Starting phenix.real_space_refine on Thu Jul 2 04:54:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9o_37377/07_2026/8w9o_37377.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9o_37377/07_2026/8w9o_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_37377/07_2026/8w9o_37377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9o_37377/07_2026/8w9o_37377.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9o_37377/07_2026/8w9o_37377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9o_37377/07_2026/8w9o_37377.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Time building chain proxies: 1.73, per 1000 atoms: 0.25 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: 0.52 Conformation dependent library (CDL) restraints added in 377.6 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: 0.16 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: 1.04 Time building geometry restraints manager: 0.70 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: 0.01 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.650 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG B 50 TYR 0.027 0.002 TYR B 158 PHE 0.014 0.002 PHE B 32 TRP 0.004 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 7032) covalent geometry : angle 0.53850 / 0.29 ( 9538) SS BOND : bond 0.00286 / 0.14 ( 2) SS BOND : angle 0.43800 / 0.21 ( 4) hydrogen bonds : bond 0.20367 / 13.20 ( 448) hydrogen bonds : angle 7.13601 / 5.20 ( 1272) *********************** 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 : 0.278 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 0.5079 time to fit residues: 63.0597 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 : 0.257 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.0050 chunk 74 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** A 440 ASN B 101 ASN B 181 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 B 440 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.152632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133858 restraints weight = 8568.353| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.67 r_work: 0.3376 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7034 Z= 0.126 Angle : 0.495 6.268 9542 Z= 0.270 Chirality : 0.039 0.135 1124 Planarity : 0.004 0.031 1150 Dihedral : 5.344 47.916 940 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.08 % Allowed : 17.35 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.29), residues: 842 helix: 1.82 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.30 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 334 TYR 0.025 0.002 TYR A 158 PHE 0.016 0.001 PHE A 408 TRP 0.003 0.001 TRP A 232 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 7032) covalent geometry : angle 0.49506 / 0.27 ( 9538) SS BOND : bond 0.00192 / 0.10 ( 2) SS BOND : angle 0.06208 / 0.03 ( 4) hydrogen bonds : bond 0.04005 / 2.62 ( 448) hydrogen bonds : angle 4.70196 / 3.38 ( 1272) *********************** 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 135 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 220 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7756 (t0) REVERT: A 248 PHE cc_start: 0.7930 (m-80) cc_final: 0.7583 (m-80) REVERT: A 343 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7846 (mp) REVERT: A 416 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7218 (mm-40) REVERT: B 152 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5490 (ttp-110) REVERT: B 220 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7123 (t0) REVERT: B 288 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6743 (mp) REVERT: B 315 GLU cc_start: 0.6266 (pm20) cc_final: 0.6046 (pm20) outliers start: 24 outliers final: 5 residues processed: 128 average time/residue: 0.4690 time to fit residues: 63.9526 Evaluate side-chains 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 220 ASN 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 152 ARG Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 302 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 5.9990 chunk 83 optimal weight: 0.0570 chunk 11 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 220 ASN A 237 GLN ** 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 220 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.150094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130911 restraints weight = 8537.656| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.68 r_work: 0.3336 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7034 Z= 0.147 Angle : 0.488 5.725 9542 Z= 0.266 Chirality : 0.039 0.134 1124 Planarity : 0.004 0.029 1150 Dihedral : 4.551 46.827 919 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.08 % Allowed : 19.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.29), residues: 842 helix: 1.86 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.35 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 262 TYR 0.022 0.002 TYR B 158 PHE 0.014 0.001 PHE A 408 TRP 0.004 0.001 TRP B 232 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 7032) covalent geometry : angle 0.48792 / 0.27 ( 9538) SS BOND : bond 0.00124 / 0.06 ( 2) SS BOND : angle 0.31416 / 0.15 ( 4) hydrogen bonds : bond 0.04034 / 2.65 ( 448) hydrogen bonds : angle 4.50892 / 3.24 ( 1272) *********************** 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 128 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 220 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7694 (t0) REVERT: A 248 PHE cc_start: 0.7956 (m-80) cc_final: 0.7530 (m-80) REVERT: A 343 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 416 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7193 (mm-40) REVERT: B 152 ARG cc_start: 0.6357 (tpp-160) cc_final: 0.5487 (ttp-110) REVERT: B 220 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7195 (t0) REVERT: B 315 GLU cc_start: 0.6372 (pm20) cc_final: 0.6098 (pm20) outliers start: 24 outliers final: 6 residues processed: 119 average time/residue: 0.4868 time to fit residues: 61.6235 Evaluate side-chains 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 220 ASN 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 264 GLU Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.0770 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 220 ASN A 237 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 101 ASN B 220 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132160 restraints weight = 8624.863| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.67 r_work: 0.3358 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7034 Z= 0.132 Angle : 0.484 7.288 9542 Z= 0.260 Chirality : 0.039 0.182 1124 Planarity : 0.003 0.027 1150 Dihedral : 4.167 19.673 916 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.70 % Allowed : 20.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.29), residues: 842 helix: 1.93 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.37 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 262 TYR 0.020 0.002 TYR B 158 PHE 0.014 0.001 PHE A 408 TRP 0.004 0.001 TRP B 232 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7032) covalent geometry : angle 0.48403 / 0.26 ( 9538) SS BOND : bond 0.00171 / 0.09 ( 2) SS BOND : angle 0.37702 / 0.20 ( 4) hydrogen bonds : bond 0.03784 / 2.50 ( 448) hydrogen bonds : angle 4.37556 / 3.15 ( 1272) *********************** 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 129 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.185 Fit side-chains REVERT: A 248 PHE cc_start: 0.7978 (m-80) cc_final: 0.7461 (m-80) REVERT: A 343 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7930 (mp) REVERT: A 416 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7163 (mm-40) REVERT: B 152 ARG cc_start: 0.6317 (tpp-160) cc_final: 0.5953 (ttp80) REVERT: B 315 GLU cc_start: 0.6385 (pm20) cc_final: 0.6070 (pm20) outliers start: 21 outliers final: 5 residues processed: 122 average time/residue: 0.4902 time to fit residues: 63.4114 Evaluate side-chains 111 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 TYR 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 416 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 0.0060 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 237 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 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 = 0.3707 r_free = 0.3707 target = 0.154232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135413 restraints weight = 8479.559| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.66 r_work: 0.3392 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7034 Z= 0.112 Angle : 0.464 5.698 9542 Z= 0.249 Chirality : 0.038 0.146 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.038 18.681 916 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.30), residues: 842 helix: 2.10 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.31 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.018 0.002 TYR B 158 PHE 0.013 0.001 PHE A 408 TRP 0.004 0.000 TRP B 232 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 7032) covalent geometry : angle 0.46385 / 0.25 ( 9538) SS BOND : bond 0.00163 / 0.08 ( 2) SS BOND : angle 0.29404 / 0.16 ( 4) hydrogen bonds : bond 0.03482 / 2.31 ( 448) hydrogen bonds : angle 4.24214 / 3.05 ( 1272) *********************** 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 145 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 248 PHE cc_start: 0.7955 (m-80) cc_final: 0.7443 (m-80) REVERT: A 343 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7879 (mp) REVERT: A 416 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7144 (mm-40) REVERT: B 257 TYR cc_start: 0.6302 (t80) cc_final: 0.6077 (t80) REVERT: B 315 GLU cc_start: 0.6478 (pm20) cc_final: 0.6163 (pm20) outliers start: 26 outliers final: 8 residues processed: 133 average time/residue: 0.4301 time to fit residues: 60.9119 Evaluate side-chains 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER 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 416 GLN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 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 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 440 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.145867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126424 restraints weight = 8554.640| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.65 r_work: 0.3312 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 7034 Z= 0.245 Angle : 0.580 6.495 9542 Z= 0.313 Chirality : 0.044 0.154 1124 Planarity : 0.004 0.029 1150 Dihedral : 4.604 23.335 916 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.98 % Allowed : 19.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.29), residues: 842 helix: 1.69 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 262 TYR 0.032 0.002 TYR B 158 PHE 0.018 0.002 PHE A 32 TRP 0.007 0.001 TRP B 499 HIS 0.006 0.002 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.25 ( 7032) covalent geometry : angle 0.57974 / 0.31 ( 9538) SS BOND : bond 0.00461 / 0.23 ( 2) SS BOND : angle 0.94476 / 0.47 ( 4) hydrogen bonds : bond 0.04476 / 3.00 ( 448) hydrogen bonds : angle 4.59909 / 3.30 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.267 Fit side-chains REVERT: A 109 LYS cc_start: 0.5851 (OUTLIER) cc_final: 0.5541 (tttt) REVERT: A 248 PHE cc_start: 0.8023 (m-80) cc_final: 0.7504 (m-80) REVERT: A 343 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8000 (mp) REVERT: A 416 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7263 (mm-40) REVERT: B 315 GLU cc_start: 0.6591 (pm20) cc_final: 0.6377 (pm20) REVERT: B 417 ASN cc_start: 0.7533 (m-40) cc_final: 0.7241 (m-40) outliers start: 31 outliers final: 13 residues processed: 131 average time/residue: 0.4534 time to fit residues: 63.5409 Evaluate side-chains 121 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 194 GLU 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 416 GLN Chi-restraints excluded: chain B residue 214 PHE 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 396 ILE Chi-restraints excluded: chain B residue 401 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 35 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.153816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135099 restraints weight = 8487.510| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.62 r_work: 0.3379 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7034 Z= 0.111 Angle : 0.479 5.657 9542 Z= 0.259 Chirality : 0.039 0.136 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.196 19.488 916 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.21 % Allowed : 19.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.29), residues: 842 helix: 2.02 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.44 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 262 TYR 0.017 0.002 TYR B 158 PHE 0.014 0.001 PHE A 408 TRP 0.004 0.000 TRP B 232 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 7032) covalent geometry : angle 0.47747 / 0.26 ( 9538) SS BOND : bond 0.00082 / 0.04 ( 2) SS BOND : angle 1.89768 / 0.99 ( 4) hydrogen bonds : bond 0.03519 / 2.34 ( 448) hydrogen bonds : angle 4.28003 / 3.08 ( 1272) *********************** 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 131 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.263 Fit side-chains REVERT: A 248 PHE cc_start: 0.7937 (m-80) cc_final: 0.7471 (m-80) REVERT: A 343 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7887 (mp) REVERT: A 416 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7175 (mm-40) REVERT: B 257 TYR cc_start: 0.6347 (t80) cc_final: 0.6102 (t80) REVERT: B 315 GLU cc_start: 0.6572 (pm20) cc_final: 0.6309 (pm20) outliers start: 25 outliers final: 10 residues processed: 124 average time/residue: 0.4377 time to fit residues: 58.1604 Evaluate side-chains 120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3706 r_free = 0.3706 target = 0.154308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135469 restraints weight = 8597.541| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.65 r_work: 0.3390 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7034 Z= 0.108 Angle : 0.481 7.775 9542 Z= 0.258 Chirality : 0.039 0.247 1124 Planarity : 0.003 0.027 1150 Dihedral : 4.168 21.880 916 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.70 % Allowed : 20.82 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.30), residues: 842 helix: 2.13 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.39 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 262 TYR 0.018 0.002 TYR B 158 PHE 0.013 0.001 PHE A 408 TRP 0.004 0.000 TRP B 232 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 7032) covalent geometry : angle 0.47952 / 0.26 ( 9538) SS BOND : bond 0.00082 / 0.04 ( 2) SS BOND : angle 1.85824 / 0.77 ( 4) hydrogen bonds : bond 0.03365 / 2.24 ( 448) hydrogen bonds : angle 4.18369 / 3.01 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 248 PHE cc_start: 0.7895 (m-80) cc_final: 0.7422 (m-80) REVERT: A 343 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7868 (mp) REVERT: A 416 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7105 (mm-40) REVERT: B 315 GLU cc_start: 0.6560 (pm20) cc_final: 0.6303 (pm20) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 0.4371 time to fit residues: 58.9347 Evaluate side-chains 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 449 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 72 optimal weight: 0.0070 chunk 3 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3704 r_free = 0.3704 target = 0.154257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135467 restraints weight = 8591.822| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.65 r_work: 0.3386 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7034 Z= 0.112 Angle : 0.479 7.819 9542 Z= 0.257 Chirality : 0.039 0.178 1124 Planarity : 0.003 0.030 1150 Dihedral : 4.173 23.427 916 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.57 % Allowed : 20.95 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.30), residues: 842 helix: 2.18 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.41 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 262 TYR 0.018 0.002 TYR B 158 PHE 0.014 0.001 PHE A 408 TRP 0.004 0.001 TRP A 232 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 7032) covalent geometry : angle 0.47788 / 0.26 ( 9538) SS BOND : bond 0.00194 / 0.09 ( 2) SS BOND : angle 1.72534 / 0.67 ( 4) hydrogen bonds : bond 0.03346 / 2.23 ( 448) hydrogen bonds : angle 4.16898 / 3.00 ( 1272) *********************** 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 128 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.261 Fit side-chains REVERT: A 343 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7896 (mp) REVERT: A 416 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7066 (mm-40) REVERT: B 152 ARG cc_start: 0.6344 (OUTLIER) cc_final: 0.5421 (ttp-110) REVERT: B 315 GLU cc_start: 0.6589 (pm20) cc_final: 0.6306 (pm20) outliers start: 20 outliers final: 12 residues processed: 119 average time/residue: 0.4418 time to fit residues: 56.2200 Evaluate side-chains 123 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 158 TYR 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 Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 449 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3706 r_free = 0.3706 target = 0.154375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135488 restraints weight = 8449.984| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.65 r_work: 0.3402 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2225 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= 0.111 Angle : 0.480 7.655 9542 Z= 0.257 Chirality : 0.039 0.176 1124 Planarity : 0.003 0.029 1150 Dihedral : 4.154 23.392 916 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.31 % Allowed : 21.34 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.29), residues: 842 helix: 2.21 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.46 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 262 TYR 0.018 0.002 TYR B 158 PHE 0.013 0.001 PHE A 408 TRP 0.004 0.001 TRP A 232 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7032) covalent geometry : angle 0.47963 / 0.26 ( 9538) SS BOND : bond 0.00105 / 0.05 ( 2) SS BOND : angle 1.35762 / 0.57 ( 4) hydrogen bonds : bond 0.03299 / 2.21 ( 448) hydrogen bonds : angle 4.14922 / 2.99 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.243 Fit side-chains REVERT: A 48 THR cc_start: 0.8334 (p) cc_final: 0.8101 (t) REVERT: A 109 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5449 (tttt) REVERT: A 248 PHE cc_start: 0.7883 (m-80) cc_final: 0.7376 (m-80) REVERT: A 343 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7883 (mp) REVERT: A 416 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7062 (mm-40) REVERT: B 152 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.5455 (ttp-110) REVERT: B 315 GLU cc_start: 0.6555 (pm20) cc_final: 0.6280 (pm20) outliers start: 18 outliers final: 11 residues processed: 115 average time/residue: 0.4435 time to fit residues: 54.5194 Evaluate side-chains 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 243 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 449 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 0.0370 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 chunk 46 optimal weight: 0.2980 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 220 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN B 101 ASN B 237 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3751 r_free = 0.3751 target = 0.158308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139689 restraints weight = 8545.212| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.65 r_work: 0.3440 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7034 Z= 0.096 Angle : 0.462 7.482 9542 Z= 0.249 Chirality : 0.038 0.172 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.032 22.127 916 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.19 % Allowed : 21.85 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.30), residues: 842 helix: 2.26 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.46 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 262 TYR 0.016 0.002 TYR B 158 PHE 0.013 0.001 PHE A 408 TRP 0.005 0.000 TRP A 232 HIS 0.004 0.001 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 ( 7032) covalent geometry : angle 0.46198 / 0.25 ( 9538) SS BOND : bond 0.00178 / 0.09 ( 2) SS BOND : angle 1.11161 / 0.47 ( 4) hydrogen bonds : bond 0.03088 / 2.05 ( 448) hydrogen bonds : angle 4.06317 / 2.93 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.89 seconds wall clock time: 39 minutes 38.10 seconds (2378.10 seconds total)