) cc_final: 0.6842 (m-80) REVERT: F 638 MET cc_start: 0.9243 (mpp) cc_final: 0.8956 (mpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2126 time to fit residues: 29.6795 Evaluate side-chains 60 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS B 267 GLN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS F 259 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10868 Z= 0.213 Angle : 0.599 7.608 14815 Z= 0.315 Chirality : 0.046 0.205 1677 Planarity : 0.005 0.053 1863 Dihedral : 5.437 62.673 1433 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.29 (0.24), residues: 1318 helix: 0.33 (0.48), residues: 114 sheet: -0.07 (0.22), residues: 549 loop : -0.26 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 447 HIS 0.011 0.001 HIS A 47 PHE 0.017 0.001 PHE F 493 TYR 0.021 0.002 TYR F 494 ARG 0.014 0.001 ARG A 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.6286 (ttp80) cc_final: 0.6068 (ttp80) REVERT: A 140 TYR cc_start: 0.8990 (m-10) cc_final: 0.8723 (m-10) REVERT: A 149 ARG cc_start: 0.8348 (mtt180) cc_final: 0.8022 (mtp180) REVERT: A 155 GLN cc_start: 0.8340 (tp-100) cc_final: 0.7899 (tp-100) REVERT: B 509 MET cc_start: 0.8959 (pmm) cc_final: 0.8727 (pmm) REVERT: F 397 THR cc_start: 0.6916 (p) cc_final: 0.6687 (p) REVERT: F 638 MET cc_start: 0.9198 (mpp) cc_final: 0.8875 (mpp) REVERT: F 733 MET cc_start: 0.9037 (mpp) cc_final: 0.8568 (tpp) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.2268 time to fit residues: 28.6252 Evaluate side-chains 58 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 40.0000 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS B 724 ASN F 269 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10868 Z= 0.304 Angle : 0.685 11.194 14815 Z= 0.362 Chirality : 0.048 0.171 1677 Planarity : 0.006 0.093 1863 Dihedral : 5.708 64.408 1433 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 27.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.76 (0.23), residues: 1318 helix: -0.81 (0.45), residues: 114 sheet: -0.37 (0.21), residues: 556 loop : -0.42 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 367 HIS 0.008 0.002 HIS F 417 PHE 0.021 0.002 PHE B 498 TYR 0.021 0.002 TYR F 302 ARG 0.006 0.001 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.8434 (m-80) cc_final: 0.8180 (m-80) REVERT: A 96 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7447 (mm-40) REVERT: A 140 TYR cc_start: 0.8960 (m-10) cc_final: 0.8754 (m-10) REVERT: A 149 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8324 (mtp180) REVERT: A 155 GLN cc_start: 0.8290 (tp-100) cc_final: 0.7878 (tp-100) REVERT: B 509 MET cc_start: 0.9009 (pmm) cc_final: 0.8784 (pmm) REVERT: B 534 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7310 (tptt) REVERT: B 638 MET cc_start: 0.9177 (mmp) cc_final: 0.8967 (mmm) REVERT: F 638 MET cc_start: 0.9186 (mpp) cc_final: 0.8846 (mpp) REVERT: F 733 MET cc_start: 0.8949 (mpp) cc_final: 0.8524 (tpp) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.2357 time to fit residues: 28.2956 Evaluate side-chains 61 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 40.0000 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 0.3980 chunk 114 optimal weight: 10.0000 chunk 34 optimal weight: 0.0980 chunk 106 optimal weight: 6.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 ASN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10868 Z= 0.222 Angle : 0.593 8.087 14815 Z= 0.315 Chirality : 0.046 0.176 1677 Planarity : 0.005 0.058 1863 Dihedral : 5.608 62.531 1433 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.73 (0.23), residues: 1318 helix: -0.48 (0.47), residues: 120 sheet: -0.46 (0.21), residues: 584 loop : -0.32 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 556 HIS 0.007 0.001 HIS F 417 PHE 0.017 0.002 PHE F 334 TYR 0.016 0.002 TYR F 302 ARG 0.020 0.001 ARG F 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.390 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: symmetry clash REVERT: A 82 TYR cc_start: 0.8394 (m-80) cc_final: 0.7987 (m-80) REVERT: A 149 ARG cc_start: 0.8642 (mtt180) cc_final: 0.8404 (mtp180) REVERT: A 155 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8149 (tp-100) REVERT: B 244 MET cc_start: 0.6866 (tmm) cc_final: 0.6623 (tmm) REVERT: B 443 MET cc_start: 0.4394 (tpt) cc_final: 0.4071 (tpt) REVERT: B 447 TRP cc_start: 0.8846 (p-90) cc_final: 0.8634 (p-90) REVERT: B 638 MET cc_start: 0.9175 (mmp) cc_final: 0.8964 (mmm) REVERT: F 397 THR cc_start: 0.7513 (p) cc_final: 0.7312 (p) REVERT: F 638 MET cc_start: 0.9188 (mpp) cc_final: 0.8829 (mpp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2382 time to fit residues: 30.1917 Evaluate side-chains 63 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 114 optimal weight: 0.2980 chunk 32 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10868 Z= 0.259 Angle : 0.629 11.264 14815 Z= 0.335 Chirality : 0.047 0.165 1677 Planarity : 0.005 0.058 1863 Dihedral : 5.709 62.223 1433 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 27.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.84 (0.23), residues: 1318 helix: -0.66 (0.46), residues: 120 sheet: -0.54 (0.21), residues: 573 loop : -0.37 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 367 HIS 0.009 0.001 HIS F 349 PHE 0.014 0.002 PHE A 62 TYR 0.021 0.002 TYR A 82 ARG 0.004 0.001 ARG F 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.8558 (m-80) cc_final: 0.8224 (m-80) REVERT: A 96 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7253 (tm-30) REVERT: A 140 TYR cc_start: 0.8895 (m-80) cc_final: 0.8460 (m-80) REVERT: A 149 ARG cc_start: 0.8712 (mtt180) cc_final: 0.8490 (mtp180) REVERT: A 155 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8176 (tp-100) REVERT: B 443 MET cc_start: 0.4615 (tpt) cc_final: 0.4259 (tpt) REVERT: B 447 TRP cc_start: 0.8839 (p-90) cc_final: 0.8595 (p-90) REVERT: B 509 MET cc_start: 0.9134 (pmm) cc_final: 0.8924 (pmm) REVERT: B 638 MET cc_start: 0.9139 (mmp) cc_final: 0.8928 (mmm) REVERT: F 638 MET cc_start: 0.9192 (mpp) cc_final: 0.8821 (mpp) REVERT: F 733 MET cc_start: 0.8883 (mpp) cc_final: 0.8328 (tpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2061 time to fit residues: 23.9092 Evaluate side-chains 60 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 50.0000 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 109 HIS B 251 ASN B 267 GLN B 363 GLN B 478 HIS ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10868 Z= 0.226 Angle : 0.606 10.241 14815 Z= 0.321 Chirality : 0.047 0.163 1677 Planarity : 0.005 0.053 1863 Dihedral : 5.701 59.905 1433 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 25.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.88 (0.24), residues: 1318 helix: -0.63 (0.46), residues: 120 sheet: -0.56 (0.21), residues: 574 loop : -0.42 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 556 HIS 0.009 0.001 HIS F 465 PHE 0.015 0.002 PHE A 62 TYR 0.017 0.002 TYR F 302 ARG 0.006 0.001 ARG F 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.8588 (m-80) cc_final: 0.8189 (m-80) REVERT: A 96 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7161 (tm-30) REVERT: A 140 TYR cc_start: 0.9072 (m-80) cc_final: 0.8658 (m-10) REVERT: A 149 ARG cc_start: 0.8784 (mtt180) cc_final: 0.8518 (mtp180) REVERT: A 155 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8177 (tp-100) REVERT: B 244 MET cc_start: 0.7131 (tmm) cc_final: 0.6882 (tpp) REVERT: B 443 MET cc_start: 0.5230 (tpt) cc_final: 0.4825 (tpt) REVERT: B 447 TRP cc_start: 0.8823 (p-90) cc_final: 0.8570 (p-90) REVERT: B 638 MET cc_start: 0.9144 (mmp) cc_final: 0.8922 (mmm) REVERT: F 638 MET cc_start: 0.9209 (mpp) cc_final: 0.8847 (mpp) REVERT: F 733 MET cc_start: 0.8714 (mpp) cc_final: 0.8192 (tpp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2259 time to fit residues: 27.7591 Evaluate side-chains 61 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.2980 chunk 72 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 chunk 58 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS A 151 GLN B 267 GLN B 349 HIS B 685 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10868 Z= 0.156 Angle : 0.563 7.736 14815 Z= 0.298 Chirality : 0.046 0.166 1677 Planarity : 0.005 0.076 1863 Dihedral : 5.401 54.784 1433 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.59 (0.24), residues: 1318 helix: -0.09 (0.47), residues: 120 sheet: -0.40 (0.21), residues: 571 loop : -0.26 (0.27), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 689 HIS 0.008 0.001 HIS B 685 PHE 0.013 0.001 PHE A 62 TYR 0.012 0.001 TYR F 424 ARG 0.005 0.000 ARG F 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.208 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 82 TYR cc_start: 0.8516 (m-80) cc_final: 0.8175 (m-80) REVERT: A 140 TYR cc_start: 0.8954 (m-80) cc_final: 0.8411 (m-80) REVERT: A 149 ARG cc_start: 0.8613 (mtt180) cc_final: 0.7941 (mtp180) REVERT: A 155 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8169 (tp-100) REVERT: B 443 MET cc_start: 0.5211 (tpt) cc_final: 0.4809 (tpt) REVERT: B 557 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8058 (pm20) REVERT: B 638 MET cc_start: 0.9229 (mmp) cc_final: 0.9018 (mmm) REVERT: F 367 TRP cc_start: 0.6921 (m100) cc_final: 0.6646 (m100) REVERT: F 397 THR cc_start: 0.7555 (p) cc_final: 0.7346 (p) REVERT: F 638 MET cc_start: 0.9140 (mpp) cc_final: 0.8766 (mpp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2129 time to fit residues: 26.9348 Evaluate side-chains 63 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 121 optimal weight: 30.0000 chunk 111 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 349 HIS ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10868 Z= 0.167 Angle : 0.555 7.452 14815 Z= 0.292 Chirality : 0.046 0.170 1677 Planarity : 0.004 0.045 1863 Dihedral : 5.294 50.411 1433 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.58 (0.24), residues: 1318 helix: -0.04 (0.48), residues: 120 sheet: -0.43 (0.21), residues: 564 loop : -0.24 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 689 HIS 0.011 0.001 HIS F 418 PHE 0.013 0.001 PHE F 334 TYR 0.013 0.001 TYR F 302 ARG 0.003 0.000 ARG F 645 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.8526 (m-80) cc_final: 0.8222 (m-80) REVERT: A 96 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7311 (tm-30) REVERT: A 140 TYR cc_start: 0.8892 (m-80) cc_final: 0.8384 (m-80) REVERT: A 149 ARG cc_start: 0.8677 (mtt180) cc_final: 0.8445 (mtp180) REVERT: A 155 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8190 (tp-100) REVERT: B 244 MET cc_start: 0.7150 (tmm) cc_final: 0.6919 (tmm) REVERT: B 443 MET cc_start: 0.5254 (tpt) cc_final: 0.4734 (tpt) REVERT: B 509 MET cc_start: 0.9113 (pmm) cc_final: 0.8913 (pmm) REVERT: B 638 MET cc_start: 0.9246 (mmp) cc_final: 0.9040 (mmm) REVERT: F 397 THR cc_start: 0.7625 (p) cc_final: 0.7419 (p) REVERT: F 638 MET cc_start: 0.9140 (mpp) cc_final: 0.8771 (mpp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2318 time to fit residues: 27.7837 Evaluate side-chains 63 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 30.0000 chunk 121 optimal weight: 30.0000 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 349 HIS ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS F 243 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10868 Z= 0.292 Angle : 0.672 7.732 14815 Z= 0.360 Chirality : 0.049 0.214 1677 Planarity : 0.006 0.070 1863 Dihedral : 5.727 47.321 1433 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 31.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1318 helix: -1.08 (0.43), residues: 125 sheet: -0.64 (0.22), residues: 550 loop : -0.51 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 689 HIS 0.009 0.002 HIS F 515 PHE 0.019 0.002 PHE F 403 TYR 0.025 0.002 TYR B 507 ARG 0.013 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.9117 (tptp) cc_final: 0.8905 (tppt) REVERT: A 96 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7371 (tm-30) REVERT: A 140 TYR cc_start: 0.8987 (m-80) cc_final: 0.8444 (m-80) REVERT: A 149 ARG cc_start: 0.8868 (mtt180) cc_final: 0.8394 (mtp180) REVERT: A 155 GLN cc_start: 0.8659 (tp-100) cc_final: 0.8286 (tp-100) REVERT: B 244 MET cc_start: 0.6768 (tmm) cc_final: 0.6520 (tmm) REVERT: B 443 MET cc_start: 0.5582 (tpt) cc_final: 0.5312 (tpp) REVERT: B 447 TRP cc_start: 0.8867 (p-90) cc_final: 0.8610 (p-90) REVERT: B 638 MET cc_start: 0.9141 (mmp) cc_final: 0.8934 (mmm) REVERT: F 367 TRP cc_start: 0.6661 (m100) cc_final: 0.6291 (m100) REVERT: F 638 MET cc_start: 0.9173 (mpp) cc_final: 0.8801 (mpp) REVERT: F 733 MET cc_start: 0.9045 (mpp) cc_final: 0.8498 (tpp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2269 time to fit residues: 27.6877 Evaluate side-chains 59 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.2980 chunk 87 optimal weight: 0.0040 chunk 131 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 349 HIS ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10868 Z= 0.210 Angle : 0.603 7.475 14815 Z= 0.320 Chirality : 0.047 0.182 1677 Planarity : 0.005 0.063 1863 Dihedral : 5.586 43.504 1433 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 26.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1318 helix: -0.63 (0.45), residues: 120 sheet: -0.67 (0.21), residues: 552 loop : -0.50 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 556 HIS 0.009 0.001 HIS F 418 PHE 0.015 0.001 PHE F 334 TYR 0.015 0.001 TYR F 302 ARG 0.003 0.000 ARG A 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.682 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 82 TYR cc_start: 0.8533 (m-80) cc_final: 0.8199 (m-80) REVERT: A 96 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7910 (tm-30) REVERT: A 140 TYR cc_start: 0.8996 (m-80) cc_final: 0.8460 (m-80) REVERT: A 155 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8290 (tp-100) REVERT: B 244 MET cc_start: 0.6920 (tmm) cc_final: 0.6659 (tmm) REVERT: B 443 MET cc_start: 0.5336 (tpt) cc_final: 0.4974 (tpt) REVERT: B 447 TRP cc_start: 0.8853 (p-90) cc_final: 0.8597 (p-90) REVERT: B 638 MET cc_start: 0.9178 (mmp) cc_final: 0.8968 (mmm) REVERT: F 638 MET cc_start: 0.9142 (mpp) cc_final: 0.8765 (mpp) REVERT: F 733 MET cc_start: 0.9126 (mpp) cc_final: 0.8580 (tpp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2268 time to fit residues: 27.7447 Evaluate side-chains 59 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 349 HIS ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.095532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.075217 restraints weight = 111349.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.074643 restraints weight = 85747.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.075081 restraints weight = 77040.533| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10868 Z= 0.324 Angle : 0.710 8.737 14815 Z= 0.380 Chirality : 0.050 0.251 1677 Planarity : 0.006 0.101 1863 Dihedral : 5.982 40.828 1433 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 36.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1318 helix: -1.37 (0.42), residues: 125 sheet: -0.86 (0.22), residues: 534 loop : -0.71 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 367 HIS 0.007 0.002 HIS F 243 PHE 0.035 0.002 PHE F 403 TYR 0.029 0.002 TYR B 507 ARG 0.012 0.001 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2068.48 seconds wall clock time: 38 minutes 35.72 seconds (2315.72 seconds total)