Starting phenix.real_space_refine on Tue Feb 13 16:01:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whz_32516/02_2024/7whz_32516.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whz_32516/02_2024/7whz_32516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whz_32516/02_2024/7whz_32516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whz_32516/02_2024/7whz_32516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whz_32516/02_2024/7whz_32516.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whz_32516/02_2024/7whz_32516.pdb" } resolution = 3.42 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= 0.015 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 4288 2.51 5 N 1142 2.21 5 O 1350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "B" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" 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: 4.29, per 1000 atoms: 0.63 Number of scatterers: 6810 At special positions: 0 Unit cell: (81.69, 94.916, 119.812, 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 1350 8.00 N 1142 7.00 C 4288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.6 seconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 23 sheets defined 2.6% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.578A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.735A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.610A pdb=" N ASP C 90 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.576A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.555A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.538A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.988A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 81 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.668A pdb=" N TYR C 59 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS C 35 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS C 96 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TRP C 112 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS C 98 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.051A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.737A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.737A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 90 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB6, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.699A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.568A pdb=" N ASN H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 68 through 69 removed outlier: 3.609A pdb=" N THR H 69 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.524A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.503A pdb=" N SER L 67 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 36 through 40 Processing sheet with id=AC5, first strand: chain 'L' and resid 36 through 40 163 hydrogen bonds defined for protein. 381 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: 1.83 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2184 1.35 - 1.47: 1977 1.47 - 1.60: 2773 1.60 - 1.73: 0 1.73 - 1.86: 40 Bond restraints: 6974 Sorted by residual: bond pdb=" C LYS L 106 " pdb=" O LYS L 106 " ideal model delta sigma weight residual 1.235 1.273 -0.038 1.13e-02 7.83e+03 1.13e+01 bond pdb=" CA THR H 117 " pdb=" CB THR H 117 " ideal model delta sigma weight residual 1.527 1.450 0.078 2.48e-02 1.63e+03 9.81e+00 bond pdb=" CA TYR D 87 " pdb=" C TYR D 87 " ideal model delta sigma weight residual 1.526 1.496 0.029 1.36e-02 5.41e+03 4.67e+00 bond pdb=" CB VAL B 50 " pdb=" CG2 VAL B 50 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.49e+00 ... (remaining 6969 not shown) Histogram of bond angle deviations from ideal: 98.90 - 106.25: 182 106.25 - 113.60: 3682 113.60 - 120.94: 3193 120.94 - 128.29: 2368 128.29 - 135.64: 52 Bond angle restraints: 9477 Sorted by residual: angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 110.17 121.04 -10.87 1.61e+00 3.86e-01 4.56e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.95 120.55 -10.60 1.59e+00 3.96e-01 4.45e+01 angle pdb=" N ASN A 394 " pdb=" CA ASN A 394 " pdb=" C ASN A 394 " ideal model delta sigma weight residual 108.99 117.30 -8.31 1.57e+00 4.06e-01 2.80e+01 angle pdb=" C GLU E 50 " pdb=" N THR E 51 " pdb=" CA THR E 51 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 angle pdb=" N LYS L 106 " pdb=" CA LYS L 106 " pdb=" C LYS L 106 " ideal model delta sigma weight residual 108.02 98.90 9.12 1.78e+00 3.16e-01 2.62e+01 ... (remaining 9472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3662 17.53 - 35.07: 361 35.07 - 52.60: 67 52.60 - 70.14: 10 70.14 - 87.67: 4 Dihedral angle restraints: 4104 sinusoidal: 1569 harmonic: 2535 Sorted by residual: dihedral pdb=" CA GLY A 447 " pdb=" C GLY A 447 " pdb=" N ASN A 448 " pdb=" CA ASN A 448 " ideal model delta harmonic sigma weight residual -180.00 -149.32 -30.68 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA GLY B 105 " pdb=" C GLY B 105 " pdb=" N SER B 106 " pdb=" CA SER B 106 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 764 0.058 - 0.116: 204 0.116 - 0.174: 44 0.174 - 0.232: 12 0.232 - 0.290: 2 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CB ILE B 70 " pdb=" CA ILE B 70 " pdb=" CG1 ILE B 70 " pdb=" CG2 ILE B 70 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA TYR E 94 " pdb=" N TYR E 94 " pdb=" C TYR E 94 " pdb=" CB TYR E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL D 58 " pdb=" CA VAL D 58 " pdb=" CG1 VAL D 58 " pdb=" CG2 VAL D 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1023 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 58 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO D 59 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 94 " 0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO E 95 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO L 46 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " 0.033 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1976 2.80 - 3.33: 5469 3.33 - 3.85: 11092 3.85 - 4.38: 12404 4.38 - 4.90: 22385 Nonbonded interactions: 53326 Sorted by model distance: nonbonded pdb=" OG SER H 102 " pdb=" O TYR H 105 " model vdw 2.276 2.440 nonbonded pdb=" O SER L 26 " pdb=" OG SER L 31 " model vdw 2.305 2.440 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 117 " model vdw 2.306 2.440 nonbonded pdb=" O ASP A 442 " pdb=" ND2 ASN A 448 " model vdw 2.321 2.520 nonbonded pdb=" OD1 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.324 2.440 ... (remaining 53321 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 'D' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) selection = (chain 'E' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) } 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=0.50 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: 4.770 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: 13.460 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.360 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.007 0.078 6974 Z= 0.470 Angle : 0.937 17.228 9477 Z= 0.536 Chirality : 0.059 0.290 1026 Planarity : 0.007 0.069 1225 Dihedral : 14.214 87.672 2478 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.40 % Allowed : 9.69 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -4.20 (0.24), residues: 873 helix: -5.10 (0.18), residues: 24 sheet: -2.74 (0.24), residues: 349 loop : -2.73 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 52 HIS 0.006 0.001 HIS B 35 PHE 0.024 0.002 PHE E 83 TYR 0.026 0.002 TYR A 453 ARG 0.007 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7602 (m-10) REVERT: B 25 SER cc_start: 0.8764 (t) cc_final: 0.8403 (m) REVERT: C 105 LEU cc_start: 0.8011 (pp) cc_final: 0.7789 (pt) REVERT: D 33 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8201 (tp) REVERT: E 70 GLU cc_start: 0.8315 (pt0) cc_final: 0.8096 (pt0) REVERT: H 62 GLN cc_start: 0.8295 (tm-30) cc_final: 0.8005 (tp40) REVERT: H 74 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7174 (tm-30) REVERT: L 67 SER cc_start: 0.7561 (t) cc_final: 0.7275 (p) outliers start: 3 outliers final: 0 residues processed: 193 average time/residue: 0.2133 time to fit residues: 52.8735 Evaluate side-chains 138 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 0.0870 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 354 ASN A 360 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN B 39 GLN C 99 HIS D 38 GLN D 100 GLN E 38 GLN L 53 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6974 Z= 0.198 Angle : 0.568 11.659 9477 Z= 0.298 Chirality : 0.044 0.176 1026 Planarity : 0.005 0.050 1225 Dihedral : 5.663 47.525 999 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.36 % Allowed : 16.42 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.25), residues: 873 helix: -5.09 (0.32), residues: 14 sheet: -2.30 (0.25), residues: 346 loop : -2.24 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS B 35 PHE 0.011 0.001 PHE E 83 TYR 0.019 0.001 TYR E 94 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9247 (t) cc_final: 0.8769 (p) REVERT: A 495 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7412 (m-10) REVERT: C 99 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7260 (m90) REVERT: H 74 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6741 (tm-30) REVERT: H 88 SER cc_start: 0.8426 (t) cc_final: 0.8086 (m) REVERT: H 90 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8401 (t0) REVERT: L 67 SER cc_start: 0.7688 (t) cc_final: 0.7469 (p) outliers start: 25 outliers final: 11 residues processed: 150 average time/residue: 0.2333 time to fit residues: 44.4101 Evaluate side-chains 138 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 69 optimal weight: 0.0020 chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 506 GLN C 99 HIS D 38 GLN L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6974 Z= 0.193 Angle : 0.558 14.213 9477 Z= 0.287 Chirality : 0.044 0.173 1026 Planarity : 0.004 0.044 1225 Dihedral : 4.968 39.051 997 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.63 % Allowed : 18.17 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.26), residues: 873 helix: -4.64 (0.59), residues: 14 sheet: -1.97 (0.26), residues: 347 loop : -1.91 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.017 0.003 HIS C 99 PHE 0.016 0.001 PHE D 71 TYR 0.019 0.001 TYR E 94 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9185 (t) cc_final: 0.8764 (p) REVERT: A 495 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7490 (m-10) REVERT: C 99 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.7338 (m170) REVERT: H 74 GLU cc_start: 0.7586 (tm-30) cc_final: 0.6864 (tm-30) REVERT: H 88 SER cc_start: 0.8530 (t) cc_final: 0.8207 (m) REVERT: L 74 SER cc_start: 0.7967 (p) cc_final: 0.7736 (t) outliers start: 27 outliers final: 11 residues processed: 150 average time/residue: 0.2243 time to fit residues: 43.0036 Evaluate side-chains 128 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 460 ASN A 506 GLN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6974 Z= 0.283 Angle : 0.588 14.394 9477 Z= 0.304 Chirality : 0.045 0.198 1026 Planarity : 0.004 0.043 1225 Dihedral : 4.929 39.075 997 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.44 % Allowed : 19.65 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.27), residues: 873 helix: -4.61 (0.65), residues: 14 sheet: -1.93 (0.26), residues: 358 loop : -1.65 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 47 HIS 0.013 0.002 HIS C 99 PHE 0.013 0.001 PHE A 377 TYR 0.020 0.001 TYR E 94 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9163 (t) cc_final: 0.8786 (p) REVERT: A 495 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7770 (m-10) REVERT: B 13 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8162 (mt0) REVERT: H 74 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7023 (tm-30) REVERT: H 88 SER cc_start: 0.8695 (t) cc_final: 0.8299 (m) REVERT: L 74 SER cc_start: 0.8293 (p) cc_final: 0.8000 (t) outliers start: 33 outliers final: 24 residues processed: 149 average time/residue: 0.2167 time to fit residues: 41.4911 Evaluate side-chains 140 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.0470 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6974 Z= 0.243 Angle : 0.568 14.221 9477 Z= 0.293 Chirality : 0.044 0.189 1026 Planarity : 0.004 0.042 1225 Dihedral : 4.797 38.155 997 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.98 % Allowed : 19.52 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.27), residues: 873 helix: -4.57 (0.68), residues: 14 sheet: -1.79 (0.26), residues: 351 loop : -1.59 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.008 0.001 HIS C 99 PHE 0.017 0.001 PHE A 377 TYR 0.020 0.001 TYR B 60 ARG 0.003 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9196 (t) cc_final: 0.8793 (p) REVERT: A 495 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7744 (m-10) REVERT: B 13 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8185 (mt0) REVERT: H 62 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7757 (tp-100) REVERT: H 87 ARG cc_start: 0.7510 (ttp-110) cc_final: 0.7238 (ttm-80) REVERT: H 88 SER cc_start: 0.8761 (t) cc_final: 0.8404 (m) REVERT: L 74 SER cc_start: 0.8353 (p) cc_final: 0.8063 (t) outliers start: 37 outliers final: 26 residues processed: 152 average time/residue: 0.2124 time to fit residues: 41.6760 Evaluate side-chains 146 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6974 Z= 0.200 Angle : 0.549 14.328 9477 Z= 0.281 Chirality : 0.044 0.181 1026 Planarity : 0.003 0.042 1225 Dihedral : 4.671 37.558 997 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.04 % Allowed : 21.67 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.27), residues: 873 helix: -4.51 (0.71), residues: 14 sheet: -1.69 (0.26), residues: 341 loop : -1.48 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.004 0.001 HIS C 99 PHE 0.016 0.001 PHE A 377 TYR 0.019 0.001 TYR E 94 ARG 0.003 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9177 (t) cc_final: 0.8744 (p) REVERT: A 495 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7601 (m-10) REVERT: B 13 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8191 (mt0) REVERT: H 62 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7735 (tp-100) REVERT: H 87 ARG cc_start: 0.7554 (ttp-110) cc_final: 0.7260 (ttm-80) REVERT: H 88 SER cc_start: 0.8822 (t) cc_final: 0.8412 (m) REVERT: L 74 SER cc_start: 0.8344 (p) cc_final: 0.8061 (t) outliers start: 30 outliers final: 24 residues processed: 147 average time/residue: 0.2136 time to fit residues: 40.6744 Evaluate side-chains 145 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6974 Z= 0.230 Angle : 0.557 14.338 9477 Z= 0.286 Chirality : 0.044 0.183 1026 Planarity : 0.003 0.042 1225 Dihedral : 4.677 37.854 997 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.44 % Allowed : 21.67 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.28), residues: 873 helix: -4.53 (0.53), residues: 20 sheet: -1.62 (0.26), residues: 345 loop : -1.39 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.007 0.001 HIS C 99 PHE 0.019 0.001 PHE A 377 TYR 0.019 0.001 TYR E 94 ARG 0.003 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9163 (t) cc_final: 0.8748 (p) REVERT: A 495 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7750 (m-10) REVERT: B 13 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8183 (mt0) REVERT: H 62 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7778 (tp-100) REVERT: H 87 ARG cc_start: 0.7599 (ttp-110) cc_final: 0.7398 (ttp80) REVERT: H 88 SER cc_start: 0.8897 (t) cc_final: 0.8413 (m) REVERT: L 74 SER cc_start: 0.8357 (p) cc_final: 0.8092 (t) outliers start: 33 outliers final: 28 residues processed: 155 average time/residue: 0.2157 time to fit residues: 43.9180 Evaluate side-chains 154 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.1980 chunk 16 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 0.0970 chunk 77 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN C 82 GLN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6974 Z= 0.156 Angle : 0.532 14.376 9477 Z= 0.272 Chirality : 0.043 0.171 1026 Planarity : 0.003 0.042 1225 Dihedral : 4.496 36.740 997 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.17 % Allowed : 22.48 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.28), residues: 873 helix: -4.51 (0.53), residues: 20 sheet: -1.49 (0.26), residues: 352 loop : -1.28 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.003 0.001 HIS C 99 PHE 0.016 0.001 PHE A 377 TYR 0.019 0.001 TYR E 94 ARG 0.003 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9137 (t) cc_final: 0.8730 (p) REVERT: A 495 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: B 13 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8170 (mt0) REVERT: H 62 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7742 (tp-100) REVERT: H 88 SER cc_start: 0.8845 (t) cc_final: 0.8380 (m) REVERT: L 68 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7371 (ptmm) REVERT: L 74 SER cc_start: 0.8258 (p) cc_final: 0.8000 (t) outliers start: 31 outliers final: 24 residues processed: 155 average time/residue: 0.2168 time to fit residues: 43.1943 Evaluate side-chains 152 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.0570 chunk 50 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6974 Z= 0.210 Angle : 0.551 14.835 9477 Z= 0.281 Chirality : 0.044 0.180 1026 Planarity : 0.003 0.042 1225 Dihedral : 4.544 37.556 997 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.31 % Allowed : 21.94 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.28), residues: 873 helix: -4.50 (0.54), residues: 20 sheet: -1.43 (0.26), residues: 351 loop : -1.26 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS C 99 PHE 0.020 0.001 PHE A 377 TYR 0.019 0.001 TYR E 94 ARG 0.002 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9146 (t) cc_final: 0.8746 (p) REVERT: A 495 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7688 (m-10) REVERT: B 13 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8162 (mt0) REVERT: H 62 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7786 (tp-100) REVERT: H 88 SER cc_start: 0.8850 (t) cc_final: 0.8404 (m) REVERT: L 68 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7569 (ptmm) REVERT: L 74 SER cc_start: 0.8288 (p) cc_final: 0.8036 (t) outliers start: 32 outliers final: 27 residues processed: 151 average time/residue: 0.2147 time to fit residues: 41.7036 Evaluate side-chains 155 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6974 Z= 0.199 Angle : 0.548 14.952 9477 Z= 0.280 Chirality : 0.044 0.176 1026 Planarity : 0.003 0.042 1225 Dihedral : 4.515 37.436 997 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.58 % Allowed : 21.67 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.28), residues: 873 helix: -4.44 (0.56), residues: 20 sheet: -1.39 (0.26), residues: 352 loop : -1.20 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS C 99 PHE 0.021 0.001 PHE A 377 TYR 0.019 0.001 TYR E 94 ARG 0.003 0.000 ARG L 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9143 (t) cc_final: 0.8745 (p) REVERT: A 449 TYR cc_start: 0.8663 (p90) cc_final: 0.8338 (p90) REVERT: A 495 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7673 (m-10) REVERT: B 13 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8172 (mt0) REVERT: H 62 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7801 (tp-100) REVERT: H 88 SER cc_start: 0.8866 (t) cc_final: 0.8418 (m) REVERT: L 68 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7587 (ptmm) REVERT: L 74 SER cc_start: 0.8289 (p) cc_final: 0.8035 (t) outliers start: 34 outliers final: 29 residues processed: 156 average time/residue: 0.2200 time to fit residues: 44.5245 Evaluate side-chains 157 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN C 82 GLN C 99 HIS D 79 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.104476 restraints weight = 9182.654| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.48 r_work: 0.3079 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6974 Z= 0.379 Angle : 0.621 14.387 9477 Z= 0.322 Chirality : 0.046 0.219 1026 Planarity : 0.004 0.044 1225 Dihedral : 4.921 39.252 997 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.44 % Allowed : 21.94 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.28), residues: 873 helix: -4.46 (0.57), residues: 20 sheet: -1.49 (0.26), residues: 348 loop : -1.27 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 47 HIS 0.008 0.002 HIS C 99 PHE 0.025 0.002 PHE A 377 TYR 0.020 0.002 TYR A 453 ARG 0.005 0.001 ARG L 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.99 seconds wall clock time: 40 minutes 2.11 seconds (2402.11 seconds total)