Starting phenix.real_space_refine on Sun Mar 10 21:32:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/03_2024/7qha_13968.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/03_2024/7qha_13968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/03_2024/7qha_13968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/03_2024/7qha_13968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/03_2024/7qha_13968.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/03_2024/7qha_13968.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 33 5.16 5 Na 2 4.78 5 C 3506 2.51 5 N 832 2.21 5 O 909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 65": "OD1" <-> "OD2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5282 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1257 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 4, 'TRANS': 148} Chain: "B" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3208 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 404} Chain: "C" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.56, per 1000 atoms: 0.67 Number of scatterers: 5282 At special positions: 0 Unit cell: (88.8769, 77.2481, 98.0138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 Na 2 11.00 O 909 8.00 N 832 7.00 C 3506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.0 seconds 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 71.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 8 through 34 Proline residue: A 16 - end of helix removed outlier: 3.510A pdb=" N ARG A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 64 removed outlier: 4.150A pdb=" N ALA A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 78 through 111 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 128 through 152 removed outlier: 3.553A pdb=" N PHE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 17 through 33 Processing helix chain 'B' and resid 37 through 47 removed outlier: 4.449A pdb=" N ALA B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 55 through 70 removed outlier: 4.097A pdb=" N PHE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 90 through 103 removed outlier: 4.129A pdb=" N VAL B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.517A pdb=" N ASP B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 142 through 145 Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.588A pdb=" N LEU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 195 removed outlier: 4.069A pdb=" N GLY B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 218 through 230 removed outlier: 4.369A pdb=" N PHE B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 250 Processing helix chain 'B' and resid 258 through 294 Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.999A pdb=" N ILE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 325 removed outlier: 3.580A pdb=" N LEU B 313 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 337 through 347 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.503A pdb=" N PHE B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.814A pdb=" N ILE A 121 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 18 through 22 removed outlier: 3.675A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 57 through 59 removed outlier: 7.033A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 1014 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: 1.42 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1596 1.35 - 1.46: 1294 1.46 - 1.58: 2458 1.58 - 1.70: 0 1.70 - 1.81: 57 Bond restraints: 5405 Sorted by residual: bond pdb=" CB ASN C 76 " pdb=" CG ASN C 76 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" CB ASP B 112 " pdb=" CG ASP B 112 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.63e-01 bond pdb=" C SER B 90 " pdb=" O SER B 90 " ideal model delta sigma weight residual 1.243 1.234 0.009 9.50e-03 1.11e+04 9.29e-01 bond pdb=" CB ASP C 30 " pdb=" CG ASP C 30 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.68e-01 bond pdb=" CB GLU B 301 " pdb=" CG GLU B 301 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.86e-01 ... (remaining 5400 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.52: 132 105.52 - 112.64: 2851 112.64 - 119.75: 1750 119.75 - 126.87: 2557 126.87 - 133.99: 62 Bond angle restraints: 7352 Sorted by residual: angle pdb=" C SER B 90 " pdb=" CA SER B 90 " pdb=" CB SER B 90 " ideal model delta sigma weight residual 117.23 110.33 6.90 1.36e+00 5.41e-01 2.58e+01 angle pdb=" C SER B 151 " pdb=" N ILE B 152 " pdb=" CA ILE B 152 " ideal model delta sigma weight residual 120.33 123.22 -2.89 8.00e-01 1.56e+00 1.31e+01 angle pdb=" CA SER B 90 " pdb=" C SER B 90 " pdb=" N LEU B 91 " ideal model delta sigma weight residual 119.98 116.95 3.03 8.50e-01 1.38e+00 1.27e+01 angle pdb=" C LYS A 64 " pdb=" N ASP A 65 " pdb=" CA ASP A 65 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.48e+00 angle pdb=" CA LEU B 421 " pdb=" CB LEU B 421 " pdb=" CG LEU B 421 " ideal model delta sigma weight residual 116.30 126.04 -9.74 3.50e+00 8.16e-02 7.75e+00 ... (remaining 7347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 2911 16.57 - 33.15: 192 33.15 - 49.72: 42 49.72 - 66.30: 7 66.30 - 82.87: 3 Dihedral angle restraints: 3155 sinusoidal: 1199 harmonic: 1956 Sorted by residual: dihedral pdb=" CA ASP C 103 " pdb=" CB ASP C 103 " pdb=" CG ASP C 103 " pdb=" OD1 ASP C 103 " ideal model delta sinusoidal sigma weight residual -30.00 -88.00 58.00 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA TYR C 94 " pdb=" C TYR C 94 " pdb=" N CYS C 95 " pdb=" CA CYS C 95 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA ILE B 228 " pdb=" C ILE B 228 " pdb=" N PHE B 229 " pdb=" CA PHE B 229 " ideal model delta harmonic sigma weight residual -180.00 -164.65 -15.35 0 5.00e+00 4.00e-02 9.42e+00 ... (remaining 3152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 623 0.039 - 0.078: 200 0.078 - 0.117: 47 0.117 - 0.155: 8 0.155 - 0.194: 2 Chirality restraints: 880 Sorted by residual: chirality pdb=" CA THR B 220 " pdb=" N THR B 220 " pdb=" C THR B 220 " pdb=" CB THR B 220 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA VAL B 399 " pdb=" N VAL B 399 " pdb=" C VAL B 399 " pdb=" CB VAL B 399 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CB THR B 220 " pdb=" CA THR B 220 " pdb=" OG1 THR B 220 " pdb=" CG2 THR B 220 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 877 not shown) Planarity restraints: 897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 76 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ASN C 76 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN C 76 " 0.013 2.00e-02 2.50e+03 pdb=" N THR C 77 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 146 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 309 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO B 310 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 310 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 310 " -0.016 5.00e-02 4.00e+02 ... (remaining 894 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1295 2.79 - 3.32: 5415 3.32 - 3.85: 8530 3.85 - 4.37: 8948 4.37 - 4.90: 16317 Nonbonded interactions: 40505 Sorted by model distance: nonbonded pdb=" OG SER C 25 " pdb=" OD1 ASN C 76 " model vdw 2.268 2.440 nonbonded pdb=" O LEU B 302 " pdb=" OG SER B 305 " model vdw 2.293 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O TYR C 98 " model vdw 2.304 2.440 nonbonded pdb=" O SER B 103 " pdb="NA NA B 501 " model vdw 2.312 2.470 nonbonded pdb=" OG SER B 380 " pdb=" O ILE B 385 " model vdw 2.316 2.440 ... (remaining 40500 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 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: 0.590 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: 3.080 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.700 Find NCS groups from input model: 0.140 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:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 0.003 0.031 5405 Z= 0.175 Angle : 0.591 9.742 7352 Z= 0.311 Chirality : 0.041 0.194 880 Planarity : 0.004 0.031 897 Dihedral : 12.232 82.871 1904 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.33), residues: 678 helix: 2.20 (0.25), residues: 428 sheet: -0.36 (0.97), residues: 35 loop : -0.50 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 108 HIS 0.004 0.001 HIS B 388 PHE 0.019 0.001 PHE B 60 TYR 0.013 0.001 TYR B 129 ARG 0.001 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8801 (ttm) cc_final: 0.8601 (ttm) REVERT: A 71 THR cc_start: 0.8147 (t) cc_final: 0.7545 (t) REVERT: A 75 ASP cc_start: 0.9189 (m-30) cc_final: 0.8825 (m-30) REVERT: B 118 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8548 (tm-30) REVERT: B 130 ASP cc_start: 0.8576 (t70) cc_final: 0.8205 (t0) REVERT: B 351 ASP cc_start: 0.8909 (p0) cc_final: 0.8662 (p0) REVERT: C 61 ASP cc_start: 0.8595 (t70) cc_final: 0.8350 (t0) REVERT: C 85 LEU cc_start: 0.8950 (mm) cc_final: 0.8664 (mm) outliers start: 0 outliers final: 1 residues processed: 137 average time/residue: 0.9418 time to fit residues: 135.6850 Evaluate side-chains 105 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 384 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5405 Z= 0.227 Angle : 0.636 11.994 7352 Z= 0.315 Chirality : 0.041 0.190 880 Planarity : 0.005 0.035 897 Dihedral : 4.104 25.839 734 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.81 % Allowed : 15.26 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.03 (0.34), residues: 678 helix: 2.39 (0.25), residues: 436 sheet: -0.60 (0.91), residues: 35 loop : -0.60 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 108 HIS 0.003 0.001 HIS B 354 PHE 0.015 0.001 PHE B 60 TYR 0.017 0.001 TYR B 425 ARG 0.008 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8457 (pm20) cc_final: 0.8230 (pm20) REVERT: A 66 ASP cc_start: 0.8916 (m-30) cc_final: 0.8572 (m-30) REVERT: A 75 ASP cc_start: 0.9228 (m-30) cc_final: 0.8932 (m-30) REVERT: B 118 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8577 (tm-30) REVERT: B 130 ASP cc_start: 0.8244 (t70) cc_final: 0.7562 (t0) REVERT: B 351 ASP cc_start: 0.8985 (p0) cc_final: 0.8662 (p0) REVERT: B 372 MET cc_start: 0.7562 (tpp) cc_final: 0.7009 (tmm) REVERT: B 418 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9031 (tm) REVERT: C 82 MET cc_start: 0.8857 (mpp) cc_final: 0.8276 (mpt) REVERT: C 85 LEU cc_start: 0.9005 (mm) cc_final: 0.8663 (mm) REVERT: C 102 ASP cc_start: 0.8667 (t0) cc_final: 0.8267 (t0) REVERT: C 108 TRP cc_start: 0.8009 (m-10) cc_final: 0.7262 (m-10) outliers start: 16 outliers final: 6 residues processed: 124 average time/residue: 1.0230 time to fit residues: 132.9898 Evaluate side-chains 111 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5405 Z= 0.282 Angle : 0.647 11.348 7352 Z= 0.321 Chirality : 0.042 0.189 880 Planarity : 0.005 0.035 897 Dihedral : 4.018 21.098 732 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.39 % Allowed : 18.60 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.13 (0.33), residues: 678 helix: 2.49 (0.25), residues: 436 sheet: -0.58 (0.90), residues: 35 loop : -0.61 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 108 HIS 0.004 0.001 HIS B 354 PHE 0.020 0.001 PHE B 340 TYR 0.011 0.001 TYR C 94 ARG 0.009 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8427 (pm20) cc_final: 0.8137 (pm20) REVERT: A 66 ASP cc_start: 0.8957 (m-30) cc_final: 0.8625 (m-30) REVERT: A 75 ASP cc_start: 0.9203 (m-30) cc_final: 0.8934 (m-30) REVERT: B 118 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8677 (tm-30) REVERT: B 130 ASP cc_start: 0.8362 (t70) cc_final: 0.7562 (t0) REVERT: B 331 LEU cc_start: 0.9332 (tp) cc_final: 0.9079 (tm) REVERT: B 351 ASP cc_start: 0.8992 (p0) cc_final: 0.8665 (p0) REVERT: B 418 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9073 (tm) REVERT: C 85 LEU cc_start: 0.9089 (mm) cc_final: 0.8750 (mm) REVERT: C 102 ASP cc_start: 0.8650 (t0) cc_final: 0.8226 (t0) REVERT: C 108 TRP cc_start: 0.8108 (m-10) cc_final: 0.7828 (m-10) outliers start: 25 outliers final: 14 residues processed: 121 average time/residue: 0.9189 time to fit residues: 117.2150 Evaluate side-chains 115 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 40 optimal weight: 0.2980 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5405 Z= 0.172 Angle : 0.626 11.256 7352 Z= 0.302 Chirality : 0.040 0.142 880 Planarity : 0.004 0.033 897 Dihedral : 3.897 20.130 732 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.33 % Allowed : 21.23 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.19 (0.33), residues: 678 helix: 2.55 (0.25), residues: 434 sheet: -0.56 (0.91), residues: 35 loop : -0.58 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 108 HIS 0.003 0.001 HIS B 354 PHE 0.009 0.001 PHE B 60 TYR 0.011 0.001 TYR C 94 ARG 0.007 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8431 (pm20) cc_final: 0.8149 (pm20) REVERT: A 66 ASP cc_start: 0.8935 (m-30) cc_final: 0.8630 (m-30) REVERT: A 75 ASP cc_start: 0.9172 (m-30) cc_final: 0.8908 (m-30) REVERT: A 126 MET cc_start: 0.9003 (ttm) cc_final: 0.8801 (ttp) REVERT: B 118 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8741 (tm-30) REVERT: B 130 ASP cc_start: 0.8313 (t70) cc_final: 0.7398 (t0) REVERT: B 331 LEU cc_start: 0.9321 (tp) cc_final: 0.9087 (tm) REVERT: B 351 ASP cc_start: 0.8979 (p0) cc_final: 0.8637 (p0) REVERT: B 418 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9025 (tm) REVERT: C 85 LEU cc_start: 0.9086 (mm) cc_final: 0.8745 (mm) REVERT: C 102 ASP cc_start: 0.8671 (t0) cc_final: 0.8262 (t0) REVERT: C 108 TRP cc_start: 0.8072 (m-10) cc_final: 0.7110 (m-10) outliers start: 19 outliers final: 8 residues processed: 117 average time/residue: 0.9551 time to fit residues: 117.6684 Evaluate side-chains 112 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5405 Z= 0.211 Angle : 0.652 10.940 7352 Z= 0.311 Chirality : 0.040 0.148 880 Planarity : 0.004 0.032 897 Dihedral : 3.879 20.666 732 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.51 % Allowed : 22.63 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.19 (0.33), residues: 678 helix: 2.57 (0.25), residues: 436 sheet: -0.74 (0.88), residues: 35 loop : -0.63 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 108 HIS 0.004 0.001 HIS B 354 PHE 0.016 0.001 PHE B 229 TYR 0.010 0.001 TYR C 94 ARG 0.007 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8438 (pm20) cc_final: 0.7990 (pm20) REVERT: A 66 ASP cc_start: 0.8949 (m-30) cc_final: 0.8643 (m-30) REVERT: A 75 ASP cc_start: 0.9175 (m-30) cc_final: 0.8912 (m-30) REVERT: B 118 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8778 (tm-30) REVERT: B 130 ASP cc_start: 0.8350 (t70) cc_final: 0.7421 (t0) REVERT: B 331 LEU cc_start: 0.9329 (tp) cc_final: 0.9114 (tm) REVERT: B 351 ASP cc_start: 0.8939 (p0) cc_final: 0.8579 (p0) REVERT: B 372 MET cc_start: 0.7605 (tpp) cc_final: 0.7009 (tmm) REVERT: B 418 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9023 (tm) REVERT: C 82 MET cc_start: 0.8875 (mpt) cc_final: 0.8587 (mpp) REVERT: C 85 LEU cc_start: 0.9094 (mm) cc_final: 0.8786 (mm) REVERT: C 102 ASP cc_start: 0.8665 (t0) cc_final: 0.8239 (t0) REVERT: C 108 TRP cc_start: 0.8096 (m-10) cc_final: 0.7839 (m-10) outliers start: 20 outliers final: 12 residues processed: 121 average time/residue: 0.9224 time to fit residues: 117.7178 Evaluate side-chains 118 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5405 Z= 0.183 Angle : 0.661 11.736 7352 Z= 0.312 Chirality : 0.040 0.148 880 Planarity : 0.004 0.033 897 Dihedral : 3.840 18.465 732 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.51 % Allowed : 24.21 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.18 (0.33), residues: 678 helix: 2.58 (0.25), residues: 433 sheet: -0.77 (0.88), residues: 35 loop : -0.62 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 108 HIS 0.003 0.001 HIS B 354 PHE 0.014 0.001 PHE B 229 TYR 0.020 0.001 TYR B 425 ARG 0.007 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8443 (pm20) cc_final: 0.8060 (pm20) REVERT: A 66 ASP cc_start: 0.8933 (m-30) cc_final: 0.8650 (m-30) REVERT: A 75 ASP cc_start: 0.9165 (m-30) cc_final: 0.8905 (m-30) REVERT: B 118 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8767 (tm-30) REVERT: B 130 ASP cc_start: 0.8340 (t70) cc_final: 0.7408 (t0) REVERT: B 268 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8510 (mm-30) REVERT: B 331 LEU cc_start: 0.9311 (tp) cc_final: 0.9108 (tm) REVERT: B 351 ASP cc_start: 0.8914 (p0) cc_final: 0.8541 (p0) REVERT: B 372 MET cc_start: 0.7710 (tpp) cc_final: 0.7040 (tmm) REVERT: B 384 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8647 (t0) REVERT: B 418 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9039 (tm) REVERT: C 85 LEU cc_start: 0.9064 (mm) cc_final: 0.8750 (mm) REVERT: C 102 ASP cc_start: 0.8653 (t0) cc_final: 0.8242 (t0) REVERT: C 108 TRP cc_start: 0.8096 (m-10) cc_final: 0.7120 (m-10) outliers start: 20 outliers final: 11 residues processed: 121 average time/residue: 0.9397 time to fit residues: 119.9309 Evaluate side-chains 118 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.0470 chunk 64 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5405 Z= 0.191 Angle : 0.658 11.701 7352 Z= 0.314 Chirality : 0.040 0.159 880 Planarity : 0.004 0.033 897 Dihedral : 3.828 18.154 732 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.33 % Allowed : 25.09 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.04 (0.33), residues: 678 helix: 2.47 (0.25), residues: 440 sheet: -0.89 (0.87), residues: 35 loop : -0.79 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 108 HIS 0.003 0.001 HIS B 354 PHE 0.010 0.001 PHE B 229 TYR 0.010 0.001 TYR B 196 ARG 0.008 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8438 (pm20) cc_final: 0.8056 (pm20) REVERT: A 66 ASP cc_start: 0.8934 (m-30) cc_final: 0.8646 (m-30) REVERT: A 75 ASP cc_start: 0.9163 (m-30) cc_final: 0.8903 (m-30) REVERT: B 118 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8763 (tm-30) REVERT: B 130 ASP cc_start: 0.8283 (t70) cc_final: 0.7287 (t0) REVERT: B 162 ASN cc_start: 0.9455 (t0) cc_final: 0.9154 (t0) REVERT: B 331 LEU cc_start: 0.9311 (tp) cc_final: 0.9107 (tm) REVERT: B 351 ASP cc_start: 0.8893 (p0) cc_final: 0.8551 (p0) REVERT: B 372 MET cc_start: 0.7756 (tpp) cc_final: 0.7081 (tmm) REVERT: B 418 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9055 (tm) REVERT: C 85 LEU cc_start: 0.9057 (mm) cc_final: 0.8751 (mm) REVERT: C 102 ASP cc_start: 0.8644 (t0) cc_final: 0.8207 (t0) REVERT: C 108 TRP cc_start: 0.8147 (m-10) cc_final: 0.7164 (m-10) outliers start: 19 outliers final: 12 residues processed: 119 average time/residue: 0.9206 time to fit residues: 115.5663 Evaluate side-chains 121 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5405 Z= 0.224 Angle : 0.702 12.085 7352 Z= 0.332 Chirality : 0.041 0.148 880 Planarity : 0.004 0.035 897 Dihedral : 3.881 18.612 732 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.81 % Allowed : 26.14 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.06 (0.33), residues: 678 helix: 2.49 (0.25), residues: 440 sheet: -0.89 (0.87), residues: 35 loop : -0.79 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 108 HIS 0.003 0.001 HIS B 354 PHE 0.021 0.001 PHE B 229 TYR 0.009 0.001 TYR C 94 ARG 0.008 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8457 (pm20) cc_final: 0.8056 (pm20) REVERT: A 66 ASP cc_start: 0.8951 (m-30) cc_final: 0.8670 (m-30) REVERT: A 75 ASP cc_start: 0.9170 (m-30) cc_final: 0.8938 (m-30) REVERT: B 118 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8782 (tm-30) REVERT: B 130 ASP cc_start: 0.8349 (t70) cc_final: 0.7504 (t0) REVERT: B 162 ASN cc_start: 0.9467 (t0) cc_final: 0.9168 (t0) REVERT: B 268 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8539 (mm-30) REVERT: B 331 LEU cc_start: 0.9317 (tp) cc_final: 0.9111 (tm) REVERT: B 351 ASP cc_start: 0.8857 (p0) cc_final: 0.8508 (p0) REVERT: B 372 MET cc_start: 0.7911 (tpp) cc_final: 0.7270 (tmm) REVERT: B 384 ASN cc_start: 0.8934 (t0) cc_final: 0.8660 (t0) REVERT: B 418 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9081 (tm) REVERT: C 85 LEU cc_start: 0.9092 (mm) cc_final: 0.8784 (mm) REVERT: C 102 ASP cc_start: 0.8649 (t0) cc_final: 0.8240 (t0) REVERT: C 108 TRP cc_start: 0.8219 (m-10) cc_final: 0.7252 (m-10) outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 0.9056 time to fit residues: 112.7796 Evaluate side-chains 121 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.0870 chunk 56 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 0.0010 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5405 Z= 0.187 Angle : 0.701 12.076 7352 Z= 0.331 Chirality : 0.040 0.167 880 Planarity : 0.004 0.032 897 Dihedral : 3.798 17.392 732 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.63 % Allowed : 27.02 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.00 (0.33), residues: 678 helix: 2.43 (0.25), residues: 440 sheet: -0.88 (0.88), residues: 35 loop : -0.78 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 108 HIS 0.002 0.001 HIS B 354 PHE 0.014 0.001 PHE B 229 TYR 0.021 0.001 TYR B 425 ARG 0.008 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8943 (m-30) cc_final: 0.8636 (m-30) REVERT: A 75 ASP cc_start: 0.9154 (m-30) cc_final: 0.8891 (m-30) REVERT: B 118 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8761 (tm-30) REVERT: B 130 ASP cc_start: 0.8602 (t70) cc_final: 0.7623 (t0) REVERT: B 162 ASN cc_start: 0.9450 (t0) cc_final: 0.9158 (t0) REVERT: B 268 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8508 (mm-30) REVERT: B 331 LEU cc_start: 0.9287 (tp) cc_final: 0.9083 (tm) REVERT: B 351 ASP cc_start: 0.8854 (p0) cc_final: 0.8496 (p0) REVERT: B 372 MET cc_start: 0.7989 (tpp) cc_final: 0.7307 (tmm) REVERT: B 384 ASN cc_start: 0.8845 (t0) cc_final: 0.8560 (t0) REVERT: C 18 LEU cc_start: 0.8592 (tm) cc_final: 0.7554 (mm) REVERT: C 82 MET cc_start: 0.8769 (mpt) cc_final: 0.8247 (mpm) REVERT: C 85 LEU cc_start: 0.9032 (mm) cc_final: 0.8680 (mm) REVERT: C 108 TRP cc_start: 0.8162 (m-10) cc_final: 0.7243 (m-10) outliers start: 15 outliers final: 11 residues processed: 121 average time/residue: 0.9012 time to fit residues: 115.0555 Evaluate side-chains 119 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.0000 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5405 Z= 0.190 Angle : 0.705 12.718 7352 Z= 0.333 Chirality : 0.041 0.205 880 Planarity : 0.004 0.033 897 Dihedral : 3.789 17.288 732 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.11 % Allowed : 27.19 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.00 (0.33), residues: 678 helix: 2.42 (0.25), residues: 441 sheet: -0.92 (0.88), residues: 35 loop : -0.77 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 108 HIS 0.002 0.001 HIS B 354 PHE 0.018 0.001 PHE B 229 TYR 0.008 0.001 TYR C 94 ARG 0.008 0.001 ARG B 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8948 (m-30) cc_final: 0.8660 (m-30) REVERT: A 75 ASP cc_start: 0.9152 (m-30) cc_final: 0.8887 (m-30) REVERT: B 118 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8762 (tm-30) REVERT: B 130 ASP cc_start: 0.8560 (t70) cc_final: 0.7534 (t0) REVERT: B 162 ASN cc_start: 0.9449 (t0) cc_final: 0.9163 (t0) REVERT: B 268 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8500 (mm-30) REVERT: B 331 LEU cc_start: 0.9294 (tp) cc_final: 0.9090 (tm) REVERT: B 351 ASP cc_start: 0.8815 (p0) cc_final: 0.8489 (p0) REVERT: B 372 MET cc_start: 0.7993 (tpp) cc_final: 0.7316 (tmm) REVERT: B 384 ASN cc_start: 0.8806 (t0) cc_final: 0.8532 (t0) REVERT: C 18 LEU cc_start: 0.8596 (tm) cc_final: 0.8016 (mm) REVERT: C 82 MET cc_start: 0.8740 (mpt) cc_final: 0.8485 (mpp) REVERT: C 85 LEU cc_start: 0.9017 (mm) cc_final: 0.8711 (mm) REVERT: C 108 TRP cc_start: 0.8177 (m-10) cc_final: 0.7258 (m-10) outliers start: 12 outliers final: 9 residues processed: 117 average time/residue: 0.9127 time to fit residues: 112.6437 Evaluate side-chains 117 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.070252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.057903 restraints weight = 14053.249| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.64 r_work: 0.2676 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5405 Z= 0.246 Angle : 0.711 11.947 7352 Z= 0.341 Chirality : 0.041 0.160 880 Planarity : 0.004 0.032 897 Dihedral : 3.878 18.541 732 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.93 % Allowed : 27.72 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.07 (0.33), residues: 678 helix: 2.48 (0.25), residues: 440 sheet: -0.80 (0.89), residues: 35 loop : -0.77 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 108 HIS 0.004 0.001 HIS B 354 PHE 0.007 0.001 PHE B 59 TYR 0.009 0.001 TYR C 94 ARG 0.008 0.001 ARG B 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2402.53 seconds wall clock time: 43 minutes 23.80 seconds (2603.80 seconds total)