Starting phenix.real_space_refine on Mon Mar 11 03:01:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp6_32676/03_2024/7wp6_32676.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp6_32676/03_2024/7wp6_32676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp6_32676/03_2024/7wp6_32676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp6_32676/03_2024/7wp6_32676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp6_32676/03_2024/7wp6_32676.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp6_32676/03_2024/7wp6_32676.pdb" } resolution = 3.81 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= -0.000 sd= 0.011 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 30 5.16 5 C 4278 2.51 5 N 1111 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 340": "OE1" <-> "OE2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ARG 408": "NH1" <-> "NH2" Residue "F ARG 466": "NH1" <-> "NH2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6748 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "D" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 930 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "I" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 875 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 791 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" 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 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.37, per 1000 atoms: 0.65 Number of scatterers: 6748 At special positions: 0 Unit cell: (77.022, 109.698, 126.036, 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 30 16.00 O 1329 8.00 N 1111 7.00 C 4278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.72 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 94 " distance=2.04 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 A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " " NAG L 201 " - " ASN L 26 " Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 18 sheets defined 1.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.893A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'I' and resid 85 through 89 removed outlier: 3.826A pdb=" N LEU I 89 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.748A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.687A pdb=" N THR B 117 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 12 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 38 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU B 46 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 59 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.108A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.617A pdb=" N THR C 63 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.618A pdb=" N THR C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 38 " --> pdb=" O ASP C 85 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP C 85 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.711A pdb=" N THR D 117 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.711A pdb=" N THR D 117 " --> pdb=" O GLU D 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.722A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.507A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.901A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.711A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE H 95 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 37 " --> pdb=" O PHE H 95 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.711A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE H 107 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.813A pdb=" N SER I 5 " --> pdb=" O LYS I 24 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS I 23 " --> pdb=" O PHE I 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP I 76 " --> pdb=" O SER I 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 30 through 31 removed outlier: 3.506A pdb=" N LYS I 36 " --> pdb=" O TYR I 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 51 through 52 removed outlier: 4.011A pdb=" N CYS I 94 " --> pdb=" O GLY I 105 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY I 105 " --> pdb=" O CYS I 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.772A pdb=" N SER L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER L 66 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.683A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP L 46 " --> pdb=" O TRP L 34 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 402 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: 1.73 Time building geometry restraints manager: 2.77 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: 2091 1.34 - 1.46: 1794 1.46 - 1.58: 2997 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 6922 Sorted by residual: bond pdb=" C TYR H 52 " pdb=" N PRO H 53 " ideal model delta sigma weight residual 1.337 1.307 0.030 1.06e-02 8.90e+03 7.91e+00 bond pdb=" CA CYS H 22 " pdb=" CB CYS H 22 " ideal model delta sigma weight residual 1.524 1.486 0.037 1.62e-02 3.81e+03 5.34e+00 bond pdb=" CA ALA L 25 " pdb=" C ALA L 25 " ideal model delta sigma weight residual 1.522 1.496 0.026 1.23e-02 6.61e+03 4.49e+00 bond pdb=" C VAL I 64 " pdb=" N PRO I 65 " ideal model delta sigma weight residual 1.331 1.356 -0.025 1.20e-02 6.94e+03 4.41e+00 bond pdb=" CA ALA F 344 " pdb=" C ALA F 344 " ideal model delta sigma weight residual 1.526 1.497 0.028 1.36e-02 5.41e+03 4.28e+00 ... (remaining 6917 not shown) Histogram of bond angle deviations from ideal: 98.61 - 106.29: 171 106.29 - 113.97: 3764 113.97 - 121.65: 3703 121.65 - 129.33: 1708 129.33 - 137.01: 52 Bond angle restraints: 9398 Sorted by residual: angle pdb=" N SER L 27 " pdb=" CA SER L 27 " pdb=" C SER L 27 " ideal model delta sigma weight residual 110.80 120.85 -10.05 2.13e+00 2.20e-01 2.22e+01 angle pdb=" C GLN I 48 " pdb=" N SER I 49 " pdb=" CA SER I 49 " ideal model delta sigma weight residual 121.27 137.01 -15.74 3.40e+00 8.65e-02 2.14e+01 angle pdb=" C TYR L 48 " pdb=" N ALA L 49 " pdb=" CA ALA L 49 " ideal model delta sigma weight residual 121.19 128.35 -7.16 1.59e+00 3.96e-01 2.03e+01 angle pdb=" N PHE I 100 " pdb=" CA PHE I 100 " pdb=" C PHE I 100 " ideal model delta sigma weight residual 109.81 119.75 -9.94 2.21e+00 2.05e-01 2.02e+01 angle pdb=" C SER B 40 " pdb=" N HIS B 41 " pdb=" CA HIS B 41 " ideal model delta sigma weight residual 122.36 128.23 -5.87 1.42e+00 4.96e-01 1.71e+01 ... (remaining 9393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 3544 16.61 - 33.21: 450 33.21 - 49.82: 75 49.82 - 66.43: 12 66.43 - 83.03: 9 Dihedral angle restraints: 4090 sinusoidal: 1608 harmonic: 2482 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 169.57 -76.57 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CA TRP C 50 " pdb=" C TRP C 50 " pdb=" N ALA C 51 " pdb=" CA ALA C 51 " ideal model delta harmonic sigma weight residual -180.00 -144.27 -35.73 0 5.00e+00 4.00e-02 5.11e+01 dihedral pdb=" CB CYS F 480 " pdb=" SG CYS F 480 " pdb=" SG CYS F 488 " pdb=" CB CYS F 488 " ideal model delta sinusoidal sigma weight residual -86.00 -133.21 47.21 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 4087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 859 0.079 - 0.159: 126 0.159 - 0.238: 14 0.238 - 0.318: 3 0.318 - 0.397: 4 Chirality restraints: 1006 Sorted by residual: chirality pdb=" CA SER L 27 " pdb=" N SER L 27 " pdb=" C SER L 27 " pdb=" CB SER L 27 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB THR C 102 " pdb=" CA THR C 102 " pdb=" OG1 THR C 102 " pdb=" CG2 THR C 102 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1003 not shown) Planarity restraints: 1201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 201 " 0.328 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG L 201 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG L 201 " 0.046 2.00e-02 2.50e+03 pdb=" N2 NAG L 201 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG L 201 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.240 2.00e-02 2.50e+03 2.05e-01 5.26e+02 pdb=" C7 NAG A 1 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.341 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.122 2.00e-02 2.50e+03 1.01e-01 1.27e+02 pdb=" C7 NAG A 2 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.162 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.018 2.00e-02 2.50e+03 ... (remaining 1198 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1243 2.76 - 3.29: 5754 3.29 - 3.83: 10868 3.83 - 4.36: 11903 4.36 - 4.90: 21382 Nonbonded interactions: 51150 Sorted by model distance: nonbonded pdb=" O ASP C 30 " pdb=" OD1 ASP C 30 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR F 478 " pdb=" O TYR I 98 " model vdw 2.254 2.440 nonbonded pdb=" O SER F 438 " pdb=" OG SER F 438 " model vdw 2.276 2.440 nonbonded pdb=" OD1 ASP F 442 " pdb=" OH TYR F 451 " model vdw 2.318 2.440 nonbonded pdb=" O THR D 114 " pdb=" OG1 THR D 114 " model vdw 2.321 2.440 ... (remaining 51145 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.250 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: 0.000 Extract box with map and model: 13.210 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.460 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.008 0.061 6922 Z= 0.493 Angle : 1.066 15.738 9398 Z= 0.594 Chirality : 0.062 0.397 1006 Planarity : 0.013 0.284 1199 Dihedral : 14.824 83.035 2501 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.45 % Favored : 90.44 % Rotamer: Outliers : 0.69 % Allowed : 12.07 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.24), residues: 847 helix: -5.32 (0.38), residues: 8 sheet: -1.64 (0.29), residues: 290 loop : -3.20 (0.21), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP I 56 HIS 0.006 0.003 HIS H 35 PHE 0.029 0.003 PHE I 100 TYR 0.032 0.003 TYR I 55 ARG 0.006 0.001 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 242 time to evaluate : 0.810 Fit side-chains REVERT: B 10 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8433 (mp0) REVERT: C 27 GLN cc_start: 0.7769 (mp10) cc_final: 0.7190 (mp10) REVERT: C 54 ARG cc_start: 0.8072 (ptp90) cc_final: 0.7803 (ptp90) REVERT: D 83 LEU cc_start: 0.9041 (mt) cc_final: 0.8733 (mp) REVERT: F 414 GLN cc_start: 0.7616 (tt0) cc_final: 0.7164 (mp10) REVERT: F 465 GLU cc_start: 0.8573 (tp30) cc_final: 0.8229 (tp30) REVERT: H 73 ASP cc_start: 0.7839 (m-30) cc_final: 0.7029 (p0) outliers start: 5 outliers final: 4 residues processed: 245 average time/residue: 0.2160 time to fit residues: 66.9458 Evaluate side-chains 194 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain I residue 42 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 10.0000 chunk 62 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN C 38 GLN C 79 GLN C 90 GLN D 62 GLN D 82 GLN F 370 ASN F 487 ASN F 493 GLN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6922 Z= 0.201 Angle : 0.660 12.638 9398 Z= 0.335 Chirality : 0.044 0.212 1006 Planarity : 0.005 0.059 1199 Dihedral : 6.145 40.937 1015 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.39 % Rotamer: Outliers : 3.16 % Allowed : 23.59 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.26), residues: 847 helix: -5.23 (0.43), residues: 8 sheet: -1.01 (0.27), residues: 352 loop : -2.83 (0.24), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 56 HIS 0.003 0.001 HIS L 33 PHE 0.026 0.002 PHE I 100 TYR 0.021 0.002 TYR I 42 ARG 0.003 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7732 (m-80) cc_final: 0.7360 (m-80) REVERT: B 89 GLU cc_start: 0.7263 (mp0) cc_final: 0.7041 (mp0) REVERT: C 18 ARG cc_start: 0.4472 (OUTLIER) cc_final: 0.3619 (ttp-110) REVERT: C 27 GLN cc_start: 0.7708 (mp10) cc_final: 0.7270 (mp10) REVERT: C 54 ARG cc_start: 0.7903 (ptp90) cc_final: 0.7557 (ptp90) REVERT: D 60 TYR cc_start: 0.8584 (m-10) cc_final: 0.8170 (m-80) REVERT: D 80 TYR cc_start: 0.7903 (m-80) cc_final: 0.7566 (m-10) REVERT: F 414 GLN cc_start: 0.7455 (tt0) cc_final: 0.6987 (mp10) REVERT: F 465 GLU cc_start: 0.8544 (tp30) cc_final: 0.8311 (tp30) REVERT: H 38 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8429 (ttmm) REVERT: I 41 TRP cc_start: 0.8569 (m100) cc_final: 0.8284 (m100) REVERT: L 38 LYS cc_start: 0.9203 (tppp) cc_final: 0.8684 (ttpt) outliers start: 23 outliers final: 15 residues processed: 213 average time/residue: 0.2072 time to fit residues: 56.0882 Evaluate side-chains 200 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN D 82 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 GLN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6922 Z= 0.255 Angle : 0.666 13.548 9398 Z= 0.335 Chirality : 0.044 0.209 1006 Planarity : 0.005 0.058 1199 Dihedral : 6.035 45.284 1015 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.32 % Favored : 92.56 % Rotamer: Outliers : 6.17 % Allowed : 22.09 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.27), residues: 847 helix: -5.18 (0.46), residues: 8 sheet: -0.78 (0.27), residues: 357 loop : -2.73 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 56 HIS 0.004 0.001 HIS L 33 PHE 0.023 0.002 PHE I 100 TYR 0.021 0.002 TYR I 42 ARG 0.003 0.001 ARG L 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 191 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 LYS cc_start: 0.9187 (tttm) cc_final: 0.8906 (tttm) REVERT: B 89 GLU cc_start: 0.7340 (mp0) cc_final: 0.7063 (mp0) REVERT: C 18 ARG cc_start: 0.4646 (OUTLIER) cc_final: 0.3833 (ttp-110) REVERT: C 54 ARG cc_start: 0.7937 (ptp90) cc_final: 0.7505 (ptp90) REVERT: D 46 GLU cc_start: 0.7382 (tt0) cc_final: 0.7160 (mt-10) REVERT: D 60 TYR cc_start: 0.8606 (m-10) cc_final: 0.8159 (m-80) REVERT: F 414 GLN cc_start: 0.7433 (tt0) cc_final: 0.6940 (mp10) REVERT: F 465 GLU cc_start: 0.8586 (tp30) cc_final: 0.8370 (tp30) REVERT: H 38 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8648 (ttmm) REVERT: I 41 TRP cc_start: 0.8584 (m100) cc_final: 0.8303 (m100) REVERT: I 95 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: L 38 LYS cc_start: 0.9236 (tppp) cc_final: 0.8679 (ttpt) outliers start: 45 outliers final: 31 residues processed: 209 average time/residue: 0.2114 time to fit residues: 56.5293 Evaluate side-chains 220 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 72 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN D 82 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6922 Z= 0.276 Angle : 0.665 13.344 9398 Z= 0.333 Chirality : 0.043 0.210 1006 Planarity : 0.004 0.055 1199 Dihedral : 6.093 50.055 1015 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.26 % Favored : 91.62 % Rotamer: Outliers : 7.54 % Allowed : 21.95 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.28), residues: 847 helix: -5.13 (0.51), residues: 8 sheet: -0.60 (0.29), residues: 338 loop : -2.63 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 56 HIS 0.003 0.001 HIS L 33 PHE 0.024 0.002 PHE I 100 TYR 0.021 0.002 TYR I 42 ARG 0.003 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 190 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.8228 (m) cc_final: 0.7835 (p) REVERT: B 63 LYS cc_start: 0.9249 (tttm) cc_final: 0.8891 (tttm) REVERT: B 89 GLU cc_start: 0.7347 (mp0) cc_final: 0.7049 (mp0) REVERT: C 18 ARG cc_start: 0.4812 (OUTLIER) cc_final: 0.3972 (ttp-110) REVERT: C 54 ARG cc_start: 0.7940 (ptp90) cc_final: 0.7497 (ptp90) REVERT: D 46 GLU cc_start: 0.7418 (tt0) cc_final: 0.7177 (mt-10) REVERT: D 60 TYR cc_start: 0.8634 (m-10) cc_final: 0.8147 (m-80) REVERT: D 88 SER cc_start: 0.8862 (m) cc_final: 0.8550 (p) REVERT: F 414 GLN cc_start: 0.7470 (tt0) cc_final: 0.6977 (mp10) REVERT: F 472 ILE cc_start: 0.6328 (mm) cc_final: 0.6104 (mm) REVERT: H 38 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8509 (ttmm) REVERT: I 21 MET cc_start: 0.5791 (mmm) cc_final: 0.5524 (mmm) REVERT: I 41 TRP cc_start: 0.8566 (m100) cc_final: 0.8322 (m100) REVERT: L 6 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7152 (mt0) REVERT: L 11 LEU cc_start: 0.8494 (mt) cc_final: 0.8236 (mt) REVERT: L 38 LYS cc_start: 0.9220 (tppp) cc_final: 0.8686 (ttpt) outliers start: 55 outliers final: 39 residues processed: 215 average time/residue: 0.2100 time to fit residues: 57.9602 Evaluate side-chains 223 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 182 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 0.0570 chunk 20 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN D 82 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6922 Z= 0.172 Angle : 0.636 12.702 9398 Z= 0.314 Chirality : 0.043 0.169 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.644 47.301 1015 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.73 % Favored : 93.15 % Rotamer: Outliers : 5.62 % Allowed : 24.97 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.28), residues: 847 helix: -4.82 (0.76), residues: 8 sheet: -0.54 (0.28), residues: 339 loop : -2.43 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 56 HIS 0.002 0.001 HIS H 35 PHE 0.020 0.001 PHE I 100 TYR 0.023 0.001 TYR F 380 ARG 0.004 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8185 (m) cc_final: 0.7839 (p) REVERT: B 38 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7681 (ttpp) REVERT: B 63 LYS cc_start: 0.9242 (tttm) cc_final: 0.8830 (tttp) REVERT: B 89 GLU cc_start: 0.7380 (mp0) cc_final: 0.7141 (mp0) REVERT: C 54 ARG cc_start: 0.7810 (ptp90) cc_final: 0.7362 (ptp90) REVERT: D 46 GLU cc_start: 0.7337 (tt0) cc_final: 0.7088 (mt-10) REVERT: D 60 TYR cc_start: 0.8623 (m-10) cc_final: 0.7812 (m-80) REVERT: D 88 SER cc_start: 0.8798 (m) cc_final: 0.8504 (p) REVERT: F 414 GLN cc_start: 0.7320 (tt0) cc_final: 0.6890 (mp10) REVERT: F 472 ILE cc_start: 0.6298 (mm) cc_final: 0.6048 (mm) REVERT: H 3 GLN cc_start: 0.8350 (tt0) cc_final: 0.7916 (tm-30) REVERT: H 38 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8454 (ttmm) REVERT: L 38 LYS cc_start: 0.9214 (tppp) cc_final: 0.8675 (ttpt) REVERT: L 76 ARG cc_start: 0.7959 (tmm-80) cc_final: 0.7466 (mmp80) outliers start: 41 outliers final: 29 residues processed: 222 average time/residue: 0.2014 time to fit residues: 57.5853 Evaluate side-chains 219 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN H 101 HIS ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6922 Z= 0.217 Angle : 0.665 12.661 9398 Z= 0.327 Chirality : 0.042 0.178 1006 Planarity : 0.004 0.055 1199 Dihedral : 5.594 45.992 1015 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.32 % Favored : 92.56 % Rotamer: Outliers : 6.31 % Allowed : 24.55 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.28), residues: 847 helix: -4.65 (0.92), residues: 8 sheet: -0.32 (0.29), residues: 329 loop : -2.29 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 41 HIS 0.002 0.001 HIS H 101 PHE 0.019 0.001 PHE I 100 TYR 0.024 0.002 TYR F 380 ARG 0.003 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.8218 (m) cc_final: 0.8010 (p) REVERT: B 63 LYS cc_start: 0.9254 (tttm) cc_final: 0.8850 (tttp) REVERT: B 89 GLU cc_start: 0.7411 (mp0) cc_final: 0.7162 (mp0) REVERT: C 18 ARG cc_start: 0.4928 (OUTLIER) cc_final: 0.4140 (ttp-110) REVERT: C 54 ARG cc_start: 0.7873 (ptp90) cc_final: 0.7418 (ptp90) REVERT: D 46 GLU cc_start: 0.7418 (tt0) cc_final: 0.7179 (mt-10) REVERT: D 60 TYR cc_start: 0.8784 (m-10) cc_final: 0.8248 (m-80) REVERT: D 88 SER cc_start: 0.8811 (m) cc_final: 0.8519 (p) REVERT: F 414 GLN cc_start: 0.7306 (tt0) cc_final: 0.6866 (mp10) REVERT: F 472 ILE cc_start: 0.6329 (mm) cc_final: 0.6114 (mm) REVERT: H 3 GLN cc_start: 0.8397 (tt0) cc_final: 0.7911 (tm-30) REVERT: H 38 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8526 (ttmm) REVERT: I 41 TRP cc_start: 0.8477 (m100) cc_final: 0.8227 (m100) REVERT: L 38 LYS cc_start: 0.9226 (tppp) cc_final: 0.8699 (ttpt) REVERT: L 76 ARG cc_start: 0.7916 (tmm-80) cc_final: 0.7332 (mmp80) outliers start: 46 outliers final: 41 residues processed: 219 average time/residue: 0.2070 time to fit residues: 58.0632 Evaluate side-chains 228 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 0.0980 chunk 57 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6922 Z= 0.192 Angle : 0.661 12.576 9398 Z= 0.325 Chirality : 0.042 0.164 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.515 48.117 1015 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 6.72 % Allowed : 24.28 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.28), residues: 847 helix: -4.50 (1.06), residues: 8 sheet: -0.34 (0.29), residues: 330 loop : -2.21 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 56 HIS 0.002 0.001 HIS H 35 PHE 0.042 0.002 PHE F 456 TYR 0.023 0.002 TYR F 380 ARG 0.004 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: B 63 LYS cc_start: 0.9292 (tttm) cc_final: 0.8902 (tttm) REVERT: B 89 GLU cc_start: 0.7419 (mp0) cc_final: 0.7174 (mp0) REVERT: C 54 ARG cc_start: 0.7825 (ptp90) cc_final: 0.7371 (ptp90) REVERT: D 23 LYS cc_start: 0.8314 (tttm) cc_final: 0.7889 (ttmm) REVERT: D 46 GLU cc_start: 0.7393 (tt0) cc_final: 0.7138 (mt-10) REVERT: D 88 SER cc_start: 0.8793 (m) cc_final: 0.8511 (p) REVERT: F 414 GLN cc_start: 0.7257 (tt0) cc_final: 0.6860 (mp10) REVERT: H 38 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8532 (ttmm) REVERT: H 80 TYR cc_start: 0.7929 (m-80) cc_final: 0.7666 (m-80) REVERT: I 21 MET cc_start: 0.5755 (mmm) cc_final: 0.5336 (mmm) REVERT: L 38 LYS cc_start: 0.9218 (tppp) cc_final: 0.8694 (ttpt) REVERT: L 76 ARG cc_start: 0.7841 (tmm-80) cc_final: 0.7221 (mmp80) outliers start: 49 outliers final: 43 residues processed: 215 average time/residue: 0.2071 time to fit residues: 56.8591 Evaluate side-chains 233 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 189 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN D 82 GLN H 3 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6922 Z= 0.285 Angle : 0.708 12.493 9398 Z= 0.350 Chirality : 0.043 0.193 1006 Planarity : 0.004 0.056 1199 Dihedral : 5.826 49.633 1015 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.09 % Favored : 90.79 % Rotamer: Outliers : 7.82 % Allowed : 23.32 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.28), residues: 847 helix: -4.43 (1.13), residues: 8 sheet: -0.33 (0.29), residues: 329 loop : -2.22 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 56 HIS 0.002 0.001 HIS L 33 PHE 0.028 0.002 PHE F 456 TYR 0.021 0.002 TYR I 42 ARG 0.003 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 181 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: B 89 GLU cc_start: 0.7451 (mp0) cc_final: 0.7195 (mp0) REVERT: C 18 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.4222 (ttp-110) REVERT: D 23 LYS cc_start: 0.8376 (tttm) cc_final: 0.7900 (ttmm) REVERT: D 46 GLU cc_start: 0.7391 (tt0) cc_final: 0.7184 (mt-10) REVERT: D 88 SER cc_start: 0.8795 (m) cc_final: 0.8494 (p) REVERT: F 414 GLN cc_start: 0.7369 (tt0) cc_final: 0.6972 (mp10) REVERT: H 38 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8534 (ttmm) REVERT: H 80 TYR cc_start: 0.8044 (m-80) cc_final: 0.7742 (m-80) REVERT: I 21 MET cc_start: 0.5728 (mmm) cc_final: 0.5427 (mmm) REVERT: I 51 LYS cc_start: 0.9019 (tptt) cc_final: 0.8814 (tptt) REVERT: I 76 ASP cc_start: 0.8365 (t70) cc_final: 0.8142 (t0) REVERT: I 97 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8149 (p90) REVERT: L 38 LYS cc_start: 0.9227 (tppp) cc_final: 0.8694 (ttpt) outliers start: 57 outliers final: 48 residues processed: 210 average time/residue: 0.2133 time to fit residues: 57.4306 Evaluate side-chains 227 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 176 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 32 optimal weight: 0.0270 chunk 57 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN H 3 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6922 Z= 0.192 Angle : 0.665 12.103 9398 Z= 0.327 Chirality : 0.043 0.164 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.607 50.263 1015 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.73 % Favored : 93.15 % Rotamer: Outliers : 6.58 % Allowed : 24.83 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.28), residues: 847 helix: -4.22 (1.33), residues: 8 sheet: -0.35 (0.29), residues: 324 loop : -2.20 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 56 HIS 0.002 0.001 HIS L 33 PHE 0.047 0.002 PHE F 456 TYR 0.022 0.002 TYR I 42 ARG 0.003 0.000 ARG L 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: B 63 LYS cc_start: 0.9313 (tttm) cc_final: 0.9001 (tttm) REVERT: B 89 GLU cc_start: 0.7452 (mp0) cc_final: 0.7207 (mp0) REVERT: D 23 LYS cc_start: 0.8351 (tttm) cc_final: 0.7935 (ttmm) REVERT: D 46 GLU cc_start: 0.7354 (tt0) cc_final: 0.7027 (mt-10) REVERT: D 88 SER cc_start: 0.8770 (m) cc_final: 0.8489 (p) REVERT: F 414 GLN cc_start: 0.7325 (tt0) cc_final: 0.6938 (mp10) REVERT: H 38 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8601 (ttmm) REVERT: H 80 TYR cc_start: 0.7985 (m-80) cc_final: 0.7694 (m-80) REVERT: L 38 LYS cc_start: 0.9221 (tppp) cc_final: 0.8684 (ttpt) outliers start: 48 outliers final: 41 residues processed: 208 average time/residue: 0.2006 time to fit residues: 53.6885 Evaluate side-chains 219 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 177 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 0.0000 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN H 3 GLN I 27 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6922 Z= 0.200 Angle : 0.680 11.738 9398 Z= 0.334 Chirality : 0.043 0.159 1006 Planarity : 0.004 0.055 1199 Dihedral : 5.584 50.880 1015 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.67 % Favored : 92.21 % Rotamer: Outliers : 6.17 % Allowed : 25.65 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.28), residues: 847 helix: -4.17 (1.37), residues: 8 sheet: -0.37 (0.29), residues: 324 loop : -2.13 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 56 HIS 0.002 0.001 HIS L 33 PHE 0.039 0.001 PHE F 456 TYR 0.022 0.002 TYR I 42 ARG 0.003 0.000 ARG L 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 0.753 Fit side-chains REVERT: B 63 LYS cc_start: 0.9313 (tttm) cc_final: 0.9034 (tttm) REVERT: B 89 GLU cc_start: 0.7444 (mp0) cc_final: 0.7206 (mp0) REVERT: D 10 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6939 (tm-30) REVERT: D 23 LYS cc_start: 0.8343 (tttm) cc_final: 0.7957 (ttmm) REVERT: D 46 GLU cc_start: 0.7222 (tt0) cc_final: 0.6961 (mt-10) REVERT: D 88 SER cc_start: 0.8764 (m) cc_final: 0.8495 (p) REVERT: F 414 GLN cc_start: 0.7322 (tt0) cc_final: 0.6989 (mp10) REVERT: H 38 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8583 (ttmm) REVERT: H 80 TYR cc_start: 0.7977 (m-80) cc_final: 0.7704 (m-80) REVERT: I 21 MET cc_start: 0.5747 (mmm) cc_final: 0.5347 (mmm) REVERT: L 38 LYS cc_start: 0.9227 (tppp) cc_final: 0.8693 (ttpt) REVERT: L 76 ARG cc_start: 0.7222 (mmp80) cc_final: 0.6864 (mmp80) outliers start: 45 outliers final: 41 residues processed: 203 average time/residue: 0.2113 time to fit residues: 55.0428 Evaluate side-chains 220 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 178 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN I 27 GLN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107187 restraints weight = 12388.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110636 restraints weight = 8064.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112971 restraints weight = 6156.328| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6922 Z= 0.234 Angle : 0.690 11.721 9398 Z= 0.340 Chirality : 0.043 0.170 1006 Planarity : 0.004 0.055 1199 Dihedral : 5.669 50.676 1015 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.62 % Favored : 91.26 % Rotamer: Outliers : 6.72 % Allowed : 25.38 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.28), residues: 847 helix: -4.22 (1.33), residues: 8 sheet: -0.37 (0.29), residues: 325 loop : -2.14 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 56 HIS 0.003 0.001 HIS L 33 PHE 0.037 0.002 PHE F 456 TYR 0.021 0.002 TYR D 32 ARG 0.003 0.000 ARG L 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2024.35 seconds wall clock time: 37 minutes 36.37 seconds (2256.37 seconds total)