Starting phenix.real_space_refine on Fri Aug 22 18:17:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9n_37376/08_2025/8w9n_37376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9n_37376/08_2025/8w9n_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_37376/08_2025/8w9n_37376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9n_37376/08_2025/8w9n_37376.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9n_37376/08_2025/8w9n_37376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9n_37376/08_2025/8w9n_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-2.0-5787/lib/python3.9/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, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.29 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: 0.61 Conformation dependent library (CDL) restraints added in 396.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.24 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: 1.07 Time building geometry restraints manager: 0.84 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: 0.01 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: 0.640 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: 0.020 Set scattering table: 0.020 Process input model: 8.540 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 aren 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 covalent geometry : bond 0.00373 ( 7032) covalent geometry : angle 0.58878 ( 9538) SS BOND : bond 0.00299 ( 2) SS BOND : angle 0.58192 ( 4) hydrogen bonds : bond 0.17400 ( 460) hydrogen bonds : angle 5.98416 ( 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 : 0.279 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: 0.6141 time to fit residues: 69.7224 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 : 0.216 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3247 r_free = 0.3247 target = 0.115457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.097120 restraints weight = 8360.187| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.42 r_work: 0.2899 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1034 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= 0.139 Angle : 0.494 6.219 9542 Z= 0.270 Chirality : 0.039 0.142 1124 Planarity : 0.004 0.029 1150 Dihedral : 4.851 50.321 924 Min Nonbonded Distance : 2.490 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 aren not related in a simple way. whole: 2.23 (0.28), residues: 842 helix: 2.38 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.52 (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 0.003 0.001 TRP B 471 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7032) covalent geometry : angle 0.49374 ( 9538) SS BOND : bond 0.00061 ( 2) SS BOND : angle 0.30897 ( 4) hydrogen bonds : bond 0.04034 ( 460) hydrogen bonds : angle 4.18453 ( 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 : 0.282 Fit side-chains REVERT: A 270 LYS cc_start: 0.7884 (mmtm) cc_final: 0.7233 (mttt) REVERT: A 343 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 416 GLN cc_start: 0.8049 (mt0) cc_final: 0.7795 (tt0) REVERT: A 419 GLN cc_start: 0.7885 (tt0) cc_final: 0.7579 (tm-30) REVERT: B 151 GLU cc_start: 0.7323 (tt0) cc_final: 0.7061 (tt0) REVERT: B 357 MET cc_start: 0.9191 (mmt) cc_final: 0.8856 (mmt) REVERT: B 419 GLN cc_start: 0.7820 (tt0) cc_final: 0.7506 (tm-30) REVERT: B 474 MET cc_start: 0.8101 (mmp) cc_final: 0.7891 (mmm) REVERT: B 494 LYS cc_start: 0.7933 (mttt) cc_final: 0.7155 (mmtt) outliers start: 22 outliers final: 5 residues processed: 112 average time/residue: 0.6049 time to fit residues: 71.2302 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 : 0.311 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 0.0010 chunk 54 optimal weight: 4.9990 chunk 83 optimal weight: 0.0060 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 = 0.3278 r_free = 0.3278 target = 0.118109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100189 restraints weight = 8353.555| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.42 r_work: 0.2951 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1458 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= 0.099 Angle : 0.432 6.085 9542 Z= 0.235 Chirality : 0.037 0.130 1124 Planarity : 0.003 0.030 1150 Dihedral : 4.423 48.910 922 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.38 % Favored : 97.51 % Rotamer: Outliers : 2.06 % Allowed : 14.40 % 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 aren not related in a simple way. whole: 2.72 (0.29), residues: 842 helix: 2.76 (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 0.003 0.000 ARG A 451 TYR 0.020 0.001 TYR A 158 PHE 0.015 0.001 PHE A 408 TRP 0.004 0.001 TRP A 254 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 7032) covalent geometry : angle 0.43204 ( 9538) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.37785 ( 4) hydrogen bonds : bond 0.03287 ( 460) hydrogen bonds : angle 3.82735 ( 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 122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.278 Fit side-chains REVERT: A 24 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8237 (mm) REVERT: A 270 LYS cc_start: 0.7775 (mmtm) cc_final: 0.7193 (mttt) REVERT: B 151 GLU cc_start: 0.7183 (tt0) cc_final: 0.6956 (tt0) REVERT: B 357 MET cc_start: 0.9105 (mmt) cc_final: 0.8834 (mmt) REVERT: B 419 GLN cc_start: 0.7780 (tt0) cc_final: 0.7509 (tm-30) REVERT: B 494 LYS cc_start: 0.7791 (mttt) cc_final: 0.7083 (mmtt) outliers start: 16 outliers final: 2 residues processed: 116 average time/residue: 0.6089 time to fit residues: 74.2935 Evaluate side-chains 97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A 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: 3.9990 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 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 = 0.3182 r_free = 0.3182 target = 0.110439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.092035 restraints weight = 8543.155| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.45 r_work: 0.2812 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 7034 Z= 0.289 Angle : 0.601 7.783 9542 Z= 0.321 Chirality : 0.045 0.163 1124 Planarity : 0.004 0.046 1150 Dihedral : 4.604 40.273 918 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 3.08 % Allowed : 13.88 % 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 aren not related in a simple way. whole: 2.14 (0.28), residues: 842 helix: 2.24 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.41 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 334 TYR 0.029 0.003 TYR A 158 PHE 0.022 0.002 PHE A 366 TRP 0.010 0.002 TRP B 471 HIS 0.007 0.002 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00693 ( 7032) covalent geometry : angle 0.60127 ( 9538) SS BOND : bond 0.00328 ( 2) SS BOND : angle 1.00764 ( 4) hydrogen bonds : bond 0.04398 ( 460) hydrogen bonds : angle 4.16454 ( 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 122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.275 Fit side-chains REVERT: A 24 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8297 (mm) REVERT: A 270 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7253 (mttt) REVERT: A 343 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8658 (mp) REVERT: A 419 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: B 150 ASP cc_start: 0.6951 (m-30) cc_final: 0.6537 (p0) REVERT: B 151 GLU cc_start: 0.7419 (tt0) cc_final: 0.7160 (tt0) REVERT: B 419 GLN cc_start: 0.7956 (tt0) cc_final: 0.7753 (tm130) REVERT: B 454 ASP cc_start: 0.7578 (t0) cc_final: 0.7304 (t0) REVERT: B 474 MET cc_start: 0.8149 (mmp) cc_final: 0.7926 (mmm) REVERT: B 494 LYS cc_start: 0.8022 (mttt) cc_final: 0.7233 (mmtm) outliers start: 24 outliers final: 9 residues processed: 114 average time/residue: 0.5706 time to fit residues: 68.6261 Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 70 SER 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: 0.9990 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.115357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.097287 restraints weight = 8474.892| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.43 r_work: 0.2907 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1554 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= 0.107 Angle : 0.458 8.331 9542 Z= 0.247 Chirality : 0.037 0.140 1124 Planarity : 0.003 0.032 1150 Dihedral : 4.075 38.962 918 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.49 % Favored : 97.39 % Rotamer: Outliers : 2.19 % Allowed : 15.04 % Favored : 82.78 % 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 aren not related in a simple way. whole: 2.67 (0.29), residues: 842 helix: 2.73 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 284 TYR 0.019 0.002 TYR A 158 PHE 0.015 0.001 PHE A 408 TRP 0.005 0.000 TRP A 232 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7032) covalent geometry : angle 0.45840 ( 9538) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.36563 ( 4) hydrogen bonds : bond 0.03268 ( 460) hydrogen bonds : angle 3.84242 ( 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 117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.260 Fit side-chains REVERT: A 24 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8251 (mm) REVERT: A 270 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7207 (mttt) REVERT: A 343 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8589 (mp) REVERT: A 419 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: B 69 MET cc_start: 0.9048 (mmt) cc_final: 0.8410 (mmt) REVERT: B 151 GLU cc_start: 0.7249 (tt0) cc_final: 0.6994 (tt0) REVERT: B 419 GLN cc_start: 0.7883 (tt0) cc_final: 0.7544 (tm-30) REVERT: B 494 LYS cc_start: 0.7915 (mttt) cc_final: 0.7175 (mmtm) outliers start: 17 outliers final: 7 residues processed: 112 average time/residue: 0.6168 time to fit residues: 72.6115 Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 A residue 347 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B 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: 3.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 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 = 0.3192 r_free = 0.3192 target = 0.111297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.092835 restraints weight = 8463.227| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.47 r_work: 0.2821 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1457 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= 0.230 Angle : 0.556 8.411 9542 Z= 0.297 Chirality : 0.042 0.165 1124 Planarity : 0.004 0.041 1150 Dihedral : 4.498 40.359 918 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.57 % Allowed : 14.91 % Favored : 82.52 % 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 aren not related in a simple way. whole: 2.27 (0.28), residues: 842 helix: 2.37 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.45 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 284 TYR 0.026 0.002 TYR A 158 PHE 0.015 0.002 PHE A 32 TRP 0.007 0.001 TRP A 471 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 7032) covalent geometry : angle 0.55624 ( 9538) SS BOND : bond 0.00224 ( 2) SS BOND : angle 0.93056 ( 4) hydrogen bonds : bond 0.04031 ( 460) hydrogen bonds : angle 4.04086 ( 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 118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.296 Fit side-chains REVERT: A 24 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8255 (mm) REVERT: A 270 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7251 (mttt) REVERT: A 343 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8600 (mp) REVERT: A 419 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: B 42 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8437 (mp) REVERT: B 151 GLU cc_start: 0.7353 (tt0) cc_final: 0.7110 (tt0) REVERT: B 419 GLN cc_start: 0.7986 (tt0) cc_final: 0.7560 (tm-30) REVERT: B 494 LYS cc_start: 0.8011 (mttt) cc_final: 0.7236 (mmtm) outliers start: 20 outliers final: 8 residues processed: 114 average time/residue: 0.6136 time to fit residues: 73.6867 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 : 0.314 ------------------------------------------------------------------------------- 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 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 42 ILE 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: 0.7980 chunk 22 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3258 r_free = 0.3258 target = 0.116326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098148 restraints weight = 8326.233| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.46 r_work: 0.2906 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1649 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= 0.106 Angle : 0.459 8.766 9542 Z= 0.248 Chirality : 0.037 0.140 1124 Planarity : 0.003 0.034 1150 Dihedral : 4.052 39.163 918 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.38 % Favored : 97.51 % Rotamer: Outliers : 2.06 % Allowed : 15.30 % Favored : 82.65 % 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 aren not related in a simple way. whole: 2.69 (0.29), residues: 842 helix: 2.73 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 415 TYR 0.019 0.002 TYR B 158 PHE 0.015 0.001 PHE A 408 TRP 0.004 0.001 TRP A 232 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7032) covalent geometry : angle 0.45888 ( 9538) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.37817 ( 4) hydrogen bonds : bond 0.03160 ( 460) hydrogen bonds : angle 3.80106 ( 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 114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.265 Fit side-chains REVERT: A 24 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8223 (mm) REVERT: A 270 LYS cc_start: 0.7769 (mmtm) cc_final: 0.7192 (mttt) REVERT: A 343 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 419 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: B 151 GLU cc_start: 0.7254 (tt0) cc_final: 0.7016 (tt0) REVERT: B 419 GLN cc_start: 0.7845 (tt0) cc_final: 0.7473 (tm-30) REVERT: B 494 LYS cc_start: 0.7880 (mttt) cc_final: 0.7139 (mmtm) outliers start: 16 outliers final: 5 residues processed: 110 average time/residue: 0.6238 time to fit residues: 72.0880 Evaluate side-chains 105 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 340 ILE 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: 1.9990 chunk 25 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 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 = 0.3195 r_free = 0.3195 target = 0.111398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.093073 restraints weight = 8584.610| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.46 r_work: 0.2842 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7034 Z= 0.235 Angle : 0.566 8.929 9542 Z= 0.302 Chirality : 0.043 0.164 1124 Planarity : 0.004 0.043 1150 Dihedral : 4.517 40.907 918 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.70 % Allowed : 14.78 % Favored : 82.52 % 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 aren not related in a simple way. whole: 2.25 (0.28), residues: 842 helix: 2.37 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.48 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 415 TYR 0.025 0.002 TYR A 158 PHE 0.015 0.002 PHE A 32 TRP 0.008 0.001 TRP A 471 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 7032) covalent geometry : angle 0.56585 ( 9538) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.90126 ( 4) hydrogen bonds : bond 0.04008 ( 460) hydrogen bonds : angle 4.03498 ( 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 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: 0.8530 (OUTLIER) cc_final: 0.8275 (mm) REVERT: A 150 ASP cc_start: 0.7146 (m-30) cc_final: 0.6648 (p0) REVERT: A 263 ASP cc_start: 0.7105 (m-30) cc_final: 0.6810 (m-30) REVERT: A 270 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7305 (mttt) REVERT: A 343 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8622 (mp) REVERT: A 419 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: B 42 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8501 (mp) REVERT: B 151 GLU cc_start: 0.7362 (tt0) cc_final: 0.7117 (tt0) REVERT: B 419 GLN cc_start: 0.7986 (tt0) cc_final: 0.7569 (tm-30) REVERT: B 494 LYS cc_start: 0.8015 (mttt) cc_final: 0.7256 (mmtm) outliers start: 21 outliers final: 9 residues processed: 119 average time/residue: 0.5757 time to fit residues: 72.2386 Evaluate side-chains 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 343 LEU 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: 0.3980 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.115224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.096930 restraints weight = 8377.636| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.46 r_work: 0.2887 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7034 Z= 0.116 Angle : 0.480 9.162 9542 Z= 0.258 Chirality : 0.038 0.138 1124 Planarity : 0.003 0.034 1150 Dihedral : 4.134 40.441 918 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.19 % Allowed : 15.30 % Favored : 82.52 % 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 aren not related in a simple way. whole: 2.63 (0.29), residues: 842 helix: 2.68 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 415 TYR 0.019 0.002 TYR B 158 PHE 0.014 0.001 PHE B 408 TRP 0.005 0.001 TRP B 232 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7032) covalent geometry : angle 0.48025 ( 9538) SS BOND : bond 0.00020 ( 2) SS BOND : angle 0.41441 ( 4) hydrogen bonds : bond 0.03250 ( 460) hydrogen bonds : angle 3.83159 ( 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 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.273 Fit side-chains REVERT: A 24 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 270 LYS cc_start: 0.7771 (mmtm) cc_final: 0.7200 (mttt) REVERT: A 343 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8578 (mp) REVERT: A 419 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: A 474 MET cc_start: 0.7656 (mpp) cc_final: 0.7331 (mmm) REVERT: B 42 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8443 (mp) REVERT: B 151 GLU cc_start: 0.7328 (tt0) cc_final: 0.7082 (tt0) REVERT: B 419 GLN cc_start: 0.7842 (tt0) cc_final: 0.7478 (tm-30) REVERT: B 420 ARG cc_start: 0.8241 (mtm180) cc_final: 0.8011 (mtm180) REVERT: B 494 LYS cc_start: 0.7882 (mttt) cc_final: 0.7146 (mmtm) outliers start: 17 outliers final: 6 residues processed: 111 average time/residue: 0.6273 time to fit residues: 73.2304 Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 340 ILE 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 A residue 419 GLN Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 340 ILE 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: 3.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.0050 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3240 r_free = 0.3240 target = 0.114948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.096729 restraints weight = 8371.790| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.46 r_work: 0.2884 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7034 Z= 0.120 Angle : 0.483 9.279 9542 Z= 0.259 Chirality : 0.038 0.136 1124 Planarity : 0.003 0.033 1150 Dihedral : 4.090 39.151 918 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 1.80 % Allowed : 15.94 % Favored : 82.26 % 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 aren not related in a simple way. whole: 2.70 (0.29), residues: 842 helix: 2.73 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.34 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 420 TYR 0.019 0.002 TYR A 158 PHE 0.014 0.001 PHE A 408 TRP 0.004 0.001 TRP B 232 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7032) covalent geometry : angle 0.48295 ( 9538) SS BOND : bond 0.00008 ( 2) SS BOND : angle 0.43957 ( 4) hydrogen bonds : bond 0.03254 ( 460) hydrogen bonds : angle 3.80348 ( 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 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.265 Fit side-chains REVERT: A 24 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8215 (mm) REVERT: A 270 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7199 (mttt) REVERT: A 343 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8560 (mp) REVERT: A 419 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: A 474 MET cc_start: 0.7648 (mpp) cc_final: 0.7341 (mmm) REVERT: B 42 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 151 GLU cc_start: 0.7318 (tt0) cc_final: 0.7069 (tt0) REVERT: B 294 LEU cc_start: 0.8723 (tp) cc_final: 0.8494 (tp) REVERT: B 419 GLN cc_start: 0.7811 (tt0) cc_final: 0.7453 (tm-30) REVERT: B 494 LYS cc_start: 0.7845 (mttt) cc_final: 0.7120 (mmtm) outliers start: 14 outliers final: 7 residues processed: 108 average time/residue: 0.6352 time to fit residues: 72.0479 Evaluate side-chains 107 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 42 ILE 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 344 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 42 ILE 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: 0.9990 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.0000 chunk 29 optimal weight: 0.9980 chunk 64 optimal weight: 0.0670 overall best weight: 0.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3252 r_free = 0.3252 target = 0.116135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.097994 restraints weight = 8405.077| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.43 r_work: 0.2916 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1772 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= 0.106 Angle : 0.472 9.338 9542 Z= 0.254 Chirality : 0.037 0.135 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.974 38.206 918 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 1.54 % Allowed : 16.45 % Favored : 82.01 % 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 aren not related in a simple way. whole: 2.80 (0.29), residues: 842 helix: 2.80 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.30 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 420 TYR 0.018 0.002 TYR B 158 PHE 0.014 0.001 PHE B 408 TRP 0.005 0.000 TRP A 232 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 7032) covalent geometry : angle 0.47230 ( 9538) SS BOND : bond 0.00056 ( 2) SS BOND : angle 0.42660 ( 4) hydrogen bonds : bond 0.03061 ( 460) hydrogen bonds : angle 3.74663 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.77 seconds wall clock time: 43 minutes 36.15 seconds (2616.15 seconds total)