Starting phenix.real_space_refine on Sat May 10 19:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9o_37377/05_2025/8w9o_37377.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9o_37377/05_2025/8w9o_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/cci-nas-00/data/ceres_data/8w9o_37377/05_2025/8w9o_37377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9o_37377/05_2025/8w9o_37377.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9o_37377/05_2025/8w9o_37377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9o_37377/05_2025/8w9o_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. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 4.53, per 1000 atoms: 0.66 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 - 3.00 Amino acid : True - 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: 1.68 Conformation dependent library (CDL) restraints added in 901.6 milliseconds 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: 0.65 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: 1.90 Time building geometry restraints manager: 1.97 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: 0.00 - 1.54: 9347 1.54 - 3.07: 156 3.07 - 4.61: 29 4.61 - 6.15: 4 6.15 - 7.69: 2 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: 0.03 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.930 Find NCS groups from input model: 0.230 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.210 ------------------------------------------------------------------------------- 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 7034 Z= 0.200 Angle : 0.538 7.685 9542 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 Details of bonding type rmsd hydrogen bonds : bond 0.20367 ( 448) hydrogen bonds : angle 7.13601 ( 1272) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.43800 ( 4) covalent geometry : bond 0.00467 ( 7032) covalent geometry : angle 0.53850 ( 9538) *********************** 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 to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.741 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 1.0560 time to fit residues: 130.9438 Evaluate side-chains 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.148146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128903 restraints weight = 8476.780| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.66 r_work: 0.3313 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 7034 Z= 0.154 Angle : 0.512 5.860 9542 Z= 0.281 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 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 448) hydrogen bonds : angle 4.79250 ( 1272) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.15625 ( 4) covalent geometry : bond 0.00331 ( 7032) covalent geometry : angle 0.51221 ( 9538) *********************** 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 to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.812 Fit side-chains REVERT: A 248 PHE cc_start: 0.7986 (m-80) cc_final: 0.7682 (m-80) REVERT: A 343 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 416 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7304 (mm-40) REVERT: B 220 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7359 (t0) REVERT: B 288 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6828 (mp) REVERT: B 315 GLU cc_start: 0.6237 (pm20) cc_final: 0.6021 (pm20) REVERT: B 417 ASN cc_start: 0.7459 (m-40) cc_final: 0.7198 (m-40) outliers start: 22 outliers final: 5 residues processed: 127 average time/residue: 1.0010 time to fit residues: 135.2566 Evaluate side-chains 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 0.0020 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 ** 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 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN B 101 ASN B 220 ASN B 237 GLN B 332 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.151398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132311 restraints weight = 8578.616| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.66 r_work: 0.3358 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7034 Z= 0.112 Angle : 0.465 5.315 9542 Z= 0.254 Chirality : 0.039 0.136 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.396 46.917 918 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.21 % Allowed : 17.99 % Favored : 78.79 % 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: 1.76 (0.29), residues: 842 helix: 1.95 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.47 (0.42), 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 0.015 0.001 PHE A 408 TYR 0.020 0.002 TYR B 158 ARG 0.004 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 448) hydrogen bonds : angle 4.38458 ( 1272) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.11315 ( 4) covalent geometry : bond 0.00232 ( 7032) covalent geometry : angle 0.46473 ( 9538) *********************** 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 140 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.771 Fit side-chains REVERT: A 237 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8433 (mm-40) REVERT: A 248 PHE cc_start: 0.7893 (m-80) cc_final: 0.7460 (m-80) REVERT: A 343 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 416 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7188 (mm-40) REVERT: B 103 TYR cc_start: 0.7344 (t80) cc_final: 0.7022 (t80) REVERT: B 152 ARG cc_start: 0.6023 (mpp-170) cc_final: 0.5527 (ttp80) REVERT: B 315 GLU cc_start: 0.6352 (pm20) cc_final: 0.6089 (pm20) REVERT: B 417 ASN cc_start: 0.7458 (m-40) cc_final: 0.7158 (m-40) outliers start: 25 outliers final: 4 residues processed: 129 average time/residue: 1.0597 time to fit residues: 145.8225 Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER 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 413 THR Chi-restraints excluded: chain A residue 416 GLN 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 7 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 237 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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.149197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129791 restraints weight = 8591.486| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.66 r_work: 0.3341 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.003 0.024 7034 Z= 0.149 Angle : 0.487 5.660 9542 Z= 0.264 Chirality : 0.040 0.136 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.206 20.773 916 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.47 % Allowed : 18.77 % 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: 1.75 (0.29), residues: 842 helix: 1.95 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.48 (0.42), 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 0.022 0.002 TYR B 158 ARG 0.002 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 448) hydrogen bonds : angle 4.36151 ( 1272) SS BOND : bond 0.00270 ( 2) SS BOND : angle 0.40184 ( 4) covalent geometry : bond 0.00332 ( 7032) covalent geometry : angle 0.48750 ( 9538) *********************** 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 133 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.814 Fit side-chains REVERT: A 109 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5673 (tttt) REVERT: A 248 PHE cc_start: 0.7963 (m-80) cc_final: 0.7477 (m-80) REVERT: A 343 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7947 (mp) REVERT: A 416 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7157 (mm-40) REVERT: B 103 TYR cc_start: 0.7446 (t80) cc_final: 0.7131 (t80) REVERT: B 152 ARG cc_start: 0.6103 (mpp-170) cc_final: 0.5609 (ttp80) REVERT: B 288 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6629 (mp) REVERT: B 315 GLU cc_start: 0.6379 (pm20) cc_final: 0.6066 (pm20) REVERT: B 417 ASN cc_start: 0.7484 (m-40) cc_final: 0.7180 (m-40) outliers start: 27 outliers final: 9 residues processed: 124 average time/residue: 1.0060 time to fit residues: 132.9055 Evaluate side-chains 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 400 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 237 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** 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 335 HIS ** 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 = 0.3651 r_free = 0.3651 target = 0.149375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130049 restraints weight = 8485.994| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.65 r_work: 0.3339 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7034 Z= 0.146 Angle : 0.493 6.483 9542 Z= 0.265 Chirality : 0.040 0.193 1124 Planarity : 0.003 0.027 1150 Dihedral : 4.206 20.515 916 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.47 % Allowed : 19.15 % 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: 1.79 (0.30), residues: 842 helix: 1.96 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.43 (0.42), residues: 274 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 0.021 0.002 TYR B 158 ARG 0.002 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 448) hydrogen bonds : angle 4.30130 ( 1272) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.46579 ( 4) covalent geometry : bond 0.00326 ( 7032) covalent geometry : angle 0.49269 ( 9538) *********************** 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 132 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.779 Fit side-chains REVERT: A 109 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.5623 (tttt) REVERT: A 248 PHE cc_start: 0.7955 (m-80) cc_final: 0.7445 (m-80) REVERT: A 343 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7949 (mp) REVERT: A 416 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7141 (mm-40) REVERT: B 103 TYR cc_start: 0.7522 (t80) cc_final: 0.7128 (t80) REVERT: B 315 GLU cc_start: 0.6459 (pm20) cc_final: 0.6180 (pm20) REVERT: B 334 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.7502 (mmm-85) REVERT: B 417 ASN cc_start: 0.7486 (m-40) cc_final: 0.7194 (m-40) outliers start: 27 outliers final: 11 residues processed: 124 average time/residue: 0.9389 time to fit residues: 124.4182 Evaluate side-chains 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 50 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 332 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.150238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130962 restraints weight = 8563.587| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.67 r_work: 0.3344 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7034 Z= 0.128 Angle : 0.478 5.915 9542 Z= 0.256 Chirality : 0.039 0.155 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.133 19.823 916 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.60 % Allowed : 19.15 % Favored : 77.25 % 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: 2.07 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.44 (0.42), 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 0.019 0.002 TYR B 158 ARG 0.007 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 448) hydrogen bonds : angle 4.22195 ( 1272) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.37403 ( 4) covalent geometry : bond 0.00285 ( 7032) covalent geometry : angle 0.47806 ( 9538) *********************** 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 136 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.717 Fit side-chains REVERT: A 109 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5611 (tttt) REVERT: A 248 PHE cc_start: 0.7933 (m-80) cc_final: 0.7452 (m-80) REVERT: A 343 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7889 (mp) REVERT: A 416 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7139 (mm-40) REVERT: B 103 TYR cc_start: 0.7555 (t80) cc_final: 0.7145 (t80) REVERT: B 315 GLU cc_start: 0.6508 (pm20) cc_final: 0.6255 (pm20) REVERT: B 417 ASN cc_start: 0.7477 (m-40) cc_final: 0.7185 (m-40) outliers start: 28 outliers final: 13 residues processed: 128 average time/residue: 0.8933 time to fit residues: 122.1969 Evaluate side-chains 118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** ** A 335 HIS ** 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 335 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.150959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131593 restraints weight = 8452.736| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.67 r_work: 0.3356 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7034 Z= 0.124 Angle : 0.477 5.391 9542 Z= 0.256 Chirality : 0.039 0.155 1124 Planarity : 0.003 0.029 1150 Dihedral : 4.105 19.682 916 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.70 % Allowed : 19.79 % Favored : 77.51 % 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: 2.11 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.38 (0.43), 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 0.013 0.001 PHE A 408 TYR 0.019 0.002 TYR B 158 ARG 0.005 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 448) hydrogen bonds : angle 4.18990 ( 1272) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.34371 ( 4) covalent geometry : bond 0.00273 ( 7032) covalent geometry : angle 0.47675 ( 9538) *********************** 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 132 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.755 Fit side-chains REVERT: A 109 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5476 (tttt) REVERT: A 248 PHE cc_start: 0.7880 (m-80) cc_final: 0.7409 (m-80) REVERT: A 343 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7862 (mp) REVERT: A 416 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7126 (mm-40) REVERT: B 103 TYR cc_start: 0.7623 (t80) cc_final: 0.7263 (t80) REVERT: B 315 GLU cc_start: 0.6510 (pm20) cc_final: 0.6235 (pm20) REVERT: B 417 ASN cc_start: 0.7462 (m-40) cc_final: 0.7153 (m-40) outliers start: 21 outliers final: 13 residues processed: 126 average time/residue: 0.9359 time to fit residues: 126.0696 Evaluate side-chains 123 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain A residue 221 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** A 335 HIS ** 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 335 HIS ** 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 = 0.3685 r_free = 0.3685 target = 0.152294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133061 restraints weight = 8562.835| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.67 r_work: 0.3364 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7034 Z= 0.114 Angle : 0.471 5.655 9542 Z= 0.253 Chirality : 0.039 0.142 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.038 19.398 916 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.57 % Allowed : 20.05 % 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: 2.03 (0.30), residues: 842 helix: 2.15 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.34 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 232 HIS 0.004 0.001 HIS B 335 PHE 0.013 0.001 PHE A 408 TYR 0.018 0.002 TYR B 158 ARG 0.005 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 448) hydrogen bonds : angle 4.14516 ( 1272) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.27449 ( 4) covalent geometry : bond 0.00247 ( 7032) covalent geometry : angle 0.47095 ( 9538) *********************** 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 131 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.765 Fit side-chains REVERT: A 109 LYS cc_start: 0.5829 (OUTLIER) cc_final: 0.5472 (tttt) REVERT: A 343 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7861 (mp) REVERT: A 416 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7092 (mm-40) REVERT: B 103 TYR cc_start: 0.7625 (t80) cc_final: 0.7226 (t80) REVERT: B 315 GLU cc_start: 0.6509 (pm20) cc_final: 0.6225 (pm20) REVERT: B 417 ASN cc_start: 0.7464 (m-40) cc_final: 0.7157 (m-40) outliers start: 20 outliers final: 11 residues processed: 126 average time/residue: 0.8965 time to fit residues: 120.7652 Evaluate side-chains 122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 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 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 17 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 79 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 335 HIS ** 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 335 HIS ** 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 = 0.3670 r_free = 0.3670 target = 0.151107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131579 restraints weight = 8681.681| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.69 r_work: 0.3344 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7034 Z= 0.123 Angle : 0.474 5.881 9542 Z= 0.256 Chirality : 0.039 0.139 1124 Planarity : 0.003 0.027 1150 Dihedral : 4.059 19.438 916 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.96 % Allowed : 20.05 % Favored : 76.99 % 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: 2.01 (0.30), residues: 842 helix: 2.13 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.35 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 232 HIS 0.004 0.001 HIS B 335 PHE 0.013 0.001 PHE A 408 TYR 0.019 0.002 TYR B 158 ARG 0.005 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 448) hydrogen bonds : angle 4.15659 ( 1272) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.32071 ( 4) covalent geometry : bond 0.00270 ( 7032) covalent geometry : angle 0.47415 ( 9538) *********************** 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 131 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.809 Fit side-chains REVERT: A 109 LYS cc_start: 0.5865 (OUTLIER) cc_final: 0.5480 (tttt) REVERT: A 343 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7866 (mp) REVERT: A 416 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7090 (mm-40) REVERT: B 103 TYR cc_start: 0.7643 (t80) cc_final: 0.7252 (t80) REVERT: B 315 GLU cc_start: 0.6505 (pm20) cc_final: 0.6218 (pm20) REVERT: B 417 ASN cc_start: 0.7466 (m-40) cc_final: 0.7144 (m-40) outliers start: 23 outliers final: 12 residues processed: 124 average time/residue: 0.9856 time to fit residues: 130.6463 Evaluate side-chains 122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.0000 overall best weight: 1.7790 ------------------------------------------------------------------------------- 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.147880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128167 restraints weight = 8709.908| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.69 r_work: 0.3309 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7034 Z= 0.183 Angle : 0.530 5.942 9542 Z= 0.285 Chirality : 0.041 0.147 1124 Planarity : 0.004 0.029 1150 Dihedral : 4.330 21.756 916 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.44 % Allowed : 20.57 % Favored : 76.99 % 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: 1.91 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.47 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 499 HIS 0.005 0.001 HIS B 335 PHE 0.014 0.002 PHE B 32 TYR 0.025 0.002 TYR A 158 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 448) hydrogen bonds : angle 4.34895 ( 1272) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.63638 ( 4) covalent geometry : bond 0.00422 ( 7032) covalent geometry : angle 0.53010 ( 9538) ********************** 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 128 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.817 Fit side-chains REVERT: A 109 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5599 (tttt) REVERT: A 343 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7951 (mp) REVERT: A 416 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7175 (mm-40) REVERT: B 103 TYR cc_start: 0.7688 (t80) cc_final: 0.7225 (t80) REVERT: B 315 GLU cc_start: 0.6595 (pm20) cc_final: 0.6277 (pm20) REVERT: B 417 ASN cc_start: 0.7477 (m-40) cc_final: 0.7214 (m-40) outliers start: 19 outliers final: 12 residues processed: 123 average time/residue: 1.0098 time to fit residues: 132.3444 Evaluate side-chains 120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 56 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 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 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 335 HIS ** 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 = 0.3684 r_free = 0.3684 target = 0.152248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132937 restraints weight = 8635.929| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.67 r_work: 0.3359 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7034 Z= 0.117 Angle : 0.480 5.977 9542 Z= 0.258 Chirality : 0.039 0.137 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.079 19.516 916 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.44 % Allowed : 20.82 % Favored : 76.74 % 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: 1.92 (0.29), residues: 842 helix: 2.08 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.41 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 232 HIS 0.004 0.001 HIS B 335 PHE 0.013 0.001 PHE A 408 TYR 0.017 0.002 TYR B 158 ARG 0.005 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 448) hydrogen bonds : angle 4.19517 ( 1272) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.32012 ( 4) covalent geometry : bond 0.00255 ( 7032) covalent geometry : angle 0.48009 ( 9538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4525.30 seconds wall clock time: 78 minutes 51.84 seconds (4731.84 seconds total)