Starting phenix.real_space_refine on Sat Aug 3 03:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/08_2024/8w9n_37376.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/08_2024/8w9n_37376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/08_2024/8w9n_37376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/08_2024/8w9n_37376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/08_2024/8w9n_37376.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/08_2024/8w9n_37376.cif" } resolution = 2.7 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= 0.006 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 40 5.16 5 Na 2 4.78 5 C 4570 2.51 5 N 1058 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6860 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3429 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 13, 'TRANS': 413} Chain breaks: 2 Chain: "B" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3429 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 13, 'TRANS': 413} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.35, per 1000 atoms: 0.63 Number of scatterers: 6860 At special positions: 0 Unit cell: (104.16, 87.42, 81.84, 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 40 16.00 Na 2 11.00 O 1190 8.00 N 1058 7.00 C 4570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 449 " - pdb=" SG CYS A 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 449 " - pdb=" SG CYS B 460 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 1 sheets defined 76.5% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 21 through 44 removed outlier: 4.132A pdb=" N LYS A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 65 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 149 through 183 Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.504A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 227 through 242 Proline residue: A 236 - end of helix removed outlier: 3.531A pdb=" N ASN A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.604A pdb=" N GLY A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 4.085A pdb=" N GLY A 276 " --> pdb=" O ASN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 308 Processing helix chain 'A' and resid 318 through 334 removed outlier: 4.105A pdb=" N ARG A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'A' and resid 398 through 414 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 426 through 440 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 472 through 488 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'B' and resid 22 through 43 Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.636A pdb=" N PHE B 77 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 93 through 111 Processing helix chain 'B' and resid 149 through 183 Processing helix chain 'B' and resid 183 through 194 removed outlier: 3.542A pdb=" N VAL B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 227 through 242 Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 262 through 271 removed outlier: 3.738A pdb=" N GLY B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 308 Processing helix chain 'B' and resid 318 through 334 removed outlier: 4.156A pdb=" N ARG B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 398 through 414 Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 426 through 440 Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 472 through 488 Processing sheet with id=AA1, first strand: chain 'A' and resid 499 through 500 460 hydrogen bonds defined for protein. 1290 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: 1.94 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2013 1.34 - 1.46: 1712 1.46 - 1.58: 3243 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 7032 Sorted by residual: bond pdb=" CA LYS B 494 " pdb=" C LYS B 494 " ideal model delta sigma weight residual 1.531 1.508 0.023 1.46e-02 4.69e+03 2.52e+00 bond pdb=" CA ASP B 454 " pdb=" C ASP B 454 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.14e-02 7.69e+03 1.49e+00 bond pdb=" N PHE B 366 " pdb=" CA PHE B 366 " ideal model delta sigma weight residual 1.463 1.447 0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" CA LYS A 494 " pdb=" C LYS A 494 " ideal model delta sigma weight residual 1.526 1.512 0.015 1.42e-02 4.96e+03 1.07e+00 bond pdb=" CA ASP A 454 " pdb=" C ASP A 454 " ideal model delta sigma weight residual 1.528 1.518 0.011 1.04e-02 9.25e+03 1.05e+00 ... (remaining 7027 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 145 106.52 - 113.39: 3849 113.39 - 120.25: 2672 120.25 - 127.12: 2818 127.12 - 133.99: 54 Bond angle restraints: 9538 Sorted by residual: angle pdb=" N THR A 43 " pdb=" CA THR A 43 " pdb=" C THR A 43 " ideal model delta sigma weight residual 111.28 115.13 -3.85 1.09e+00 8.42e-01 1.25e+01 angle pdb=" N THR A 445 " pdb=" CA THR A 445 " pdb=" C THR A 445 " ideal model delta sigma weight residual 112.89 108.75 4.14 1.24e+00 6.50e-01 1.11e+01 angle pdb=" N GLY B 442 " pdb=" CA GLY B 442 " pdb=" C GLY B 442 " ideal model delta sigma weight residual 114.85 110.75 4.10 1.35e+00 5.49e-01 9.23e+00 angle pdb=" N ALA B 498 " pdb=" CA ALA B 498 " pdb=" C ALA B 498 " ideal model delta sigma weight residual 113.20 109.69 3.51 1.21e+00 6.83e-01 8.43e+00 angle pdb=" N LEU A 176 " pdb=" CA LEU A 176 " pdb=" C LEU A 176 " ideal model delta sigma weight residual 111.36 108.27 3.09 1.09e+00 8.42e-01 8.01e+00 ... (remaining 9533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3653 17.70 - 35.41: 325 35.41 - 53.11: 83 53.11 - 70.81: 7 70.81 - 88.51: 6 Dihedral angle restraints: 4074 sinusoidal: 1584 harmonic: 2490 Sorted by residual: dihedral pdb=" CA ARG B 334 " pdb=" C ARG B 334 " pdb=" N HIS B 335 " pdb=" CA HIS B 335 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ARG A 334 " pdb=" C ARG A 334 " pdb=" N HIS A 335 " pdb=" CA HIS A 335 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ILE A 42 " pdb=" C ILE A 42 " pdb=" N THR A 43 " pdb=" CA THR A 43 " ideal model delta harmonic sigma weight residual -180.00 -162.70 -17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 4071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 623 0.030 - 0.060: 370 0.060 - 0.089: 88 0.089 - 0.119: 33 0.119 - 0.149: 10 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CA VAL A 453 " pdb=" N VAL A 453 " pdb=" C VAL A 453 " pdb=" CB VAL A 453 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA SER B 68 " pdb=" N SER B 68 " pdb=" C SER B 68 " pdb=" CB SER B 68 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA HIS B 335 " pdb=" N HIS B 335 " pdb=" C HIS B 335 " pdb=" CB HIS B 335 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1121 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 158 " 0.009 2.00e-02 2.50e+03 8.29e-03 1.37e+00 pdb=" CG TYR A 158 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 158 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 158 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 158 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 158 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 158 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 472 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO A 473 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 158 " -0.009 2.00e-02 2.50e+03 7.97e-03 1.27e+00 pdb=" CG TYR B 158 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 158 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 158 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 158 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 158 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 158 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 158 " 0.000 2.00e-02 2.50e+03 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 395 2.73 - 3.27: 7462 3.27 - 3.82: 12390 3.82 - 4.36: 15206 4.36 - 4.90: 25437 Nonbonded interactions: 60890 Sorted by model distance: nonbonded pdb=" O ALA A 39 " pdb=" OG1 THR A 43 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASP B 150 " pdb=" OH TYR B 267 " model vdw 2.247 3.040 nonbonded pdb=" O LEU B 256 " pdb=" OG1 THR B 260 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR A 339 " pdb=" O VAL A 341 " model vdw 2.270 3.040 nonbonded pdb=" NH2 ARG A 334 " pdb=" O PRO A 361 " model vdw 2.286 3.120 ... (remaining 60885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.830 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.004 0.033 7032 Z= 0.235 Angle : 0.589 6.359 9538 Z= 0.364 Chirality : 0.040 0.149 1124 Planarity : 0.003 0.028 1150 Dihedral : 14.675 88.512 2464 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 0.64 % Allowed : 15.17 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.28), residues: 842 helix: 1.58 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -0.69 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 471 HIS 0.006 0.002 HIS A 335 PHE 0.019 0.001 PHE B 23 TYR 0.020 0.002 TYR A 158 ARG 0.004 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.833 Fit side-chains REVERT: A 270 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7516 (mttt) REVERT: A 419 GLN cc_start: 0.7463 (tt0) cc_final: 0.7113 (tm-30) REVERT: A 454 ASP cc_start: 0.7436 (t0) cc_final: 0.7206 (t0) REVERT: A 494 LYS cc_start: 0.7513 (mttt) cc_final: 0.7121 (mmtt) REVERT: B 357 MET cc_start: 0.9040 (mmt) cc_final: 0.8839 (mmt) REVERT: B 419 GLN cc_start: 0.7305 (tt0) cc_final: 0.7010 (tm-30) REVERT: B 494 LYS cc_start: 0.7617 (mttt) cc_final: 0.7136 (mmtt) outliers start: 5 outliers final: 4 residues processed: 108 average time/residue: 1.2717 time to fit residues: 144.5957 Evaluate side-chains 98 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 340 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 76 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: A 79 ASN A 181 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 237 GLN B 300 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7032 Z= 0.162 Angle : 0.478 6.291 9538 Z= 0.262 Chirality : 0.038 0.137 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.750 49.868 924 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.57 % Allowed : 14.14 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.28), residues: 842 helix: 2.45 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.52 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.005 0.001 HIS B 335 PHE 0.016 0.001 PHE A 408 TYR 0.028 0.002 TYR A 158 ARG 0.004 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.856 Fit side-chains REVERT: A 270 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7174 (mttt) REVERT: A 343 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 357 MET cc_start: 0.9197 (mmt) cc_final: 0.8983 (mmt) REVERT: A 416 GLN cc_start: 0.7667 (mt0) cc_final: 0.7441 (tt0) REVERT: A 419 GLN cc_start: 0.7576 (tt0) cc_final: 0.7356 (tm-30) REVERT: B 151 GLU cc_start: 0.7153 (tt0) cc_final: 0.6878 (tt0) REVERT: B 357 MET cc_start: 0.9219 (mmt) cc_final: 0.8952 (mmt) REVERT: B 474 MET cc_start: 0.7966 (mmp) cc_final: 0.7737 (mmm) REVERT: B 494 LYS cc_start: 0.7770 (mttt) cc_final: 0.7110 (mmtt) outliers start: 20 outliers final: 4 residues processed: 112 average time/residue: 1.1685 time to fit residues: 138.3032 Evaluate side-chains 96 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7032 Z= 0.203 Angle : 0.486 6.167 9538 Z= 0.261 Chirality : 0.039 0.142 1124 Planarity : 0.003 0.030 1150 Dihedral : 4.385 37.828 920 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.49 % Favored : 97.39 % Rotamer: Outliers : 2.31 % Allowed : 13.88 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.28), residues: 842 helix: 2.58 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 PHE 0.013 0.001 PHE A 408 TYR 0.024 0.002 TYR A 158 ARG 0.004 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.764 Fit side-chains REVERT: A 24 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 44 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.7062 (tttt) REVERT: A 270 LYS cc_start: 0.7801 (mmtm) cc_final: 0.7214 (mttt) REVERT: A 343 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8680 (mp) REVERT: B 151 GLU cc_start: 0.7270 (tt0) cc_final: 0.7012 (tt0) REVERT: B 357 MET cc_start: 0.9201 (mmt) cc_final: 0.8921 (mmt) REVERT: B 474 MET cc_start: 0.7979 (mmp) cc_final: 0.7756 (mmm) REVERT: B 494 LYS cc_start: 0.7824 (mttt) cc_final: 0.7191 (mmtt) outliers start: 18 outliers final: 6 residues processed: 106 average time/residue: 1.2213 time to fit residues: 136.4725 Evaluate side-chains 103 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 340 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7032 Z= 0.193 Angle : 0.473 6.264 9538 Z= 0.255 Chirality : 0.038 0.143 1124 Planarity : 0.003 0.032 1150 Dihedral : 4.358 37.829 920 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.83 % Allowed : 14.27 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.28), residues: 842 helix: 2.63 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.32 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.005 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.023 0.002 TYR A 158 ARG 0.004 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.842 Fit side-chains REVERT: A 24 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 270 LYS cc_start: 0.7737 (mmtm) cc_final: 0.7166 (mttt) REVERT: A 343 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8676 (mp) REVERT: A 419 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: B 151 GLU cc_start: 0.7255 (tt0) cc_final: 0.7007 (tt0) REVERT: B 419 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: B 474 MET cc_start: 0.8014 (mmp) cc_final: 0.7793 (mmm) REVERT: B 494 LYS cc_start: 0.7854 (mttt) cc_final: 0.7241 (mmtm) outliers start: 22 outliers final: 7 residues processed: 115 average time/residue: 1.1793 time to fit residues: 143.1566 Evaluate side-chains 110 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 419 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7032 Z= 0.151 Angle : 0.447 7.586 9538 Z= 0.241 Chirality : 0.037 0.136 1124 Planarity : 0.003 0.033 1150 Dihedral : 4.188 36.686 920 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.57 % Allowed : 14.40 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.29), residues: 842 helix: 2.82 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.32 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.005 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.019 0.002 TYR A 158 ARG 0.004 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.833 Fit side-chains REVERT: A 24 LEU cc_start: 0.8455 (tp) cc_final: 0.8227 (mm) REVERT: A 270 LYS cc_start: 0.7715 (mmtm) cc_final: 0.7128 (mttt) REVERT: A 343 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8654 (mp) REVERT: A 419 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: B 70 SER cc_start: 0.8785 (t) cc_final: 0.8491 (p) REVERT: B 151 GLU cc_start: 0.7180 (tt0) cc_final: 0.6931 (tt0) REVERT: B 294 LEU cc_start: 0.8831 (tp) cc_final: 0.8587 (tp) REVERT: B 419 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: B 494 LYS cc_start: 0.7795 (mttt) cc_final: 0.7172 (mmtm) outliers start: 20 outliers final: 5 residues processed: 118 average time/residue: 1.2644 time to fit residues: 157.2910 Evaluate side-chains 105 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 419 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7032 Z= 0.346 Angle : 0.557 7.462 9538 Z= 0.296 Chirality : 0.042 0.158 1124 Planarity : 0.004 0.045 1150 Dihedral : 4.178 23.869 916 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.70 % Allowed : 14.78 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.28), residues: 842 helix: 2.41 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.40 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 471 HIS 0.006 0.002 HIS B 335 PHE 0.017 0.002 PHE A 366 TYR 0.026 0.002 TYR A 158 ARG 0.004 0.001 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.815 Fit side-chains REVERT: A 24 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8268 (mm) REVERT: A 270 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7264 (mttt) REVERT: A 343 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8670 (mp) REVERT: A 419 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 151 GLU cc_start: 0.7313 (tt0) cc_final: 0.7050 (tt0) REVERT: B 419 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: B 494 LYS cc_start: 0.7933 (mttt) cc_final: 0.7293 (mmtm) outliers start: 21 outliers final: 10 residues processed: 112 average time/residue: 1.1373 time to fit residues: 134.7448 Evaluate side-chains 111 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 419 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7032 Z= 0.168 Angle : 0.472 7.752 9538 Z= 0.252 Chirality : 0.038 0.144 1124 Planarity : 0.003 0.034 1150 Dihedral : 3.833 19.838 916 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 15.81 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.29), residues: 842 helix: 2.71 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.34 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.004 0.001 HIS A 335 PHE 0.015 0.001 PHE A 408 TYR 0.019 0.002 TYR B 158 ARG 0.005 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.722 Fit side-chains REVERT: A 24 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8234 (mm) REVERT: A 270 LYS cc_start: 0.7750 (mmtm) cc_final: 0.7220 (mttt) REVERT: A 343 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8648 (mp) REVERT: A 419 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: B 69 MET cc_start: 0.9161 (mmt) cc_final: 0.8657 (mmt) REVERT: B 151 GLU cc_start: 0.7275 (tt0) cc_final: 0.7022 (tt0) REVERT: B 419 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: B 494 LYS cc_start: 0.7828 (mttt) cc_final: 0.7203 (mmtm) outliers start: 16 outliers final: 7 residues processed: 111 average time/residue: 1.2050 time to fit residues: 140.9597 Evaluate side-chains 110 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 419 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7032 Z= 0.277 Angle : 0.534 7.731 9538 Z= 0.283 Chirality : 0.040 0.155 1124 Planarity : 0.004 0.040 1150 Dihedral : 4.103 24.080 916 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.31 % Allowed : 15.68 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.29), residues: 842 helix: 2.54 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 232 HIS 0.005 0.001 HIS A 335 PHE 0.013 0.002 PHE A 408 TYR 0.023 0.002 TYR B 158 ARG 0.004 0.001 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.835 Fit side-chains REVERT: A 24 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8255 (mm) REVERT: A 270 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7242 (mttt) REVERT: A 284 ARG cc_start: 0.8080 (tpp80) cc_final: 0.7866 (tpp80) REVERT: A 343 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8662 (mp) REVERT: A 419 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: B 151 GLU cc_start: 0.7296 (tt0) cc_final: 0.7042 (tt0) REVERT: B 419 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: B 494 LYS cc_start: 0.7900 (mttt) cc_final: 0.7269 (mmtm) outliers start: 18 outliers final: 9 residues processed: 111 average time/residue: 1.2138 time to fit residues: 142.0590 Evaluate side-chains 111 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 419 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7032 Z= 0.168 Angle : 0.479 7.751 9538 Z= 0.255 Chirality : 0.038 0.141 1124 Planarity : 0.003 0.034 1150 Dihedral : 3.833 20.276 916 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.83 % Allowed : 15.04 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.29), residues: 842 helix: 2.73 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 232 HIS 0.004 0.001 HIS A 335 PHE 0.014 0.001 PHE A 408 TYR 0.019 0.002 TYR B 158 ARG 0.005 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.803 Fit side-chains REVERT: A 24 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8227 (mm) REVERT: A 270 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7195 (mttt) REVERT: A 343 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8635 (mp) REVERT: A 419 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: A 474 MET cc_start: 0.7749 (mpp) cc_final: 0.7467 (mmm) REVERT: B 69 MET cc_start: 0.9141 (mmt) cc_final: 0.8699 (mmt) REVERT: B 151 GLU cc_start: 0.7218 (tt0) cc_final: 0.6964 (tt0) REVERT: B 294 LEU cc_start: 0.8826 (tp) cc_final: 0.8596 (tp) REVERT: B 419 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: B 494 LYS cc_start: 0.7805 (mttt) cc_final: 0.7192 (mmtm) outliers start: 22 outliers final: 8 residues processed: 116 average time/residue: 1.1211 time to fit residues: 137.3689 Evaluate side-chains 111 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 419 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7032 Z= 0.238 Angle : 0.520 7.808 9538 Z= 0.277 Chirality : 0.039 0.147 1124 Planarity : 0.004 0.035 1150 Dihedral : 4.016 23.219 916 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 1.80 % Allowed : 16.45 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.29), residues: 842 helix: 2.62 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.005 0.001 HIS A 335 PHE 0.013 0.001 PHE B 408 TYR 0.021 0.002 TYR B 158 ARG 0.008 0.001 ARG B 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.811 Fit side-chains REVERT: A 24 LEU cc_start: 0.8465 (tp) cc_final: 0.8240 (mm) REVERT: A 270 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7240 (mttt) REVERT: A 342 ASP cc_start: 0.8681 (t0) cc_final: 0.8453 (t0) REVERT: A 343 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8632 (mp) REVERT: A 419 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: A 474 MET cc_start: 0.7764 (mpp) cc_final: 0.7467 (mmm) REVERT: B 151 GLU cc_start: 0.7288 (tt0) cc_final: 0.7032 (tt0) REVERT: B 494 LYS cc_start: 0.7885 (mttt) cc_final: 0.7258 (mmtm) outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 1.2346 time to fit residues: 141.7617 Evaluate side-chains 110 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** 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 = 0.3245 r_free = 0.3245 target = 0.115260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.097054 restraints weight = 8284.627| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.45 r_work: 0.2890 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7032 Z= 0.167 Angle : 0.487 7.767 9538 Z= 0.260 Chirality : 0.038 0.139 1124 Planarity : 0.003 0.033 1150 Dihedral : 3.847 20.704 916 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 1.67 % Allowed : 16.84 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.29), residues: 842 helix: 2.71 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.30 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.004 0.001 HIS A 335 PHE 0.013 0.001 PHE A 408 TYR 0.019 0.002 TYR B 158 ARG 0.007 0.001 ARG B 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.59 seconds wall clock time: 52 minutes 20.15 seconds (3140.15 seconds total)