Starting phenix.real_space_refine on Sun Mar 10 16:10:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/03_2024/7wb5_32395.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/03_2024/7wb5_32395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/03_2024/7wb5_32395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/03_2024/7wb5_32395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/03_2024/7wb5_32395.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/03_2024/7wb5_32395.pdb" } resolution = 3.7 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= 0.022 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 15 5.16 5 C 2077 2.51 5 N 533 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 65": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 364": "OD1" <-> "OD2" Residue "R TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 389": "OD1" <-> "OD2" Residue "R GLU 406": "OE1" <-> "OE2" Residue "R ARG 408": "NH1" <-> "NH2" Residue "R TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 471": "OE1" <-> "OE2" Residue "R TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3256 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.32, per 1000 atoms: 0.71 Number of scatterers: 3256 At special positions: 0 Unit cell: (72.36, 88.56, 72.36, 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 15 16.00 O 631 8.00 N 533 7.00 C 2077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 570.0 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 12 sheets defined 4.4% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 364 through 370 removed outlier: 4.598A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.682A pdb=" N LYS H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.906A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.533A pdb=" N TRP H 50 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.846A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU L 73 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.595A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.572A pdb=" N GLN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.884A pdb=" N ILE R 434 " --> pdb=" O VAL R 511 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS R 432 " --> pdb=" O LEU R 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474 73 hydrogen bonds defined for protein. 171 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: 0.82 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 734 1.33 - 1.45: 857 1.45 - 1.57: 1735 1.57 - 1.69: 1 1.69 - 1.82: 18 Bond restraints: 3345 Sorted by residual: bond pdb=" CA SER R 438 " pdb=" CB SER R 438 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.35e-02 5.49e+03 1.53e+01 bond pdb=" CA SER R 349 " pdb=" CB SER R 349 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.64e-02 3.72e+03 1.43e+01 bond pdb=" N LEU R 452 " pdb=" CA LEU R 452 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" N VAL R 433 " pdb=" CA VAL R 433 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N LYS R 378 " pdb=" CA LYS R 378 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 ... (remaining 3340 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.46: 54 104.46 - 112.01: 1454 112.01 - 119.57: 1347 119.57 - 127.13: 1665 127.13 - 134.69: 28 Bond angle restraints: 4548 Sorted by residual: angle pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.52e+01 angle pdb=" CA TRP R 436 " pdb=" CB TRP R 436 " pdb=" CG TRP R 436 " ideal model delta sigma weight residual 113.60 123.83 -10.23 1.90e+00 2.77e-01 2.90e+01 angle pdb=" CA PHE R 400 " pdb=" CB PHE R 400 " pdb=" CG PHE R 400 " ideal model delta sigma weight residual 113.80 118.30 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N PRO L 80 " pdb=" CD PRO L 80 " pdb=" CG PRO L 80 " ideal model delta sigma weight residual 103.20 96.90 6.30 1.50e+00 4.44e-01 1.77e+01 angle pdb=" N LEU R 387 " pdb=" CA LEU R 387 " pdb=" C LEU R 387 " ideal model delta sigma weight residual 114.75 109.56 5.19 1.26e+00 6.30e-01 1.69e+01 ... (remaining 4543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 1718 21.52 - 43.04: 173 43.04 - 64.55: 66 64.55 - 86.07: 12 86.07 - 107.59: 12 Dihedral angle restraints: 1981 sinusoidal: 801 harmonic: 1180 Sorted by residual: dihedral pdb=" CA VAL L 29 " pdb=" C VAL L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta harmonic sigma weight residual 180.00 -139.90 -40.10 0 5.00e+00 4.00e-02 6.43e+01 dihedral pdb=" CA PHE H 106 " pdb=" C PHE H 106 " pdb=" N ASP H 107 " pdb=" CA ASP H 107 " ideal model delta harmonic sigma weight residual 180.00 -146.68 -33.32 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.78 -43.78 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 1978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 417 0.119 - 0.238: 63 0.238 - 0.356: 5 0.356 - 0.475: 0 0.475 - 0.593: 2 Chirality restraints: 487 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.29e+01 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN R 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.81e+00 ... (remaining 484 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.304 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" C7 NAG A 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.009 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.453 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.292 2.00e-02 2.50e+03 2.51e-01 7.91e+02 pdb=" C7 NAG A 1 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.443 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.111 5.00e-02 4.00e+02 1.57e-01 3.92e+01 pdb=" N PRO L 80 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.076 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 281 2.73 - 3.27: 3255 3.27 - 3.82: 5356 3.82 - 4.36: 6706 4.36 - 4.90: 11080 Nonbonded interactions: 26678 Sorted by model distance: nonbonded pdb=" O ILE L 21 " pdb=" OG1 THR L 72 " model vdw 2.188 2.440 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.216 2.440 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 113 " model vdw 2.319 2.440 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.405 2.440 nonbonded pdb=" O VAL H 76 " pdb=" OG SER H 77 " model vdw 2.421 2.440 ... (remaining 26673 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: 3.010 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: 12.900 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.011 0.132 3345 Z= 0.690 Angle : 1.407 12.925 4548 Z= 0.926 Chirality : 0.090 0.593 487 Planarity : 0.018 0.262 581 Dihedral : 21.949 107.591 1220 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 2.24 % Allowed : 18.16 % Favored : 79.60 % Rotamer: Outliers : 14.00 % Allowed : 7.43 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -4.90 (0.36), residues: 402 helix: -4.22 (0.64), residues: 21 sheet: -3.58 (0.39), residues: 121 loop : -3.14 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.006 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.023 0.003 PHE R 400 TYR 0.024 0.003 TYR L 49 ARG 0.007 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 125 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: H 83 ILE cc_start: 0.9173 (tt) cc_final: 0.8932 (tt) REVERT: L 74 THR cc_start: 0.7091 (m) cc_final: 0.6553 (m) REVERT: L 79 GLN cc_start: 0.8296 (mp10) cc_final: 0.7818 (mp10) REVERT: R 369 TYR cc_start: 0.7978 (t80) cc_final: 0.7755 (t80) REVERT: R 387 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8498 (tt) REVERT: R 454 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7654 (mtp-110) REVERT: R 493 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7989 (tm-30) outliers start: 49 outliers final: 12 residues processed: 150 average time/residue: 0.1799 time to fit residues: 31.4844 Evaluate side-chains 122 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 422 ASN Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 454 ARG Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 493 GLN Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3345 Z= 0.270 Angle : 0.805 8.250 4548 Z= 0.410 Chirality : 0.049 0.160 487 Planarity : 0.007 0.083 581 Dihedral : 17.938 96.580 544 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.45 % Favored : 89.05 % Rotamer: Outliers : 8.00 % Allowed : 18.86 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.54 (0.36), residues: 402 helix: -3.72 (0.66), residues: 21 sheet: -3.21 (0.42), residues: 113 loop : -3.02 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.027 0.002 PHE R 515 TYR 0.020 0.002 TYR L 49 ARG 0.006 0.001 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8427 (m-80) cc_final: 0.8029 (m-10) REVERT: L 31 ASN cc_start: 0.8109 (p0) cc_final: 0.7470 (t0) REVERT: L 79 GLN cc_start: 0.8288 (mp10) cc_final: 0.7600 (mp10) REVERT: L 100 GLN cc_start: 0.7463 (tm-30) cc_final: 0.7078 (tm-30) REVERT: R 387 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8398 (tt) REVERT: R 408 ARG cc_start: 0.8787 (mtm110) cc_final: 0.8116 (ptm160) REVERT: R 414 GLN cc_start: 0.7952 (tp40) cc_final: 0.7330 (tp-100) REVERT: R 462 LYS cc_start: 0.8525 (pptt) cc_final: 0.8076 (ptmm) REVERT: R 493 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: R 516 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7435 (pp20) outliers start: 28 outliers final: 21 residues processed: 125 average time/residue: 0.1897 time to fit residues: 27.8242 Evaluate side-chains 125 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 422 ASN Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 460 ASN Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 493 GLN Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3345 Z= 0.249 Angle : 0.734 9.227 4548 Z= 0.368 Chirality : 0.048 0.220 487 Planarity : 0.006 0.078 581 Dihedral : 15.386 85.548 538 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.44 % Favored : 88.06 % Rotamer: Outliers : 7.43 % Allowed : 20.00 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.08 (0.38), residues: 402 helix: -3.79 (0.70), residues: 21 sheet: -2.56 (0.47), residues: 110 loop : -2.85 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.014 0.002 PHE R 515 TYR 0.020 0.002 TYR H 105 ARG 0.003 0.001 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8432 (m-80) cc_final: 0.8072 (m-10) REVERT: L 31 ASN cc_start: 0.8015 (p0) cc_final: 0.7429 (t0) REVERT: L 79 GLN cc_start: 0.8327 (mp10) cc_final: 0.7944 (mp10) REVERT: L 100 GLN cc_start: 0.7381 (tm-30) cc_final: 0.7068 (tm-30) REVERT: R 387 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8373 (tt) REVERT: R 408 ARG cc_start: 0.8832 (mtm110) cc_final: 0.8307 (ptm160) REVERT: R 414 GLN cc_start: 0.7961 (tp40) cc_final: 0.7462 (tp-100) REVERT: R 466 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6268 (ptp-110) REVERT: R 493 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7421 (tm-30) outliers start: 26 outliers final: 23 residues processed: 123 average time/residue: 0.1759 time to fit residues: 25.5311 Evaluate side-chains 121 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 460 ASN Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 0.0270 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 3345 Z= 0.417 Angle : 0.801 8.726 4548 Z= 0.406 Chirality : 0.050 0.246 487 Planarity : 0.007 0.082 581 Dihedral : 13.400 73.960 526 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.43 % Favored : 86.32 % Rotamer: Outliers : 10.00 % Allowed : 19.43 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.22 (0.38), residues: 402 helix: -3.83 (0.74), residues: 21 sheet: -2.99 (0.43), residues: 126 loop : -2.71 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP H 109 HIS 0.002 0.002 HIS L 34 PHE 0.010 0.002 PHE R 515 TYR 0.028 0.002 TYR L 49 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 0.394 Fit side-chains REVERT: H 60 TYR cc_start: 0.8568 (m-80) cc_final: 0.8124 (m-10) REVERT: L 31 ASN cc_start: 0.8135 (p0) cc_final: 0.7467 (t0) REVERT: L 62 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7270 (p90) REVERT: L 79 GLN cc_start: 0.8431 (mp10) cc_final: 0.8072 (mp10) REVERT: L 100 GLN cc_start: 0.7437 (tm-30) cc_final: 0.7060 (tm-30) REVERT: R 387 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8584 (tt) REVERT: R 408 ARG cc_start: 0.8854 (mtm110) cc_final: 0.8339 (ptm160) REVERT: R 414 GLN cc_start: 0.7934 (tp40) cc_final: 0.7487 (tp-100) REVERT: R 466 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6115 (ptp-110) REVERT: R 508 TYR cc_start: 0.6885 (m-80) cc_final: 0.6187 (m-80) outliers start: 35 outliers final: 27 residues processed: 116 average time/residue: 0.1778 time to fit residues: 24.2653 Evaluate side-chains 121 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 393 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 460 ASN Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3345 Z= 0.252 Angle : 0.730 8.781 4548 Z= 0.365 Chirality : 0.047 0.237 487 Planarity : 0.006 0.080 581 Dihedral : 11.825 59.378 526 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.19 % Favored : 88.56 % Rotamer: Outliers : 10.00 % Allowed : 20.00 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.06 (0.37), residues: 402 helix: -3.79 (0.77), residues: 21 sheet: -2.57 (0.47), residues: 114 loop : -2.80 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.024 0.002 PHE R 392 TYR 0.019 0.002 TYR L 49 ARG 0.003 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.7793 (t70) cc_final: 0.7409 (m-30) REVERT: H 34 MET cc_start: 0.8914 (tpp) cc_final: 0.8687 (tpp) REVERT: H 43 GLN cc_start: 0.7137 (mp10) cc_final: 0.6687 (mp10) REVERT: H 60 TYR cc_start: 0.8456 (m-80) cc_final: 0.8027 (m-10) REVERT: L 62 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7185 (p90) REVERT: L 79 GLN cc_start: 0.8399 (mp10) cc_final: 0.8052 (mp10) REVERT: L 100 GLN cc_start: 0.7432 (tm-30) cc_final: 0.7088 (tm-30) REVERT: R 387 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8508 (tt) REVERT: R 408 ARG cc_start: 0.8853 (mtm110) cc_final: 0.8336 (ptm160) REVERT: R 414 GLN cc_start: 0.7897 (tp40) cc_final: 0.7377 (tp-100) REVERT: R 453 TYR cc_start: 0.8705 (p90) cc_final: 0.8482 (p90) REVERT: R 508 TYR cc_start: 0.6547 (m-80) cc_final: 0.6152 (m-80) outliers start: 35 outliers final: 27 residues processed: 119 average time/residue: 0.1619 time to fit residues: 22.9070 Evaluate side-chains 117 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 460 ASN Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3345 Z= 0.273 Angle : 0.736 8.837 4548 Z= 0.368 Chirality : 0.047 0.200 487 Planarity : 0.006 0.079 581 Dihedral : 10.599 51.245 525 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.70 % Favored : 89.05 % Rotamer: Outliers : 9.14 % Allowed : 20.57 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.04 (0.37), residues: 402 helix: -3.70 (0.84), residues: 19 sheet: -2.58 (0.45), residues: 117 loop : -2.79 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.017 0.002 PHE R 392 TYR 0.020 0.002 TYR L 49 ARG 0.004 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 31 ASP cc_start: 0.7769 (t70) cc_final: 0.7563 (m-30) REVERT: H 43 GLN cc_start: 0.7138 (mp10) cc_final: 0.6678 (mp10) REVERT: H 60 TYR cc_start: 0.8403 (m-80) cc_final: 0.8075 (m-10) REVERT: L 62 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7238 (p90) REVERT: L 79 GLN cc_start: 0.8422 (mp10) cc_final: 0.7998 (mp10) REVERT: L 100 GLN cc_start: 0.7444 (tm-30) cc_final: 0.7104 (tm-30) REVERT: R 380 TYR cc_start: 0.7736 (m-10) cc_final: 0.7441 (m-10) REVERT: R 387 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8531 (tt) REVERT: R 408 ARG cc_start: 0.8868 (mtm110) cc_final: 0.8337 (ptm160) REVERT: R 414 GLN cc_start: 0.7652 (tp40) cc_final: 0.7112 (tp-100) REVERT: R 466 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6130 (ptp-110) REVERT: R 508 TYR cc_start: 0.6637 (m-80) cc_final: 0.6251 (m-80) outliers start: 32 outliers final: 26 residues processed: 115 average time/residue: 0.1762 time to fit residues: 23.8710 Evaluate side-chains 122 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 460 ASN Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3345 Z= 0.273 Angle : 0.734 8.249 4548 Z= 0.370 Chirality : 0.047 0.159 487 Planarity : 0.006 0.077 581 Dihedral : 9.778 53.569 522 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 10.00 % Allowed : 20.86 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.96 (0.37), residues: 402 helix: -3.59 (0.90), residues: 18 sheet: -2.55 (0.46), residues: 114 loop : -2.74 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.015 0.002 PHE R 392 TYR 0.024 0.002 TYR H 32 ARG 0.004 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7148 (mp10) cc_final: 0.6673 (mp10) REVERT: H 60 TYR cc_start: 0.8397 (m-80) cc_final: 0.8017 (m-10) REVERT: L 62 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7251 (p90) REVERT: L 79 GLN cc_start: 0.8427 (mp10) cc_final: 0.7992 (mp10) REVERT: L 100 GLN cc_start: 0.7417 (tm-30) cc_final: 0.7090 (tm-30) REVERT: R 380 TYR cc_start: 0.7810 (m-10) cc_final: 0.7237 (m-10) REVERT: R 387 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8551 (tt) REVERT: R 408 ARG cc_start: 0.8847 (mtm110) cc_final: 0.8236 (ptm160) REVERT: R 414 GLN cc_start: 0.7568 (tp40) cc_final: 0.6874 (tp40) REVERT: R 454 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7260 (mtp85) REVERT: R 467 ASP cc_start: 0.7466 (p0) cc_final: 0.6982 (p0) outliers start: 35 outliers final: 27 residues processed: 116 average time/residue: 0.1764 time to fit residues: 24.1660 Evaluate side-chains 122 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 460 ASN Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3345 Z= 0.325 Angle : 0.781 7.592 4548 Z= 0.396 Chirality : 0.047 0.169 487 Planarity : 0.006 0.079 581 Dihedral : 9.529 57.559 522 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 8.86 % Allowed : 23.14 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.00 (0.37), residues: 402 helix: -3.59 (0.89), residues: 18 sheet: -2.55 (0.47), residues: 108 loop : -2.80 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.016 0.002 PHE R 392 TYR 0.025 0.002 TYR H 105 ARG 0.005 0.001 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7161 (mp10) cc_final: 0.6675 (mp10) REVERT: H 60 TYR cc_start: 0.8457 (m-80) cc_final: 0.8036 (m-10) REVERT: L 62 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7343 (p90) REVERT: L 79 GLN cc_start: 0.8452 (mp10) cc_final: 0.7983 (mp10) REVERT: L 100 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7148 (tm-30) REVERT: R 387 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8579 (tt) REVERT: R 408 ARG cc_start: 0.8876 (mtm110) cc_final: 0.8264 (ptm160) REVERT: R 414 GLN cc_start: 0.7581 (tp40) cc_final: 0.6856 (tp-100) REVERT: R 454 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7159 (mtp85) REVERT: R 467 ASP cc_start: 0.7455 (p0) cc_final: 0.7079 (p0) outliers start: 31 outliers final: 29 residues processed: 109 average time/residue: 0.1862 time to fit residues: 24.0801 Evaluate side-chains 121 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 460 ASN Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0020 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3345 Z= 0.226 Angle : 0.739 6.984 4548 Z= 0.373 Chirality : 0.045 0.164 487 Planarity : 0.006 0.079 581 Dihedral : 9.130 55.517 522 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 8.86 % Allowed : 23.14 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.85 (0.37), residues: 402 helix: -3.66 (0.85), residues: 18 sheet: -2.35 (0.47), residues: 108 loop : -2.73 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.016 0.001 PHE R 392 TYR 0.026 0.002 TYR H 105 ARG 0.004 0.000 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 96 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7212 (mp10) cc_final: 0.6730 (mp10) REVERT: H 60 TYR cc_start: 0.8361 (m-80) cc_final: 0.7963 (m-10) REVERT: L 62 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7236 (p90) REVERT: L 79 GLN cc_start: 0.8461 (mp10) cc_final: 0.7943 (mp10) REVERT: L 100 GLN cc_start: 0.7410 (tm-30) cc_final: 0.7118 (tm-30) REVERT: R 387 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8554 (tt) REVERT: R 454 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7314 (mtp85) REVERT: R 467 ASP cc_start: 0.7307 (p0) cc_final: 0.7095 (p0) outliers start: 31 outliers final: 29 residues processed: 115 average time/residue: 0.1788 time to fit residues: 24.9009 Evaluate side-chains 125 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 455 LEU Chi-restraints excluded: chain R residue 460 ASN Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.0020 chunk 4 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 overall best weight: 0.2226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3345 Z= 0.170 Angle : 0.736 11.085 4548 Z= 0.366 Chirality : 0.045 0.138 487 Planarity : 0.006 0.080 581 Dihedral : 8.540 52.612 522 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 7.43 % Allowed : 24.86 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.62 (0.38), residues: 402 helix: -3.93 (0.75), residues: 18 sheet: -2.12 (0.49), residues: 107 loop : -2.57 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 109 HIS 0.003 0.002 HIS L 34 PHE 0.016 0.001 PHE R 392 TYR 0.025 0.002 TYR H 105 ARG 0.004 0.000 ARG R 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.378 Fit side-chains REVERT: H 43 GLN cc_start: 0.7228 (mp10) cc_final: 0.6728 (mp10) REVERT: H 60 TYR cc_start: 0.8244 (m-80) cc_final: 0.7980 (m-10) REVERT: L 62 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7143 (p90) REVERT: L 79 GLN cc_start: 0.8452 (mp10) cc_final: 0.7891 (mp10) REVERT: L 100 GLN cc_start: 0.7253 (tm-30) cc_final: 0.7020 (tm-30) REVERT: R 387 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8515 (tt) REVERT: R 408 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8378 (ptm160) REVERT: R 454 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7467 (mtp85) outliers start: 26 outliers final: 22 residues processed: 113 average time/residue: 0.1693 time to fit residues: 22.7087 Evaluate side-chains 120 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.0170 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 ASN ** R 474 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 = 0.3943 r_free = 0.3943 target = 0.151263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129771 restraints weight = 4961.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130026 restraints weight = 4141.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131305 restraints weight = 3624.081| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3345 Z= 0.220 Angle : 0.740 10.933 4548 Z= 0.373 Chirality : 0.046 0.185 487 Planarity : 0.006 0.079 581 Dihedral : 8.076 51.484 520 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 6.57 % Allowed : 26.00 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.54 (0.38), residues: 402 helix: -4.32 (0.68), residues: 20 sheet: -2.00 (0.49), residues: 107 loop : -2.48 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.015 0.001 PHE R 392 TYR 0.024 0.002 TYR H 105 ARG 0.004 0.001 ARG H 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1455.48 seconds wall clock time: 26 minutes 52.96 seconds (1612.96 seconds total)