Starting phenix.real_space_refine on Sun Mar 10 21:28:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws7_32749/03_2024/7ws7_32749.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws7_32749/03_2024/7ws7_32749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws7_32749/03_2024/7ws7_32749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws7_32749/03_2024/7ws7_32749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws7_32749/03_2024/7ws7_32749.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws7_32749/03_2024/7ws7_32749.pdb" } resolution = 3.4 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= -0.003 sd= 0.026 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 22 5.16 5 C 3294 2.51 5 N 869 2.21 5 O 1024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 516": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5209 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 192} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.37, per 1000 atoms: 0.65 Number of scatterers: 5209 At special positions: 0 Unit cell: (77.08, 100.04, 120.54, 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 22 16.00 O 1024 8.00 N 869 7.00 C 3294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 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 Links applied BETA1-4 " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG O 1 " - " ASN B 343 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 939.4 milliseconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 17 sheets defined 8.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.619A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.711A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.733A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.672A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.581A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.603A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.908A pdb=" N ASP K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.877A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.786A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.494A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.761A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.860A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.701A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 98 through 99 removed outlier: 6.424A pdb=" N LYS G 98 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.804A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.164A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.926A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR J 98 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.672A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR K 112 " --> pdb=" O LYS K 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.672A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR K 94 " --> pdb=" O THR K 117 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 384 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: 1.46 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1672 1.34 - 1.46: 1353 1.46 - 1.58: 2285 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 5338 Sorted by residual: bond pdb=" N ASP B 442 " pdb=" CA ASP B 442 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.10e-02 8.26e+03 1.06e+01 bond pdb=" N VAL B 445 " pdb=" CA VAL B 445 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.36e+00 bond pdb=" N VAL B 382 " pdb=" CA VAL B 382 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.80e+00 bond pdb=" N PHE B 392 " pdb=" CA PHE B 392 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.09e-02 8.42e+03 7.67e+00 bond pdb=" N GLU K 103 " pdb=" CA GLU K 103 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.16e-02 7.43e+03 7.64e+00 ... (remaining 5333 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.45: 147 106.45 - 113.34: 2750 113.34 - 120.23: 1912 120.23 - 127.12: 2385 127.12 - 134.01: 59 Bond angle restraints: 7253 Sorted by residual: angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 113.53 110.01 3.52 9.80e-01 1.04e+00 1.29e+01 angle pdb=" N LYS B 386 " pdb=" CA LYS B 386 " pdb=" C LYS B 386 " ideal model delta sigma weight residual 112.92 108.82 4.10 1.23e+00 6.61e-01 1.11e+01 angle pdb=" CA VAL B 445 " pdb=" C VAL B 445 " pdb=" O VAL B 445 " ideal model delta sigma weight residual 120.95 117.63 3.32 1.04e+00 9.25e-01 1.02e+01 angle pdb=" C ARG B 509 " pdb=" CA ARG B 509 " pdb=" CB ARG B 509 " ideal model delta sigma weight residual 109.72 104.73 4.99 1.66e+00 3.63e-01 9.04e+00 angle pdb=" CA SER F 67 " pdb=" C SER F 67 " pdb=" O SER F 67 " ideal model delta sigma weight residual 121.45 118.28 3.17 1.07e+00 8.73e-01 8.76e+00 ... (remaining 7248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 2954 21.97 - 43.94: 185 43.94 - 65.91: 15 65.91 - 87.88: 13 87.88 - 109.85: 4 Dihedral angle restraints: 3171 sinusoidal: 1236 harmonic: 1935 Sorted by residual: dihedral pdb=" C1 NAG O 2 " pdb=" C2 NAG O 2 " pdb=" C3 NAG O 2 " pdb=" O3 NAG O 2 " ideal model delta sinusoidal sigma weight residual -175.09 -65.24 -109.85 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C1 NAG O 2 " pdb=" C2 NAG O 2 " pdb=" C3 NAG O 2 " pdb=" C4 NAG O 2 " ideal model delta sinusoidal sigma weight residual -52.39 56.91 -109.30 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" N2 NAG O 2 " pdb=" C2 NAG O 2 " pdb=" C3 NAG O 2 " pdb=" O3 NAG O 2 " ideal model delta sinusoidal sigma weight residual 62.25 170.61 -108.36 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 3168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 690 0.078 - 0.155: 89 0.155 - 0.232: 6 0.232 - 0.310: 0 0.310 - 0.387: 1 Chirality restraints: 786 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ARG B 509 " pdb=" N ARG B 509 " pdb=" C ARG B 509 " pdb=" CB ARG B 509 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL B 382 " pdb=" CA VAL B 382 " pdb=" CG1 VAL B 382 " pdb=" CG2 VAL B 382 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 783 not shown) Planarity restraints: 938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.095 2.00e-02 2.50e+03 1.38e-01 2.40e+02 pdb=" CG ASN B 343 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.243 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN F 79 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.87e+00 pdb=" N PRO F 80 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 80 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 387 " -0.010 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C LEU B 387 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 387 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 388 " -0.013 2.00e-02 2.50e+03 ... (remaining 935 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 14 2.44 - 3.05: 3147 3.05 - 3.67: 7333 3.67 - 4.28: 10603 4.28 - 4.90: 18849 Nonbonded interactions: 39946 Sorted by model distance: nonbonded pdb=" OD1 ASN B 343 " pdb=" O7 NAG O 1 " model vdw 1.820 3.040 nonbonded pdb=" OH TYR F 97 " pdb=" O ILE G 104 " model vdw 2.134 2.440 nonbonded pdb=" OD1 ASP B 420 " pdb=" ND2 ASN B 460 " model vdw 2.185 2.520 nonbonded pdb=" NH1 ARG F 61 " pdb=" OD2 ASP F 82 " model vdw 2.304 2.520 nonbonded pdb=" NH2 ARG K 67 " pdb=" OD2 ASP K 90 " model vdw 2.316 2.520 ... (remaining 39941 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 'F' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' } 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: 7.380 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: 26.950 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.840 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 0.064 5338 Z= 0.314 Angle : 0.712 5.729 7253 Z= 0.433 Chirality : 0.050 0.387 786 Planarity : 0.004 0.070 937 Dihedral : 14.978 109.847 1922 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -1.78 (0.32), residues: 661 helix: -3.72 (0.75), residues: 27 sheet: -0.67 (0.32), residues: 280 loop : -1.37 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 47 HIS 0.001 0.000 HIS G 35 PHE 0.013 0.001 PHE J 83 TYR 0.019 0.001 TYR F 49 ARG 0.007 0.001 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.627 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2451 time to fit residues: 42.7577 Evaluate side-chains 118 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN K 77 ASN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 5338 Z= 0.392 Angle : 0.692 8.382 7253 Z= 0.354 Chirality : 0.049 0.343 786 Planarity : 0.004 0.039 937 Dihedral : 8.775 76.009 779 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.77 % Allowed : 11.70 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.32), residues: 661 helix: -3.60 (0.83), residues: 27 sheet: -0.44 (0.32), residues: 291 loop : -1.48 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 47 HIS 0.002 0.001 HIS K 35 PHE 0.018 0.002 PHE B 377 TYR 0.017 0.001 TYR B 495 ARG 0.006 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 0.568 Fit side-chains REVERT: K 91 THR cc_start: 0.8784 (p) cc_final: 0.8556 (p) outliers start: 10 outliers final: 7 residues processed: 133 average time/residue: 0.2057 time to fit residues: 33.8752 Evaluate side-chains 128 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5338 Z= 0.222 Angle : 0.606 9.017 7253 Z= 0.305 Chirality : 0.046 0.309 786 Planarity : 0.004 0.035 937 Dihedral : 6.610 49.316 779 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.60 % Allowed : 17.55 % Favored : 80.85 % 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: -1.69 (0.32), residues: 661 helix: -3.54 (0.84), residues: 27 sheet: -0.37 (0.31), residues: 291 loop : -1.58 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 47 HIS 0.002 0.001 HIS K 35 PHE 0.012 0.001 PHE B 392 TYR 0.011 0.001 TYR B 495 ARG 0.005 0.000 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: K 54 ASN cc_start: 0.8060 (p0) cc_final: 0.7771 (p0) outliers start: 9 outliers final: 6 residues processed: 134 average time/residue: 0.2168 time to fit residues: 35.9737 Evaluate side-chains 123 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 49 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 5338 Z= 0.365 Angle : 0.664 8.304 7253 Z= 0.336 Chirality : 0.047 0.301 786 Planarity : 0.004 0.037 937 Dihedral : 6.105 43.572 779 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.37 % Allowed : 18.79 % Favored : 77.84 % 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: -1.68 (0.32), residues: 661 helix: -3.50 (0.83), residues: 27 sheet: -0.40 (0.31), residues: 305 loop : -1.58 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 47 HIS 0.002 0.001 HIS K 35 PHE 0.031 0.002 PHE B 392 TYR 0.016 0.001 TYR B 495 ARG 0.005 0.001 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: K 54 ASN cc_start: 0.8156 (p0) cc_final: 0.7805 (p0) REVERT: K 91 THR cc_start: 0.8852 (p) cc_final: 0.8644 (p) outliers start: 19 outliers final: 12 residues processed: 137 average time/residue: 0.2111 time to fit residues: 35.8812 Evaluate side-chains 134 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 49 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 0.0000 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5338 Z= 0.207 Angle : 0.616 8.187 7253 Z= 0.308 Chirality : 0.045 0.284 786 Planarity : 0.004 0.035 937 Dihedral : 5.705 39.115 779 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.84 % Allowed : 20.57 % Favored : 76.60 % 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: -1.38 (0.32), residues: 661 helix: -3.51 (0.82), residues: 27 sheet: -0.05 (0.32), residues: 279 loop : -1.43 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 47 HIS 0.002 0.001 HIS K 35 PHE 0.031 0.001 PHE B 392 TYR 0.010 0.001 TYR B 495 ARG 0.006 0.000 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: K 54 ASN cc_start: 0.8036 (p0) cc_final: 0.7817 (p0) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 0.2084 time to fit residues: 34.1481 Evaluate side-chains 128 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 82 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 0.0040 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5338 Z= 0.140 Angle : 0.587 7.900 7253 Z= 0.292 Chirality : 0.044 0.270 786 Planarity : 0.003 0.033 937 Dihedral : 5.290 35.426 779 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.95 % Allowed : 21.99 % Favored : 76.06 % 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: -1.36 (0.32), residues: 661 helix: -3.27 (0.73), residues: 33 sheet: -0.03 (0.32), residues: 267 loop : -1.36 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS K 35 PHE 0.020 0.001 PHE B 392 TYR 0.008 0.001 TYR G 95 ARG 0.005 0.000 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 0.495 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 133 average time/residue: 0.2039 time to fit residues: 33.6431 Evaluate side-chains 127 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 34 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5338 Z= 0.237 Angle : 0.609 8.103 7253 Z= 0.304 Chirality : 0.045 0.269 786 Planarity : 0.003 0.033 937 Dihedral : 5.178 32.521 779 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.13 % Allowed : 22.34 % Favored : 75.53 % 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: -1.29 (0.32), residues: 661 helix: -3.50 (0.81), residues: 27 sheet: -0.01 (0.32), residues: 279 loop : -1.34 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 113 HIS 0.003 0.001 HIS K 35 PHE 0.021 0.001 PHE B 392 TYR 0.011 0.001 TYR B 495 ARG 0.006 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: B 474 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7198 (tm-30) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.2153 time to fit residues: 34.0099 Evaluate side-chains 128 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5338 Z= 0.203 Angle : 0.600 7.645 7253 Z= 0.300 Chirality : 0.045 0.263 786 Planarity : 0.003 0.033 937 Dihedral : 5.055 30.001 779 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.84 % Allowed : 21.99 % Favored : 75.18 % 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: -1.25 (0.32), residues: 661 helix: -3.51 (0.80), residues: 27 sheet: 0.03 (0.32), residues: 277 loop : -1.32 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 47 HIS 0.002 0.001 HIS K 35 PHE 0.019 0.001 PHE B 392 TYR 0.009 0.001 TYR B 495 ARG 0.007 0.000 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.583 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 131 average time/residue: 0.2059 time to fit residues: 33.7725 Evaluate side-chains 133 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5338 Z= 0.200 Angle : 0.610 7.344 7253 Z= 0.306 Chirality : 0.044 0.254 786 Planarity : 0.003 0.033 937 Dihedral : 4.886 26.106 779 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.66 % Allowed : 21.81 % Favored : 75.53 % 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: -1.19 (0.32), residues: 661 helix: -3.31 (0.72), residues: 33 sheet: 0.11 (0.32), residues: 277 loop : -1.27 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 47 HIS 0.002 0.001 HIS K 35 PHE 0.018 0.001 PHE B 392 TYR 0.009 0.001 TYR B 495 ARG 0.006 0.000 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: B 516 GLU cc_start: 0.7464 (mp0) cc_final: 0.7095 (mp0) outliers start: 15 outliers final: 14 residues processed: 130 average time/residue: 0.2049 time to fit residues: 33.0408 Evaluate side-chains 134 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5338 Z= 0.210 Angle : 0.612 7.376 7253 Z= 0.308 Chirality : 0.045 0.249 786 Planarity : 0.003 0.033 937 Dihedral : 4.828 23.406 779 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.48 % Allowed : 21.99 % Favored : 75.53 % 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: -1.19 (0.32), residues: 661 helix: -3.34 (0.71), residues: 33 sheet: 0.10 (0.32), residues: 278 loop : -1.27 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 47 HIS 0.002 0.001 HIS K 35 PHE 0.017 0.001 PHE B 392 TYR 0.009 0.001 TYR B 369 ARG 0.006 0.000 ARG K 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: B 516 GLU cc_start: 0.7477 (mp0) cc_final: 0.7109 (mp0) outliers start: 14 outliers final: 13 residues processed: 128 average time/residue: 0.2067 time to fit residues: 33.0350 Evaluate side-chains 129 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.0020 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073099 restraints weight = 12087.017| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.89 r_work: 0.2945 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5338 Z= 0.170 Angle : 0.592 7.061 7253 Z= 0.298 Chirality : 0.044 0.240 786 Planarity : 0.003 0.032 937 Dihedral : 4.617 22.380 779 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.84 % Allowed : 21.81 % Favored : 75.35 % 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: -1.21 (0.32), residues: 661 helix: -3.34 (0.70), residues: 33 sheet: 0.08 (0.33), residues: 267 loop : -1.24 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS K 35 PHE 0.014 0.001 PHE B 392 TYR 0.008 0.001 TYR G 95 ARG 0.006 0.000 ARG G 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.09 seconds wall clock time: 37 minutes 39.90 seconds (2259.90 seconds total)