Starting phenix.real_space_refine on Mon Mar 11 03:42:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/03_2024/8w9n_37376.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/03_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_37376/03_2024/8w9n_37376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/03_2024/8w9n_37376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/03_2024/8w9n_37376.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9n_37376/03_2024/8w9n_37376.pdb" } 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-5265/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: 4.43, per 1000 atoms: 0.65 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: 2.70 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: 0.63 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: 2.04 Time building geometry restraints manager: 2.93 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 2.440 nonbonded pdb=" OD1 ASP B 150 " pdb=" OH TYR B 267 " model vdw 2.247 2.440 nonbonded pdb=" O LEU B 256 " pdb=" OG1 THR B 260 " model vdw 2.258 2.440 nonbonded pdb=" OG1 THR A 339 " pdb=" O VAL A 341 " model vdw 2.270 2.440 nonbonded pdb=" NH2 ARG A 334 " pdb=" O PRO A 361 " model vdw 2.286 2.520 ... (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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 2.340 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 22.470 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.040 ------------------------------------------------------------------------------- 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 : 0.742 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: 1.2049 time to fit residues: 137.2822 Evaluate side-chains 98 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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: 4.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 181 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN B 181 ASN B 237 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: 0.8340 moved from start: 0.0920 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= 0.183 Angle : 0.478 6.307 9538 Z= 0.261 Chirality : 0.038 0.144 1124 Planarity : 0.003 0.029 1150 Dihedral : 4.754 49.967 924 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 2.57 % Allowed : 14.65 % Favored : 82.78 % 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: 2.28 (0.28), residues: 842 helix: 2.43 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.55 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.005 0.001 HIS B 335 PHE 0.015 0.001 PHE A 408 TYR 0.028 0.002 TYR A 158 ARG 0.002 0.000 ARG A 284 *********************** 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 113 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.793 Fit side-chains REVERT: A 24 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8295 (mm) REVERT: A 270 LYS cc_start: 0.7847 (mmtm) cc_final: 0.7209 (mttt) REVERT: A 343 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8689 (mp) REVERT: A 416 GLN cc_start: 0.7700 (mt0) cc_final: 0.7487 (tt0) REVERT: A 419 GLN cc_start: 0.7587 (tt0) cc_final: 0.7342 (tm-30) REVERT: B 151 GLU cc_start: 0.7322 (tt0) cc_final: 0.7055 (tt0) REVERT: B 357 MET cc_start: 0.9253 (mmt) cc_final: 0.8955 (mmt) REVERT: B 474 MET cc_start: 0.7989 (mmp) cc_final: 0.7759 (mmm) REVERT: B 494 LYS cc_start: 0.7714 (mttt) cc_final: 0.7067 (mmtt) outliers start: 20 outliers final: 4 residues processed: 107 average time/residue: 1.1801 time to fit residues: 133.4679 Evaluate side-chains 97 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 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 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 396 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: 0.9980 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7032 Z= 0.165 Angle : 0.452 6.167 9538 Z= 0.244 Chirality : 0.037 0.140 1124 Planarity : 0.003 0.030 1150 Dihedral : 3.976 36.742 918 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 1.80 % Allowed : 15.04 % Favored : 83.16 % 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: 2.62 (0.29), residues: 842 helix: 2.69 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 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 0.003 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 108 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.784 Fit side-chains REVERT: A 24 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8265 (mm) REVERT: A 270 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7140 (mttt) REVERT: A 343 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8697 (mp) REVERT: A 416 GLN cc_start: 0.7853 (mt0) cc_final: 0.7556 (tp40) REVERT: B 151 GLU cc_start: 0.7263 (tt0) cc_final: 0.7012 (tt0) REVERT: B 357 MET cc_start: 0.9233 (mmt) cc_final: 0.8901 (mmt) REVERT: B 474 MET cc_start: 0.7976 (mmp) cc_final: 0.7758 (mmm) REVERT: B 494 LYS cc_start: 0.7778 (mttt) cc_final: 0.7130 (mmtt) outliers start: 14 outliers final: 4 residues processed: 103 average time/residue: 1.2144 time to fit residues: 131.9692 Evaluate side-chains 96 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 343 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 ** 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: 0.1235 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= 0.249 Angle : 0.501 6.487 9538 Z= 0.269 Chirality : 0.040 0.153 1124 Planarity : 0.003 0.033 1150 Dihedral : 4.001 23.955 916 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 2.83 % Allowed : 14.14 % 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: 2.49 (0.28), residues: 842 helix: 2.56 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.41 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 PHE 0.014 0.002 PHE A 366 TYR 0.024 0.002 TYR A 158 ARG 0.002 0.000 ARG A 284 *********************** 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 120 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.818 Fit side-chains REVERT: A 24 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8282 (mm) REVERT: A 44 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7143 (tttt) REVERT: A 270 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7172 (mttt) REVERT: A 343 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8682 (mp) REVERT: A 419 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: B 151 GLU cc_start: 0.7291 (tt0) cc_final: 0.6834 (tt0) REVERT: B 357 MET cc_start: 0.9197 (mmt) cc_final: 0.8875 (mmt) REVERT: B 419 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: B 454 ASP cc_start: 0.7352 (t0) cc_final: 0.7072 (t0) REVERT: B 494 LYS cc_start: 0.7907 (mttt) cc_final: 0.7260 (mmtm) outliers start: 22 outliers final: 8 residues processed: 111 average time/residue: 1.1682 time to fit residues: 137.1770 Evaluate side-chains 109 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 68 SER Chi-restraints excluded: chain A residue 100 LEU 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 A residue 419 GLN Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 343 LEU 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: 0.5980 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7032 Z= 0.177 Angle : 0.462 6.035 9538 Z= 0.248 Chirality : 0.038 0.146 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.825 21.685 916 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 2.57 % Allowed : 14.27 % Favored : 83.16 % 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: 2.63 (0.29), residues: 842 helix: 2.71 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.45 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.005 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.021 0.002 TYR A 158 ARG 0.004 0.000 ARG A 284 *********************** 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 115 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.813 Fit side-chains REVERT: A 24 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8239 (mm) REVERT: A 44 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7124 (tttt) REVERT: A 270 LYS cc_start: 0.7733 (mmtm) cc_final: 0.7218 (mttt) REVERT: A 343 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 416 GLN cc_start: 0.7947 (mt0) cc_final: 0.7658 (tp40) REVERT: A 419 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: B 151 GLU cc_start: 0.7066 (tt0) cc_final: 0.6834 (tt0) REVERT: B 357 MET cc_start: 0.9182 (mmt) cc_final: 0.8825 (mmt) REVERT: B 474 MET cc_start: 0.7971 (mmp) cc_final: 0.7770 (mmm) REVERT: B 494 LYS cc_start: 0.7829 (mttt) cc_final: 0.7228 (mmtm) outliers start: 20 outliers final: 9 residues processed: 108 average time/residue: 1.2794 time to fit residues: 145.9100 Evaluate side-chains 104 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 68 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 273 ASN 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 A residue 419 GLN Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8339 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7032 Z= 0.151 Angle : 0.444 5.844 9538 Z= 0.239 Chirality : 0.037 0.141 1124 Planarity : 0.003 0.031 1150 Dihedral : 3.712 20.780 916 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.70 % Allowed : 14.65 % Favored : 82.65 % 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: 2.75 (0.29), residues: 842 helix: 2.81 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.005 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.020 0.002 TYR A 158 ARG 0.003 0.000 ARG A 284 *********************** 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 115 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.917 Fit side-chains REVERT: A 24 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8234 (mm) REVERT: A 270 LYS cc_start: 0.7722 (mmtm) cc_final: 0.7193 (mttt) REVERT: A 343 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8693 (mp) REVERT: A 416 GLN cc_start: 0.7941 (mt0) cc_final: 0.7651 (tp40) REVERT: A 419 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: B 151 GLU cc_start: 0.7069 (tt0) cc_final: 0.6844 (tt0) REVERT: B 294 LEU cc_start: 0.8822 (tp) cc_final: 0.8586 (tp) REVERT: B 357 MET cc_start: 0.9211 (mmt) cc_final: 0.8840 (mmt) REVERT: B 419 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: B 494 LYS cc_start: 0.7803 (mttt) cc_final: 0.7204 (mmtm) outliers start: 21 outliers final: 5 residues processed: 107 average time/residue: 1.2817 time to fit residues: 144.5410 Evaluate side-chains 103 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 343 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 273 ASN 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: 2.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7032 Z= 0.173 Angle : 0.461 7.212 9538 Z= 0.247 Chirality : 0.037 0.143 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.742 21.434 916 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 2.57 % Allowed : 15.04 % Favored : 82.39 % 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: 2.75 (0.29), residues: 842 helix: 2.81 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.44 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.005 0.001 HIS B 335 PHE 0.013 0.001 PHE A 408 TYR 0.020 0.002 TYR A 158 ARG 0.004 0.000 ARG B 420 *********************** 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 115 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.803 Fit side-chains REVERT: A 24 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8238 (mm) REVERT: A 44 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6943 (tptt) REVERT: A 270 LYS cc_start: 0.7723 (mmtm) cc_final: 0.7187 (mttt) REVERT: A 343 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8701 (mp) REVERT: A 416 GLN cc_start: 0.8008 (mt0) cc_final: 0.7685 (tp40) REVERT: A 419 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: B 294 LEU cc_start: 0.8826 (tp) cc_final: 0.8594 (tp) REVERT: B 357 MET cc_start: 0.9205 (mmt) cc_final: 0.8812 (mmt) REVERT: B 419 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: B 494 LYS cc_start: 0.7770 (mttt) cc_final: 0.7186 (mmtm) outliers start: 20 outliers final: 9 residues processed: 108 average time/residue: 1.1407 time to fit residues: 130.2857 Evaluate side-chains 107 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 42 ILE Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 273 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1464 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= 0.213 Angle : 0.484 7.270 9538 Z= 0.259 Chirality : 0.039 0.149 1124 Planarity : 0.003 0.033 1150 Dihedral : 3.835 22.438 916 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.96 % Allowed : 15.04 % 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: 2.66 (0.29), residues: 842 helix: 2.72 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.43 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 PHE 0.013 0.001 PHE A 408 TYR 0.022 0.002 TYR A 158 ARG 0.005 0.000 ARG B 420 *********************** 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 119 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.841 Fit side-chains REVERT: A 24 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8243 (mm) REVERT: A 44 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6836 (tptt) REVERT: A 270 LYS cc_start: 0.7700 (mmtm) cc_final: 0.7132 (mttt) REVERT: A 343 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 416 GLN cc_start: 0.8023 (mt0) cc_final: 0.7707 (tp40) REVERT: A 419 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: B 294 LEU cc_start: 0.8826 (tp) cc_final: 0.8593 (tp) REVERT: B 357 MET cc_start: 0.9208 (mmt) cc_final: 0.8771 (mmt) REVERT: B 419 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: B 420 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7947 (mtm180) REVERT: B 494 LYS cc_start: 0.7837 (mttt) cc_final: 0.7231 (mmtm) outliers start: 23 outliers final: 8 residues processed: 111 average time/residue: 1.1489 time to fit residues: 135.1302 Evaluate side-chains 108 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 42 ILE Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 273 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** 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: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7032 Z= 0.183 Angle : 0.472 7.401 9538 Z= 0.253 Chirality : 0.038 0.148 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.791 21.674 916 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 2.57 % Allowed : 15.42 % 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: 2.72 (0.29), residues: 842 helix: 2.76 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 232 HIS 0.005 0.001 HIS B 335 PHE 0.013 0.001 PHE A 408 TYR 0.020 0.002 TYR A 158 ARG 0.005 0.000 ARG B 420 *********************** 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 115 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.807 Fit side-chains REVERT: A 24 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8239 (mm) REVERT: A 270 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7136 (mttt) REVERT: A 343 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 416 GLN cc_start: 0.8020 (mt0) cc_final: 0.7701 (tp40) REVERT: A 419 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 294 LEU cc_start: 0.8826 (tp) cc_final: 0.8580 (tp) REVERT: B 357 MET cc_start: 0.9212 (mmt) cc_final: 0.8772 (mmt) REVERT: B 419 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: B 420 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7939 (mtm180) REVERT: B 494 LYS cc_start: 0.7818 (mttt) cc_final: 0.7214 (mmtm) outliers start: 20 outliers final: 10 residues processed: 109 average time/residue: 1.1156 time to fit residues: 128.7111 Evaluate side-chains 108 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 42 ILE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 273 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7032 Z= 0.185 Angle : 0.478 8.426 9538 Z= 0.256 Chirality : 0.038 0.147 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.800 21.836 916 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 15.94 % 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: 2.70 (0.29), residues: 842 helix: 2.74 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.39 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 232 HIS 0.005 0.001 HIS B 335 PHE 0.013 0.001 PHE A 408 TYR 0.020 0.002 TYR B 158 ARG 0.004 0.000 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 111 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.801 Fit side-chains REVERT: A 24 LEU cc_start: 0.8479 (tp) cc_final: 0.8243 (mm) REVERT: A 270 LYS cc_start: 0.7689 (mmtm) cc_final: 0.7125 (mttt) REVERT: A 343 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8704 (mp) REVERT: A 416 GLN cc_start: 0.8023 (mt0) cc_final: 0.7706 (tp40) REVERT: A 419 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: B 294 LEU cc_start: 0.8825 (tp) cc_final: 0.8575 (tp) REVERT: B 315 GLU cc_start: 0.7939 (tp30) cc_final: 0.7693 (mm-30) REVERT: B 357 MET cc_start: 0.9205 (mmt) cc_final: 0.8765 (mmt) REVERT: B 419 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: B 494 LYS cc_start: 0.7781 (mttt) cc_final: 0.7195 (mmtm) outliers start: 16 outliers final: 11 residues processed: 107 average time/residue: 1.2554 time to fit residues: 141.6798 Evaluate side-chains 106 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 273 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.0870 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.098936 restraints weight = 8313.469| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.44 r_work: 0.2911 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7032 Z= 0.137 Angle : 0.454 8.279 9538 Z= 0.244 Chirality : 0.037 0.143 1124 Planarity : 0.003 0.031 1150 Dihedral : 3.666 20.034 916 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.06 % Allowed : 16.07 % Favored : 81.88 % 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: 2.83 (0.29), residues: 842 helix: 2.88 (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 0.004 0.001 TRP A 232 HIS 0.004 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.018 0.001 TYR B 158 ARG 0.006 0.000 ARG B 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.86 seconds wall clock time: 48 minutes 32.53 seconds (2912.53 seconds total)