Starting phenix.real_space_refine on Thu Jul 2 04:53:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9n_37376/07_2026/8w9n_37376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9n_37376/07_2026/8w9n_37376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9n_37376/07_2026/8w9n_37376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9n_37376/07_2026/8w9n_37376.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9n_37376/07_2026/8w9n_37376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9n_37376/07_2026/8w9n_37376.cif" } resolution = 2.7 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 S 40 5.16 5 Na 2 4.78 5 C 4570 2.51 5 N 1058 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 6860 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3429 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 13, 'TRANS': 413} Chain breaks: 2 Chain: "B" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3429 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 13, 'TRANS': 413} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Time building chain proxies: 1.64, per 1000 atoms: 0.24 Number of scatterers: 6860 At special positions: 0 Unit cell: (104.16, 87.42, 81.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 Na 2 11.00 O 1190 8.00 N 1058 7.00 C 4570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 449 " - pdb=" SG CYS A 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 449 " - pdb=" SG CYS B 460 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.60 Conformation dependent library (CDL) restraints added in 446.4 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: 48 helices and 1 sheets defined 76.5% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 21 through 44 removed outlier: 4.132A pdb=" N LYS A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 65 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 149 through 183 Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.504A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 227 through 242 Proline residue: A 236 - end of helix removed outlier: 3.531A pdb=" N ASN A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.604A pdb=" N GLY A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 4.085A pdb=" N GLY A 276 " --> pdb=" O ASN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 308 Processing helix chain 'A' and resid 318 through 334 removed outlier: 4.105A pdb=" N ARG A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'A' and resid 398 through 414 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 426 through 440 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 472 through 488 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'B' and resid 22 through 43 Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.636A pdb=" N PHE B 77 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 93 through 111 Processing helix chain 'B' and resid 149 through 183 Processing helix chain 'B' and resid 183 through 194 removed outlier: 3.542A pdb=" N VAL B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 227 through 242 Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 262 through 271 removed outlier: 3.738A pdb=" N GLY B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 308 Processing helix chain 'B' and resid 318 through 334 removed outlier: 4.156A pdb=" N ARG B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 398 through 414 Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 426 through 440 Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 472 through 488 Processing sheet with id=AA1, first strand: chain 'A' and resid 499 through 500 460 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2013 1.34 - 1.46: 1712 1.46 - 1.58: 3243 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 7032 Sorted by residual: bond pdb=" CA LYS B 494 " pdb=" C LYS B 494 " ideal model delta sigma weight residual 1.531 1.508 0.023 1.46e-02 4.69e+03 2.52e+00 bond pdb=" CA ASP B 454 " pdb=" C ASP B 454 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.14e-02 7.69e+03 1.49e+00 bond pdb=" N PHE B 366 " pdb=" CA PHE B 366 " ideal model delta sigma weight residual 1.463 1.447 0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" CA LYS A 494 " pdb=" C LYS A 494 " ideal model delta sigma weight residual 1.526 1.512 0.015 1.42e-02 4.96e+03 1.07e+00 bond pdb=" CA ASP A 454 " pdb=" C ASP A 454 " ideal model delta sigma weight residual 1.528 1.518 0.011 1.04e-02 9.25e+03 1.05e+00 ... (remaining 7027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 9142 1.27 - 2.54: 315 2.54 - 3.82: 62 3.82 - 5.09: 14 5.09 - 6.36: 5 Bond angle restraints: 9538 Sorted by residual: angle pdb=" N THR A 43 " pdb=" CA THR A 43 " pdb=" C THR A 43 " ideal model delta sigma weight residual 111.28 115.13 -3.85 1.09e+00 8.42e-01 1.25e+01 angle pdb=" N THR A 445 " pdb=" CA THR A 445 " pdb=" C THR A 445 " ideal model delta sigma weight residual 112.89 108.75 4.14 1.24e+00 6.50e-01 1.11e+01 angle pdb=" N GLY B 442 " pdb=" CA GLY B 442 " pdb=" C GLY B 442 " ideal model delta sigma weight residual 114.85 110.75 4.10 1.35e+00 5.49e-01 9.23e+00 angle pdb=" N ALA B 498 " pdb=" CA ALA B 498 " pdb=" C ALA B 498 " ideal model delta sigma weight residual 113.20 109.69 3.51 1.21e+00 6.83e-01 8.43e+00 angle pdb=" N LEU A 176 " pdb=" CA LEU A 176 " pdb=" C LEU A 176 " ideal model delta sigma weight residual 111.36 108.27 3.09 1.09e+00 8.42e-01 8.01e+00 ... (remaining 9533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3653 17.70 - 35.41: 325 35.41 - 53.11: 83 53.11 - 70.81: 7 70.81 - 88.51: 6 Dihedral angle restraints: 4074 sinusoidal: 1584 harmonic: 2490 Sorted by residual: dihedral pdb=" CA ARG B 334 " pdb=" C ARG B 334 " pdb=" N HIS B 335 " pdb=" CA HIS B 335 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ARG A 334 " pdb=" C ARG A 334 " pdb=" N HIS A 335 " pdb=" CA HIS A 335 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ILE A 42 " pdb=" C ILE A 42 " pdb=" N THR A 43 " pdb=" CA THR A 43 " ideal model delta harmonic sigma weight residual -180.00 -162.70 -17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 4071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 623 0.030 - 0.060: 370 0.060 - 0.089: 88 0.089 - 0.119: 33 0.119 - 0.149: 10 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CA VAL A 453 " pdb=" N VAL A 453 " pdb=" C VAL A 453 " pdb=" CB VAL A 453 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA SER B 68 " pdb=" N SER B 68 " pdb=" C SER B 68 " pdb=" CB SER B 68 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA HIS B 335 " pdb=" N HIS B 335 " pdb=" C HIS B 335 " pdb=" CB HIS B 335 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1121 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 158 " 0.009 2.00e-02 2.50e+03 8.29e-03 1.37e+00 pdb=" CG TYR A 158 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 158 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 158 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 158 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 158 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 158 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 472 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO A 473 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 158 " -0.009 2.00e-02 2.50e+03 7.97e-03 1.27e+00 pdb=" CG TYR B 158 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 158 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 158 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 158 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 158 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 158 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 158 " 0.000 2.00e-02 2.50e+03 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 395 2.73 - 3.27: 7462 3.27 - 3.82: 12390 3.82 - 4.36: 15206 4.36 - 4.90: 25437 Nonbonded interactions: 60890 Sorted by model distance: nonbonded pdb=" O ALA A 39 " pdb=" OG1 THR A 43 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASP B 150 " pdb=" OH TYR B 267 " model vdw 2.247 3.040 nonbonded pdb=" O LEU B 256 " pdb=" OG1 THR B 260 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR A 339 " pdb=" O VAL A 341 " model vdw 2.270 3.040 nonbonded pdb=" NH2 ARG A 334 " pdb=" O PRO A 361 " model vdw 2.286 3.120 ... (remaining 60885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.210 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7034 Z= 0.184 Angle : 0.589 6.359 9542 Z= 0.364 Chirality : 0.040 0.149 1124 Planarity : 0.003 0.028 1150 Dihedral : 14.675 88.512 2464 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 0.64 % Allowed : 15.17 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.27 (0.28), residues: 842 helix: 1.58 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -0.69 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 497 TYR 0.020 0.002 TYR A 158 PHE 0.019 0.001 PHE B 23 TRP 0.005 0.001 TRP B 471 HIS 0.006 0.002 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 ( 7032) covalent geometry : angle 0.58878 / 0.36 ( 9538) SS BOND : bond 0.00299 / 0.15 ( 2) SS BOND : angle 0.58192 / 0.30 ( 4) hydrogen bonds : bond 0.17400 / 11.31 ( 460) hydrogen bonds : angle 5.98416 / 4.31 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.244 Fit side-chains REVERT: A 270 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7516 (mttt) REVERT: A 419 GLN cc_start: 0.7463 (tt0) cc_final: 0.7113 (tm-30) REVERT: A 454 ASP cc_start: 0.7436 (t0) cc_final: 0.7206 (t0) REVERT: A 494 LYS cc_start: 0.7513 (mttt) cc_final: 0.7121 (mmtt) REVERT: B 357 MET cc_start: 0.9040 (mmt) cc_final: 0.8839 (mmt) REVERT: B 419 GLN cc_start: 0.7305 (tt0) cc_final: 0.7010 (tm-30) REVERT: B 494 LYS cc_start: 0.7617 (mttt) cc_final: 0.7136 (mmtt) outliers start: 5 outliers final: 4 residues processed: 108 average time/residue: 0.5481 time to fit residues: 62.3688 Evaluate side-chains 98 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 340 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 181 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 237 GLN B 271 ASN B 300 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.097283 restraints weight = 8353.894| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.41 r_work: 0.2900 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7034 Z= 0.140 Angle : 0.494 6.211 9542 Z= 0.270 Chirality : 0.039 0.141 1124 Planarity : 0.004 0.029 1150 Dihedral : 4.845 50.321 924 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.83 % Allowed : 13.88 % Favored : 83.29 % 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: 2.24 (0.28), residues: 842 helix: 2.39 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.53 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 451 TYR 0.029 0.002 TYR A 158 PHE 0.015 0.001 PHE A 408 TRP 0.004 0.001 TRP A 232 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7032) covalent geometry : angle 0.49370 / 0.27 ( 9538) SS BOND : bond 0.00096 / 0.05 ( 2) SS BOND : angle 0.31279 / 0.12 ( 4) hydrogen bonds : bond 0.04016 / 2.66 ( 460) hydrogen bonds : angle 4.17728 / 2.97 ( 1290) *********************** 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 118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.244 Fit side-chains REVERT: A 270 LYS cc_start: 0.7889 (mmtm) cc_final: 0.7238 (mttt) REVERT: A 343 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8672 (mp) REVERT: A 416 GLN cc_start: 0.8043 (mt0) cc_final: 0.7792 (tt0) REVERT: A 419 GLN cc_start: 0.7883 (tt0) cc_final: 0.7581 (tm-30) REVERT: B 151 GLU cc_start: 0.7347 (tt0) cc_final: 0.7080 (tt0) REVERT: B 357 MET cc_start: 0.9195 (mmt) cc_final: 0.8853 (mmt) REVERT: B 419 GLN cc_start: 0.7816 (tt0) cc_final: 0.7504 (tm-30) REVERT: B 474 MET cc_start: 0.8114 (mmp) cc_final: 0.7903 (mmm) REVERT: B 494 LYS cc_start: 0.7929 (mttt) cc_final: 0.7154 (mmtt) outliers start: 22 outliers final: 5 residues processed: 112 average time/residue: 0.5356 time to fit residues: 63.2932 Evaluate side-chains 97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.114659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.096598 restraints weight = 8368.138| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.41 r_work: 0.2890 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7034 Z= 0.140 Angle : 0.480 6.303 9542 Z= 0.259 Chirality : 0.039 0.144 1124 Planarity : 0.003 0.030 1150 Dihedral : 4.726 50.348 922 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.49 % Favored : 97.39 % Rotamer: Outliers : 2.19 % Allowed : 14.14 % Favored : 83.68 % 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: 2.51 (0.28), residues: 842 helix: 2.59 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.43 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 451 TYR 0.023 0.002 TYR A 158 PHE 0.014 0.001 PHE A 408 TRP 0.005 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7032) covalent geometry : angle 0.47980 / 0.26 ( 9538) SS BOND : bond 0.00012 / 0.01 ( 2) SS BOND : angle 0.55718 / 0.24 ( 4) hydrogen bonds : bond 0.03718 / 2.47 ( 460) hydrogen bonds : angle 3.96562 / 2.83 ( 1290) *********************** 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 117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.266 Fit side-chains REVERT: A 24 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 44 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7045 (tttt) REVERT: A 270 LYS cc_start: 0.7876 (mmtm) cc_final: 0.7267 (mttt) REVERT: A 343 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8655 (mp) REVERT: A 419 GLN cc_start: 0.7881 (tt0) cc_final: 0.7630 (tm-30) REVERT: B 151 GLU cc_start: 0.7328 (tt0) cc_final: 0.7084 (tt0) REVERT: B 419 GLN cc_start: 0.7829 (tt0) cc_final: 0.7559 (tm-30) REVERT: B 474 MET cc_start: 0.8116 (mmp) cc_final: 0.7914 (mmm) REVERT: B 494 LYS cc_start: 0.7965 (mttt) cc_final: 0.7213 (mmtt) outliers start: 17 outliers final: 6 residues processed: 110 average time/residue: 0.5575 time to fit residues: 64.6143 Evaluate side-chains 105 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 340 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.111746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.093543 restraints weight = 8505.036| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.42 r_work: 0.2844 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7034 Z= 0.206 Angle : 0.536 7.384 9542 Z= 0.288 Chirality : 0.041 0.162 1124 Planarity : 0.004 0.039 1150 Dihedral : 4.671 39.520 920 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.70 % Allowed : 13.75 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.30 (0.28), residues: 842 helix: 2.38 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.39 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 284 TYR 0.025 0.002 TYR B 158 PHE 0.016 0.002 PHE A 366 TRP 0.007 0.001 TRP B 232 HIS 0.006 0.002 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 7032) covalent geometry : angle 0.53586 / 0.29 ( 9538) SS BOND : bond 0.00186 / 0.09 ( 2) SS BOND : angle 0.76492 / 0.33 ( 4) hydrogen bonds : bond 0.04001 / 2.64 ( 460) hydrogen bonds : angle 4.05261 / 2.89 ( 1290) *********************** 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 124 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.262 Fit side-chains REVERT: A 24 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8285 (mm) REVERT: A 44 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7224 (pptt) REVERT: A 270 LYS cc_start: 0.7849 (mmtm) cc_final: 0.7256 (mttt) REVERT: A 343 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8676 (mp) REVERT: A 419 GLN cc_start: 0.8027 (tt0) cc_final: 0.7709 (tm-30) REVERT: B 150 ASP cc_start: 0.6829 (m-30) cc_final: 0.6476 (p0) REVERT: B 151 GLU cc_start: 0.7361 (tt0) cc_final: 0.6894 (tt0) REVERT: B 454 ASP cc_start: 0.7596 (t0) cc_final: 0.7306 (t0) REVERT: B 494 LYS cc_start: 0.8035 (mttt) cc_final: 0.7284 (mmtm) outliers start: 21 outliers final: 8 residues processed: 117 average time/residue: 0.5040 time to fit residues: 62.1825 Evaluate side-chains 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 340 ILE 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 42 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 83 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0050 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.098984 restraints weight = 8450.343| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.42 r_work: 0.2928 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7034 Z= 0.100 Angle : 0.440 6.514 9542 Z= 0.238 Chirality : 0.037 0.140 1124 Planarity : 0.003 0.032 1150 Dihedral : 4.204 37.895 920 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.49 % Favored : 97.39 % Rotamer: Outliers : 1.93 % Allowed : 15.04 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.74 (0.29), residues: 842 helix: 2.78 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.018 0.002 TYR B 158 PHE 0.015 0.001 PHE A 408 TRP 0.005 0.000 TRP A 232 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 7032) covalent geometry : angle 0.44020 / 0.24 ( 9538) SS BOND : bond 0.00050 / 0.02 ( 2) SS BOND : angle 0.29711 / 0.12 ( 4) hydrogen bonds : bond 0.03119 / 2.09 ( 460) hydrogen bonds : angle 3.79289 / 2.70 ( 1290) *********************** 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 120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.267 Fit side-chains REVERT: A 24 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 270 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7174 (mttt) REVERT: A 419 GLN cc_start: 0.7989 (tt0) cc_final: 0.7730 (tm-30) REVERT: B 69 MET cc_start: 0.9020 (mmt) cc_final: 0.8450 (mmt) REVERT: B 151 GLU cc_start: 0.7216 (tt0) cc_final: 0.6976 (tt0) REVERT: B 419 GLN cc_start: 0.7690 (tm130) cc_final: 0.7249 (tm-30) REVERT: B 494 LYS cc_start: 0.7887 (mttt) cc_final: 0.7047 (mmtm) outliers start: 15 outliers final: 4 residues processed: 115 average time/residue: 0.5307 time to fit residues: 64.3978 Evaluate side-chains 103 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.096401 restraints weight = 8435.539| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.42 r_work: 0.2886 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7034 Z= 0.135 Angle : 0.478 7.416 9542 Z= 0.256 Chirality : 0.038 0.135 1124 Planarity : 0.003 0.033 1150 Dihedral : 4.059 37.498 918 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.19 % Allowed : 15.42 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.70 (0.29), residues: 842 helix: 2.72 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.33 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 334 TYR 0.021 0.002 TYR A 158 PHE 0.013 0.001 PHE B 408 TRP 0.005 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7032) covalent geometry : angle 0.47811 / 0.26 ( 9538) SS BOND : bond 0.00056 / 0.03 ( 2) SS BOND : angle 0.53265 / 0.22 ( 4) hydrogen bonds : bond 0.03395 / 2.25 ( 460) hydrogen bonds : angle 3.81451 / 2.72 ( 1290) *********************** 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 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.257 Fit side-chains REVERT: A 24 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8244 (mm) REVERT: A 44 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6863 (tptt) REVERT: A 270 LYS cc_start: 0.7814 (mmtm) cc_final: 0.7195 (mttt) REVERT: A 343 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8574 (mp) REVERT: A 419 GLN cc_start: 0.8010 (tt0) cc_final: 0.7731 (tm-30) REVERT: B 151 GLU cc_start: 0.7324 (tt0) cc_final: 0.7082 (tt0) REVERT: B 294 LEU cc_start: 0.8759 (tp) cc_final: 0.8537 (tp) REVERT: B 419 GLN cc_start: 0.7702 (tm130) cc_final: 0.7279 (tm-30) REVERT: B 494 LYS cc_start: 0.7870 (mttt) cc_final: 0.7141 (mmtm) outliers start: 17 outliers final: 7 residues processed: 114 average time/residue: 0.5167 time to fit residues: 62.1162 Evaluate side-chains 111 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.100279 restraints weight = 8347.962| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.46 r_work: 0.2939 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7034 Z= 0.095 Angle : 0.440 7.474 9542 Z= 0.237 Chirality : 0.037 0.140 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.808 35.825 918 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.49 % Favored : 97.39 % Rotamer: Outliers : 1.67 % Allowed : 15.94 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.93 (0.29), residues: 842 helix: 2.92 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.28 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 334 TYR 0.018 0.001 TYR B 158 PHE 0.014 0.001 PHE A 408 TRP 0.005 0.000 TRP A 232 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 ( 7032) covalent geometry : angle 0.44021 / 0.24 ( 9538) SS BOND : bond 0.00068 / 0.03 ( 2) SS BOND : angle 0.32614 / 0.14 ( 4) hydrogen bonds : bond 0.02957 / 1.98 ( 460) hydrogen bonds : angle 3.69162 / 2.63 ( 1290) *********************** 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 118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.236 Fit side-chains REVERT: A 24 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8214 (mm) REVERT: A 44 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6547 (tptt) REVERT: A 270 LYS cc_start: 0.7732 (mmtm) cc_final: 0.7175 (mttt) REVERT: A 419 GLN cc_start: 0.7978 (tt0) cc_final: 0.7733 (tm-30) REVERT: B 70 SER cc_start: 0.8700 (t) cc_final: 0.8391 (p) REVERT: B 151 GLU cc_start: 0.7202 (tt0) cc_final: 0.6973 (tt0) REVERT: B 294 LEU cc_start: 0.8726 (tp) cc_final: 0.8470 (tp) REVERT: B 419 GLN cc_start: 0.7681 (tm130) cc_final: 0.7267 (tm-30) REVERT: B 494 LYS cc_start: 0.7701 (mttt) cc_final: 0.6948 (mmtm) outliers start: 13 outliers final: 2 residues processed: 115 average time/residue: 0.5256 time to fit residues: 63.5727 Evaluate side-chains 104 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 70 optimal weight: 0.0570 chunk 65 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 59 optimal weight: 0.0670 chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.097458 restraints weight = 8521.141| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.46 r_work: 0.2885 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1691 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= 0.133 Angle : 0.488 7.398 9542 Z= 0.260 Chirality : 0.038 0.131 1124 Planarity : 0.003 0.033 1150 Dihedral : 3.754 20.445 916 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 1.80 % Allowed : 16.45 % Favored : 81.75 % 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: 2.82 (0.29), residues: 842 helix: 2.80 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.25 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 334 TYR 0.020 0.002 TYR A 158 PHE 0.013 0.001 PHE B 408 TRP 0.005 0.001 TRP B 232 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7032) covalent geometry : angle 0.48775 / 0.26 ( 9538) SS BOND : bond 0.00056 / 0.03 ( 2) SS BOND : angle 0.50136 / 0.21 ( 4) hydrogen bonds : bond 0.03306 / 2.19 ( 460) hydrogen bonds : angle 3.75810 / 2.68 ( 1290) *********************** 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 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.270 Fit side-chains REVERT: A 24 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8223 (mm) REVERT: A 44 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6647 (tptt) REVERT: A 270 LYS cc_start: 0.7758 (mmtm) cc_final: 0.7192 (mttt) REVERT: A 343 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 419 GLN cc_start: 0.8015 (tt0) cc_final: 0.7755 (tm-30) REVERT: A 474 MET cc_start: 0.7675 (mpp) cc_final: 0.7395 (mmm) REVERT: B 151 GLU cc_start: 0.7250 (tt0) cc_final: 0.7014 (tt0) REVERT: B 294 LEU cc_start: 0.8736 (tp) cc_final: 0.8500 (tp) REVERT: B 494 LYS cc_start: 0.7813 (mttt) cc_final: 0.7118 (mmtm) outliers start: 14 outliers final: 5 residues processed: 112 average time/residue: 0.5208 time to fit residues: 61.4546 Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.098635 restraints weight = 8406.262| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.46 r_work: 0.2911 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7034 Z= 0.107 Angle : 0.465 7.480 9542 Z= 0.248 Chirality : 0.037 0.131 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.667 18.500 916 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 1.54 % Allowed : 16.84 % Favored : 81.62 % 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: 2.89 (0.29), residues: 842 helix: 2.88 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.27 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 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 A 232 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 7032) covalent geometry : angle 0.46521 / 0.25 ( 9538) SS BOND : bond 0.00027 / 0.01 ( 2) SS BOND : angle 0.40110 / 0.17 ( 4) hydrogen bonds : bond 0.03079 / 2.05 ( 460) hydrogen bonds : angle 3.71381 / 2.65 ( 1290) *********************** 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 110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.309 Fit side-chains REVERT: A 24 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8218 (mm) REVERT: A 270 LYS cc_start: 0.7737 (mmtm) cc_final: 0.7178 (mttt) REVERT: A 343 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8565 (mp) REVERT: A 419 GLN cc_start: 0.7989 (tt0) cc_final: 0.7736 (tm-30) REVERT: B 151 GLU cc_start: 0.7214 (tt0) cc_final: 0.6984 (tt0) REVERT: B 294 LEU cc_start: 0.8722 (tp) cc_final: 0.8473 (tp) REVERT: B 494 LYS cc_start: 0.7792 (mttt) cc_final: 0.7072 (mmtm) outliers start: 12 outliers final: 4 residues processed: 108 average time/residue: 0.5586 time to fit residues: 63.5054 Evaluate side-chains 104 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.115097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096805 restraints weight = 8382.561| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.45 r_work: 0.2881 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1723 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= 0.135 Angle : 0.495 7.411 9542 Z= 0.264 Chirality : 0.038 0.132 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.814 20.796 916 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 1.16 % Allowed : 17.22 % Favored : 81.62 % 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: 2.76 (0.29), residues: 842 helix: 2.76 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.29 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 334 TYR 0.020 0.002 TYR B 158 PHE 0.013 0.001 PHE A 408 TRP 0.005 0.001 TRP B 232 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7032) covalent geometry : angle 0.49481 / 0.26 ( 9538) SS BOND : bond 0.00057 / 0.03 ( 2) SS BOND : angle 0.54212 / 0.23 ( 4) hydrogen bonds : bond 0.03317 / 2.19 ( 460) hydrogen bonds : angle 3.77186 / 2.70 ( 1290) ********************** 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 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.274 Fit side-chains REVERT: A 24 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8231 (mm) REVERT: A 270 LYS cc_start: 0.7768 (mmtm) cc_final: 0.7193 (mttt) REVERT: A 343 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8580 (mp) REVERT: A 419 GLN cc_start: 0.8021 (tt0) cc_final: 0.7784 (tm-30) REVERT: A 474 MET cc_start: 0.7696 (mpp) cc_final: 0.7402 (mmm) REVERT: B 151 GLU cc_start: 0.7248 (tt0) cc_final: 0.7007 (tt0) REVERT: B 294 LEU cc_start: 0.8738 (tp) cc_final: 0.8508 (tp) REVERT: B 494 LYS cc_start: 0.7828 (mttt) cc_final: 0.7105 (mmtm) outliers start: 9 outliers final: 5 residues processed: 105 average time/residue: 0.5968 time to fit residues: 65.7120 Evaluate side-chains 106 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098184 restraints weight = 8388.333| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.44 r_work: 0.2891 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1754 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= 0.129 Angle : 0.494 7.516 9542 Z= 0.264 Chirality : 0.038 0.131 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.808 20.178 916 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 1.16 % Allowed : 17.48 % Favored : 81.36 % 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: 2.79 (0.29), residues: 842 helix: 2.77 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.26 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 420 TYR 0.019 0.002 TYR B 158 PHE 0.013 0.001 PHE A 408 TRP 0.005 0.001 TRP B 232 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7032) covalent geometry : angle 0.49429 / 0.26 ( 9538) SS BOND : bond 0.00033 / 0.02 ( 2) SS BOND : angle 0.51162 / 0.22 ( 4) hydrogen bonds : bond 0.03261 / 2.16 ( 460) hydrogen bonds : angle 3.77234 / 2.70 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.80 seconds wall clock time: 39 minutes 33.88 seconds (2373.88 seconds total)