Starting phenix.real_space_refine on Sat Aug 3 03:34:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/08_2024/8w9o_37377.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/08_2024/8w9o_37377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/08_2024/8w9o_37377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/08_2024/8w9o_37377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/08_2024/8w9o_37377.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/08_2024/8w9o_37377.cif" } resolution = 2.8 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 K 4 8.98 5 S 40 5.16 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 94": "OE1" <-> "OE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 371": "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: 6862 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.02, per 1000 atoms: 0.59 Number of scatterers: 6862 At special positions: 0 Unit cell: (103.23, 89.28, 85.56, 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) K 4 19.00 S 40 16.00 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: 2.69 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: 43 helices and 2 sheets defined 72.7% alpha, 0.5% 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 43 Processing helix chain 'A' and resid 52 through 65 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 149 through 183 Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.794A pdb=" N VAL A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 3.713A 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 Processing helix chain 'A' and resid 244 through 261 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 282 through 308 Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.617A pdb=" N LEU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.231A 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 454 through 458 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 472 through 488 Processing helix chain 'B' and resid 22 through 43 Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 149 through 183 Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.767A pdb=" N VAL B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 3.672A 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 261 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 through 308 Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.532A pdb=" N LEU B 323 " --> pdb=" O SER B 319 " (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 removed outlier: 3.539A pdb=" N GLN B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 440 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 365 through 366 Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 500 448 hydrogen bonds defined for protein. 1272 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: 1.87 Time building geometry restraints manager: 2.89 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: 2004 1.34 - 1.45: 1203 1.45 - 1.57: 3761 1.57 - 1.69: 0 1.69 - 1.80: 64 Bond restraints: 7032 Sorted by residual: bond pdb=" CB THR B 71 " pdb=" CG2 THR B 71 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.29e+00 bond pdb=" CG LYS A 184 " pdb=" CD LYS A 184 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" C MET A 367 " pdb=" O MET A 367 " ideal model delta sigma weight residual 1.242 1.230 0.012 1.16e-02 7.43e+03 1.06e+00 bond pdb=" CB LYS A 184 " pdb=" CG LYS A 184 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CG LYS B 184 " pdb=" CD LYS B 184 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.40e-01 ... (remaining 7027 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.36: 139 106.36 - 113.28: 3837 113.28 - 120.19: 2546 120.19 - 127.10: 2961 127.10 - 134.01: 55 Bond angle restraints: 9538 Sorted by residual: angle pdb=" CB LYS A 184 " pdb=" CG LYS A 184 " pdb=" CD LYS A 184 " ideal model delta sigma weight residual 111.30 118.99 -7.69 2.30e+00 1.89e-01 1.12e+01 angle pdb=" CB LYS B 184 " pdb=" CG LYS B 184 " pdb=" CD LYS B 184 " ideal model delta sigma weight residual 111.30 117.99 -6.69 2.30e+00 1.89e-01 8.45e+00 angle pdb=" CA TYR A 158 " pdb=" CB TYR A 158 " pdb=" CG TYR A 158 " ideal model delta sigma weight residual 113.90 118.63 -4.73 1.80e+00 3.09e-01 6.91e+00 angle pdb=" CA TYR B 158 " pdb=" CB TYR B 158 " pdb=" CG TYR B 158 " ideal model delta sigma weight residual 113.90 118.41 -4.51 1.80e+00 3.09e-01 6.29e+00 angle pdb=" CA GLU A 194 " pdb=" CB GLU A 194 " pdb=" CG GLU A 194 " ideal model delta sigma weight residual 114.10 118.55 -4.45 2.00e+00 2.50e-01 4.95e+00 ... (remaining 9533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3560 17.36 - 34.72: 387 34.72 - 52.08: 111 52.08 - 69.44: 9 69.44 - 86.80: 7 Dihedral angle restraints: 4074 sinusoidal: 1584 harmonic: 2490 Sorted by residual: 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 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 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 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA THR B 65 " pdb=" C THR B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 4071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 618 0.030 - 0.059: 354 0.059 - 0.089: 105 0.089 - 0.118: 38 0.118 - 0.148: 9 Chirality restraints: 1124 Sorted by residual: 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 5.48e-01 chirality pdb=" CG LEU B 323 " pdb=" CB LEU B 323 " pdb=" CD1 LEU B 323 " pdb=" CD2 LEU B 323 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE B 195 " pdb=" N ILE B 195 " pdb=" C ILE B 195 " pdb=" CB ILE B 195 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1121 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 158 " -0.013 2.00e-02 2.50e+03 1.11e-02 2.48e+00 pdb=" CG TYR B 158 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 158 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 158 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 158 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 158 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 158 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 158 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 158 " 0.013 2.00e-02 2.50e+03 1.11e-02 2.48e+00 pdb=" CG TYR A 158 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 158 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 158 " 0.002 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 " 0.002 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=" CB ASP A 188 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.38e+00 pdb=" CG ASP A 188 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP A 188 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP A 188 " 0.007 2.00e-02 2.50e+03 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 2007 2.80 - 3.39: 7906 3.39 - 3.97: 13899 3.97 - 4.56: 20701 4.56 - 5.14: 28082 Nonbonded interactions: 72595 Sorted by model distance: nonbonded pdb=" O VAL A 427 " pdb=" OG1 THR A 431 " model vdw 2.217 3.040 nonbonded pdb=" O ALA B 39 " pdb=" OG1 THR B 43 " model vdw 2.252 3.040 nonbonded pdb=" O LYS B 155 " pdb=" OG SER B 159 " model vdw 2.263 3.040 nonbonded pdb=" O ASN A 169 " pdb=" OG SER A 173 " model vdw 2.264 3.040 nonbonded pdb=" OD1 ASP A 150 " pdb=" OH TYR A 267 " model vdw 2.267 3.040 ... (remaining 72590 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.870 Find NCS groups from input model: 0.190 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:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.005 0.038 7032 Z= 0.296 Angle : 0.539 7.685 9538 Z= 0.290 Chirality : 0.041 0.148 1124 Planarity : 0.003 0.027 1150 Dihedral : 15.896 86.800 2464 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.31 % Allowed : 19.41 % Favored : 78.28 % 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: 0.95 (0.29), residues: 842 helix: 1.39 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.68 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 PHE 0.014 0.002 PHE B 32 TYR 0.027 0.002 TYR B 158 ARG 0.003 0.000 ARG B 50 *********************** 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 122 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.714 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 1.0519 time to fit residues: 130.7901 Evaluate side-chains 113 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 444 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 211 ASN A 220 ASN A 237 GLN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 211 ASN B 220 ASN B 237 GLN B 300 GLN B 332 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 426 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7032 Z= 0.210 Angle : 0.512 5.860 9538 Z= 0.282 Chirality : 0.040 0.143 1124 Planarity : 0.004 0.029 1150 Dihedral : 5.591 47.710 940 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.83 % Allowed : 17.87 % Favored : 79.31 % 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: 1.42 (0.29), residues: 842 helix: 1.68 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.56 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.004 0.001 HIS B 335 PHE 0.015 0.001 PHE A 408 TYR 0.028 0.002 TYR A 158 ARG 0.004 0.001 ARG B 152 *********************** 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 132 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.836 Fit side-chains REVERT: A 248 PHE cc_start: 0.8059 (m-80) cc_final: 0.7780 (m-80) REVERT: A 343 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8007 (mp) REVERT: A 416 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7271 (mm-40) REVERT: B 220 ASN cc_start: 0.7687 (OUTLIER) cc_final: 0.7481 (t0) REVERT: B 288 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6928 (mp) REVERT: B 417 ASN cc_start: 0.7525 (m-40) cc_final: 0.7266 (m-40) outliers start: 22 outliers final: 5 residues processed: 127 average time/residue: 0.9908 time to fit residues: 133.7559 Evaluate side-chains 112 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 302 LEU 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: 7.9990 chunk 23 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 237 GLN A 242 ASN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 HIS B 101 ASN B 220 ASN B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS B 416 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7032 Z= 0.329 Angle : 0.556 6.179 9538 Z= 0.302 Chirality : 0.043 0.152 1124 Planarity : 0.004 0.030 1150 Dihedral : 4.835 48.042 918 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.73 % Allowed : 18.25 % Favored : 78.02 % 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: 1.22 (0.29), residues: 842 helix: 1.55 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -0.68 (0.41), residues: 278 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 0.002 PHE A 32 TYR 0.033 0.002 TYR A 158 ARG 0.003 0.000 ARG A 46 *********************** 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 138 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.816 Fit side-chains REVERT: A 248 PHE cc_start: 0.8066 (m-80) cc_final: 0.7704 (m-80) REVERT: A 343 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8031 (mp) REVERT: A 416 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7525 (mm110) REVERT: B 103 TYR cc_start: 0.7379 (t80) cc_final: 0.6880 (t80) REVERT: B 288 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6908 (mp) REVERT: B 417 ASN cc_start: 0.7546 (m-40) cc_final: 0.7276 (m-40) outliers start: 29 outliers final: 11 residues processed: 129 average time/residue: 1.0229 time to fit residues: 140.2415 Evaluate side-chains 120 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 396 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 237 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 101 ASN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 332 ASN B 416 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7032 Z= 0.253 Angle : 0.520 6.122 9538 Z= 0.282 Chirality : 0.041 0.174 1124 Planarity : 0.004 0.030 1150 Dihedral : 4.757 48.452 918 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.88 % Allowed : 17.35 % Favored : 77.76 % 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: 1.34 (0.29), residues: 842 helix: 1.63 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.63 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.003 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.026 0.002 TYR A 158 ARG 0.004 0.000 ARG B 334 *********************** 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 149 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 111 time to evaluate : 0.699 Fit side-chains REVERT: A 109 LYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5649 (tttt) REVERT: A 237 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8542 (mm-40) REVERT: A 248 PHE cc_start: 0.8053 (m-80) cc_final: 0.7608 (m-80) REVERT: A 343 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8010 (mp) REVERT: A 416 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7491 (mm110) REVERT: B 103 TYR cc_start: 0.7416 (t80) cc_final: 0.6860 (t80) REVERT: B 417 ASN cc_start: 0.7569 (m-40) cc_final: 0.7290 (m-40) outliers start: 38 outliers final: 13 residues processed: 134 average time/residue: 0.9826 time to fit residues: 140.3884 Evaluate side-chains 122 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 237 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7032 Z= 0.251 Angle : 0.525 6.047 9538 Z= 0.283 Chirality : 0.041 0.157 1124 Planarity : 0.004 0.030 1150 Dihedral : 4.761 48.337 918 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.98 % Allowed : 18.25 % Favored : 77.76 % 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: 1.39 (0.29), residues: 842 helix: 1.68 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.63 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.003 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.026 0.002 TYR A 158 ARG 0.003 0.000 ARG B 334 *********************** 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 142 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 109 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5686 (tttt) REVERT: A 248 PHE cc_start: 0.8037 (m-80) cc_final: 0.7598 (m-80) REVERT: A 343 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8009 (mp) REVERT: A 416 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7185 (mm-40) REVERT: B 103 TYR cc_start: 0.7475 (t80) cc_final: 0.6914 (t80) REVERT: B 417 ASN cc_start: 0.7569 (m-40) cc_final: 0.7297 (m-40) outliers start: 31 outliers final: 13 residues processed: 131 average time/residue: 0.9835 time to fit residues: 137.1732 Evaluate side-chains 121 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.0010 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 237 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN B 101 ASN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 332 ASN B 416 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7032 Z= 0.154 Angle : 0.472 5.477 9538 Z= 0.256 Chirality : 0.039 0.138 1124 Planarity : 0.003 0.030 1150 Dihedral : 4.546 47.761 918 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.96 % Allowed : 19.15 % Favored : 77.89 % 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: 1.80 (0.29), residues: 842 helix: 1.98 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.47 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 232 HIS 0.003 0.001 HIS B 165 PHE 0.015 0.001 PHE A 408 TYR 0.017 0.002 TYR B 158 ARG 0.005 0.000 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 141 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.798 Fit side-chains REVERT: A 248 PHE cc_start: 0.8011 (m-80) cc_final: 0.7573 (m-80) REVERT: A 343 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7901 (mp) REVERT: A 416 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7142 (mm-40) REVERT: B 103 TYR cc_start: 0.7502 (t80) cc_final: 0.7045 (t80) REVERT: B 417 ASN cc_start: 0.7545 (m-40) cc_final: 0.7264 (m-40) outliers start: 23 outliers final: 9 residues processed: 134 average time/residue: 0.9208 time to fit residues: 132.0656 Evaluate side-chains 119 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 449 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 237 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1845 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= 0.170 Angle : 0.478 5.445 9538 Z= 0.258 Chirality : 0.039 0.154 1124 Planarity : 0.004 0.031 1150 Dihedral : 4.525 47.148 918 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.60 % Allowed : 20.31 % Favored : 76.09 % 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: 1.87 (0.29), residues: 842 helix: 2.05 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.47 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.003 0.001 HIS B 335 PHE 0.017 0.001 PHE B 477 TYR 0.019 0.002 TYR B 158 ARG 0.004 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 139 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.850 Fit side-chains REVERT: A 237 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8517 (mm-40) REVERT: A 248 PHE cc_start: 0.7986 (m-80) cc_final: 0.7493 (m-80) REVERT: A 343 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7932 (mp) REVERT: A 416 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7120 (mm-40) REVERT: B 103 TYR cc_start: 0.7522 (t80) cc_final: 0.7042 (t80) REVERT: B 417 ASN cc_start: 0.7551 (m-40) cc_final: 0.7265 (m-40) outliers start: 28 outliers final: 14 residues processed: 130 average time/residue: 0.9225 time to fit residues: 128.1642 Evaluate side-chains 122 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 449 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 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 101 ASN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 220 ASN B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7032 Z= 0.167 Angle : 0.494 9.173 9538 Z= 0.263 Chirality : 0.039 0.220 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.482 46.780 918 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.21 % Allowed : 20.82 % Favored : 75.96 % 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: 1.90 (0.30), residues: 842 helix: 2.08 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.47 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 232 HIS 0.003 0.001 HIS B 165 PHE 0.014 0.001 PHE A 408 TYR 0.018 0.002 TYR B 158 ARG 0.004 0.000 ARG B 334 *********************** 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 133 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.797 Fit side-chains REVERT: A 248 PHE cc_start: 0.7976 (m-80) cc_final: 0.7482 (m-80) REVERT: A 343 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7933 (mp) REVERT: A 416 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7117 (mm-40) REVERT: B 103 TYR cc_start: 0.7556 (t80) cc_final: 0.7098 (t80) REVERT: B 417 ASN cc_start: 0.7554 (m-40) cc_final: 0.7260 (m-40) outliers start: 25 outliers final: 15 residues processed: 125 average time/residue: 0.9319 time to fit residues: 124.4945 Evaluate side-chains 124 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 449 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7032 Z= 0.155 Angle : 0.486 8.326 9538 Z= 0.259 Chirality : 0.039 0.183 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.395 46.063 918 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.70 % Allowed : 21.47 % Favored : 75.84 % 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: 1.97 (0.30), residues: 842 helix: 2.13 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.45 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 232 HIS 0.003 0.001 HIS B 165 PHE 0.014 0.001 PHE A 408 TYR 0.018 0.002 TYR B 158 ARG 0.004 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 133 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.794 Fit side-chains REVERT: A 248 PHE cc_start: 0.7955 (m-80) cc_final: 0.7500 (m-80) REVERT: A 343 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7934 (mp) REVERT: A 416 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7064 (mm-40) REVERT: B 103 TYR cc_start: 0.7539 (t80) cc_final: 0.7114 (t80) REVERT: B 417 ASN cc_start: 0.7541 (m-40) cc_final: 0.7243 (m-40) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 0.9321 time to fit residues: 125.3954 Evaluate side-chains 119 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 449 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 83 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7032 Z= 0.193 Angle : 0.509 7.834 9538 Z= 0.271 Chirality : 0.040 0.170 1124 Planarity : 0.004 0.030 1150 Dihedral : 4.217 23.199 916 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.44 % Allowed : 22.11 % Favored : 75.45 % 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: 1.90 (0.30), residues: 842 helix: 2.08 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.46 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.003 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.020 0.002 TYR B 158 ARG 0.004 0.000 ARG B 152 ********************** 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 123 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.783 Fit side-chains REVERT: A 343 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7984 (mp) REVERT: A 416 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7103 (mm-40) REVERT: B 103 TYR cc_start: 0.7566 (t80) cc_final: 0.7106 (t80) REVERT: B 417 ASN cc_start: 0.7564 (m-40) cc_final: 0.7226 (t0) outliers start: 19 outliers final: 13 residues processed: 118 average time/residue: 0.9252 time to fit residues: 116.6170 Evaluate side-chains 119 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 449 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN B 101 ASN B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.153027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133996 restraints weight = 8427.590| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.61 r_work: 0.3373 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7032 Z= 0.171 Angle : 0.498 7.720 9538 Z= 0.266 Chirality : 0.039 0.167 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.161 22.866 916 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.44 % Allowed : 22.11 % Favored : 75.45 % 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: 1.94 (0.29), residues: 842 helix: 2.13 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.46 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.003 0.001 HIS B 165 PHE 0.014 0.001 PHE A 408 TYR 0.019 0.002 TYR B 158 ARG 0.005 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.62 seconds wall clock time: 49 minutes 43.50 seconds (2983.50 seconds total)