Starting phenix.real_space_refine on Mon Mar 11 03:40:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/03_2024/8w9o_37377.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/03_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_37377/03_2024/8w9o_37377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/03_2024/8w9o_37377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/03_2024/8w9o_37377.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9o_37377/03_2024/8w9o_37377.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.29, per 1000 atoms: 0.63 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: 2.98 Conformation dependent library (CDL) restraints added in 1.3 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: 0.73 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: 1.98 Time building geometry restraints manager: 3.16 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 2.440 nonbonded pdb=" O ALA B 39 " pdb=" OG1 THR B 43 " model vdw 2.252 2.440 nonbonded pdb=" O LYS B 155 " pdb=" OG SER B 159 " model vdw 2.263 2.440 nonbonded pdb=" O ASN A 169 " pdb=" OG SER A 173 " model vdw 2.264 2.440 nonbonded pdb=" OD1 ASP A 150 " pdb=" OH TYR A 267 " model vdw 2.267 2.440 ... (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 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: 0.770 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: 2.490 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.540 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.320 ------------------------------------------------------------------------------- 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 : 0.873 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 1.0654 time to fit residues: 132.2921 Evaluate side-chains 113 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B 101 ASN B 211 ASN B 220 ASN B 237 GLN B 300 GLN B 332 ASN B 416 GLN B 426 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7032 Z= 0.305 Angle : 0.553 6.472 9538 Z= 0.301 Chirality : 0.042 0.147 1124 Planarity : 0.004 0.030 1150 Dihedral : 5.863 48.603 940 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.08 % Allowed : 18.77 % Favored : 78.15 % 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: 1.15 (0.29), residues: 842 helix: 1.50 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.70 (0.40), residues: 280 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 408 TYR 0.035 0.002 TYR A 158 ARG 0.003 0.000 ARG B 50 *********************** 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 133 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.819 Fit side-chains REVERT: A 248 PHE cc_start: 0.8083 (m-80) cc_final: 0.7809 (m-80) REVERT: A 343 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 416 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7723 (mm110) REVERT: B 35 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7619 (mp) REVERT: B 103 TYR cc_start: 0.7266 (t80) cc_final: 0.6821 (t80) REVERT: B 288 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6972 (mp) outliers start: 24 outliers final: 7 residues processed: 126 average time/residue: 1.0446 time to fit residues: 139.7603 Evaluate side-chains 117 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 194 GLU 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 416 GLN Chi-restraints excluded: chain B residue 35 LEU 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: 5.9990 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN A 237 GLN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN B 101 ASN B 220 ASN B 237 GLN B 332 ASN B 416 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1341 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= 0.149 Angle : 0.460 5.284 9538 Z= 0.250 Chirality : 0.038 0.136 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.492 48.587 919 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.34 % Allowed : 19.28 % Favored : 77.38 % 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: 1.71 (0.29), residues: 842 helix: 1.94 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.57 (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 0.015 0.001 PHE A 408 TYR 0.017 0.002 TYR B 158 ARG 0.003 0.000 ARG A 497 *********************** 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 143 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 248 PHE cc_start: 0.8015 (m-80) cc_final: 0.7581 (m-80) REVERT: A 343 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 416 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7169 (mm-40) REVERT: B 152 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.5679 (ttp-110) outliers start: 26 outliers final: 7 residues processed: 133 average time/residue: 0.9810 time to fit residues: 138.8856 Evaluate side-chains 115 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 198 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 152 ARG Chi-restraints excluded: chain B residue 264 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 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 B 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1387 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= 0.195 Angle : 0.480 5.573 9538 Z= 0.258 Chirality : 0.039 0.135 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.504 47.674 918 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.86 % Allowed : 20.31 % 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: 1.74 (0.29), residues: 842 helix: 1.99 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.60 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.004 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.021 0.002 TYR A 158 ARG 0.002 0.000 ARG A 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 138 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 109 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5642 (tttt) REVERT: A 248 PHE cc_start: 0.8039 (m-80) cc_final: 0.7618 (m-80) REVERT: A 343 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7992 (mp) REVERT: A 416 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7189 (mm-40) REVERT: B 152 ARG cc_start: 0.6435 (tpp-160) cc_final: 0.5962 (ttp80) REVERT: B 417 ASN cc_start: 0.7582 (m-40) cc_final: 0.7308 (m-40) outliers start: 30 outliers final: 11 residues processed: 129 average time/residue: 1.0960 time to fit residues: 150.2730 Evaluate side-chains 118 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 198 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 A residue 444 THR Chi-restraints excluded: chain B residue 250 VAL 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 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: 6.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 101 ASN B 237 GLN B 335 HIS B 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1555 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= 0.176 Angle : 0.475 6.740 9538 Z= 0.254 Chirality : 0.039 0.208 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.437 47.398 918 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.47 % Allowed : 20.31 % Favored : 76.22 % 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: 1.86 (0.29), residues: 842 helix: 2.08 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.57 (0.41), residues: 276 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 0.014 0.001 PHE A 408 TYR 0.020 0.002 TYR B 158 ARG 0.002 0.000 ARG A 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 134 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 109 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5622 (tttt) REVERT: A 248 PHE cc_start: 0.8054 (m-80) cc_final: 0.7554 (m-80) REVERT: A 343 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.7980 (mp) REVERT: A 416 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7186 (mm-40) REVERT: B 417 ASN cc_start: 0.7560 (m-40) cc_final: 0.7289 (m-40) outliers start: 27 outliers final: 14 residues processed: 126 average time/residue: 1.1566 time to fit residues: 154.4980 Evaluate side-chains 120 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 198 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 A residue 444 THR 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 444 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 237 GLN B 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7032 Z= 0.213 Angle : 0.490 5.661 9538 Z= 0.262 Chirality : 0.040 0.157 1124 Planarity : 0.003 0.029 1150 Dihedral : 4.517 47.351 918 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.86 % Allowed : 20.69 % 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: 1.82 (0.29), residues: 842 helix: 2.05 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.58 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.004 0.001 HIS B 165 PHE 0.014 0.001 PHE A 408 TYR 0.022 0.002 TYR A 158 ARG 0.002 0.000 ARG A 497 *********************** 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 139 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8003 (m-30) cc_final: 0.7745 (m-30) REVERT: A 109 LYS cc_start: 0.5964 (OUTLIER) cc_final: 0.5573 (mtmm) REVERT: A 248 PHE cc_start: 0.8058 (m-80) cc_final: 0.7586 (m-80) REVERT: A 343 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 416 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7187 (mm-40) REVERT: B 417 ASN cc_start: 0.7573 (m-40) cc_final: 0.7304 (m-40) outliers start: 30 outliers final: 15 residues processed: 132 average time/residue: 0.9697 time to fit residues: 137.7852 Evaluate side-chains 126 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 339 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 A residue 444 THR 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 444 THR 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: 3.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 242 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 416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1578 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= 0.213 Angle : 0.495 5.651 9538 Z= 0.265 Chirality : 0.040 0.155 1124 Planarity : 0.003 0.029 1150 Dihedral : 4.530 47.555 918 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.34 % Allowed : 21.21 % 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: 1.81 (0.29), residues: 842 helix: 2.04 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.58 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.004 0.001 HIS B 165 PHE 0.013 0.001 PHE A 408 TYR 0.022 0.002 TYR B 158 ARG 0.002 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 134 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8005 (m-30) cc_final: 0.7762 (m-30) REVERT: A 109 LYS cc_start: 0.5856 (OUTLIER) cc_final: 0.5460 (mtmm) REVERT: A 248 PHE cc_start: 0.8021 (m-80) cc_final: 0.7563 (m-80) REVERT: A 343 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 416 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7187 (mm-40) REVERT: B 417 ASN cc_start: 0.7551 (m-40) cc_final: 0.7294 (m-40) outliers start: 26 outliers final: 15 residues processed: 126 average time/residue: 1.0962 time to fit residues: 146.5533 Evaluate side-chains 125 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 198 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 A residue 444 THR 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 444 THR 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: 3.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 70 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 242 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 416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7032 Z= 0.159 Angle : 0.470 5.535 9538 Z= 0.251 Chirality : 0.039 0.148 1124 Planarity : 0.003 0.029 1150 Dihedral : 4.379 47.145 918 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.21 % Allowed : 21.59 % Favored : 75.19 % 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: 1.97 (0.30), residues: 842 helix: 2.17 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.52 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 232 HIS 0.004 0.001 HIS B 272 PHE 0.014 0.001 PHE A 408 TYR 0.018 0.002 TYR B 158 ARG 0.003 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 140 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7931 (m-30) cc_final: 0.7690 (m-30) REVERT: A 109 LYS cc_start: 0.5837 (OUTLIER) cc_final: 0.5541 (tttt) REVERT: A 248 PHE cc_start: 0.7955 (m-80) cc_final: 0.7529 (m-80) REVERT: A 343 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7982 (mp) REVERT: A 415 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6675 (ptp-170) REVERT: A 416 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7203 (mm-40) REVERT: B 417 ASN cc_start: 0.7546 (m-40) cc_final: 0.7289 (m-40) outliers start: 25 outliers final: 14 residues processed: 134 average time/residue: 1.0399 time to fit residues: 147.9988 Evaluate side-chains 128 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 194 GLU 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 415 ARG Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 444 THR 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 444 THR 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: 2.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 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: 0.7873 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7032 Z= 0.152 Angle : 0.478 8.994 9538 Z= 0.253 Chirality : 0.039 0.225 1124 Planarity : 0.003 0.030 1150 Dihedral : 4.339 46.959 918 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.21 % Allowed : 21.47 % Favored : 75.32 % 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: 2.05 (0.30), residues: 842 helix: 2.22 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.48 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.004 0.001 HIS B 272 PHE 0.014 0.001 PHE A 408 TYR 0.018 0.002 TYR B 158 ARG 0.004 0.000 ARG B 187 *********************** 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 137 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7919 (m-30) cc_final: 0.7660 (m-30) REVERT: A 109 LYS cc_start: 0.5728 (OUTLIER) cc_final: 0.5415 (tttt) REVERT: A 343 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7973 (mp) REVERT: A 415 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.6559 (ptp-170) REVERT: A 416 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7191 (mm-40) REVERT: B 417 ASN cc_start: 0.7545 (m-40) cc_final: 0.7263 (m-40) outliers start: 25 outliers final: 15 residues processed: 131 average time/residue: 1.1234 time to fit residues: 156.1551 Evaluate side-chains 127 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 194 GLU 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 415 ARG Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 444 THR 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 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 220 ASN ** A 242 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1896 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= 0.163 Angle : 0.475 8.343 9538 Z= 0.253 Chirality : 0.039 0.187 1124 Planarity : 0.003 0.029 1150 Dihedral : 4.360 47.019 918 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.08 % Allowed : 22.11 % Favored : 74.81 % 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: 2.05 (0.30), residues: 842 helix: 2.22 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.48 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.004 0.001 HIS A 335 PHE 0.014 0.001 PHE A 408 TYR 0.019 0.002 TYR B 158 ARG 0.002 0.000 ARG A 262 ********************** 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 136 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7921 (m-30) cc_final: 0.7664 (m-30) REVERT: A 109 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5411 (tttt) REVERT: A 343 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7984 (mp) REVERT: A 415 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6581 (ptp-170) REVERT: A 416 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7193 (mm-40) REVERT: B 417 ASN cc_start: 0.7551 (m-40) cc_final: 0.7210 (t0) outliers start: 24 outliers final: 16 residues processed: 129 average time/residue: 1.0026 time to fit residues: 137.5538 Evaluate side-chains 128 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 194 GLU 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 415 ARG Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 220 ASN 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 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130711 restraints weight = 8490.883| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.66 r_work: 0.3334 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7032 Z= 0.204 Angle : 0.498 7.901 9538 Z= 0.265 Chirality : 0.040 0.173 1124 Planarity : 0.003 0.030 1150 Dihedral : 4.497 47.344 918 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.83 % Allowed : 22.62 % Favored : 74.55 % 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: 1.91 (0.30), residues: 842 helix: 2.10 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.50 (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 165 PHE 0.013 0.001 PHE A 408 TYR 0.022 0.002 TYR A 158 ARG 0.002 0.000 ARG A 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.83 seconds wall clock time: 50 minutes 39.59 seconds (3039.59 seconds total)