Starting phenix.real_space_refine on Sat May 10 19:26:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9n_37376/05_2025/8w9n_37376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9n_37376/05_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_37376/05_2025/8w9n_37376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9n_37376/05_2025/8w9n_37376.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9n_37376/05_2025/8w9n_37376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9n_37376/05_2025/8w9n_37376.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.50, per 1000 atoms: 0.66 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: 1.75 Conformation dependent library (CDL) restraints added in 994.2 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: 0.74 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: 2.01 Time building geometry restraints manager: 2.03 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: 0.04 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.980 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (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 TRP 0.005 0.001 TRP B 471 HIS 0.006 0.002 HIS A 335 PHE 0.019 0.001 PHE B 23 TYR 0.020 0.002 TYR A 158 ARG 0.004 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.17400 ( 460) hydrogen bonds : angle 5.98416 ( 1290) SS BOND : bond 0.00299 ( 2) SS BOND : angle 0.58192 ( 4) covalent geometry : bond 0.00373 ( 7032) covalent geometry : angle 0.58878 ( 9538) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.818 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: 1.2125 time to fit residues: 138.0386 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 : 0.788 ------------------------------------------------------------------------------- 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 70 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 237 GLN B 300 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.117275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.098921 restraints weight = 8225.203| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.44 r_work: 0.2919 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1100 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= 0.121 Angle : 0.478 6.291 9542 Z= 0.262 Chirality : 0.038 0.137 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.750 49.868 924 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.57 % Allowed : 14.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.28), residues: 842 helix: 2.45 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.52 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.005 0.001 HIS B 335 PHE 0.016 0.001 PHE A 408 TYR 0.028 0.002 TYR A 158 ARG 0.004 0.000 ARG A 451 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 460) hydrogen bonds : angle 4.12712 ( 1290) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.25964 ( 4) covalent geometry : bond 0.00260 ( 7032) covalent geometry : angle 0.47840 ( 9538) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.787 Fit side-chains REVERT: A 270 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7200 (mttt) REVERT: A 343 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 357 MET cc_start: 0.9174 (mmt) cc_final: 0.8972 (mmt) REVERT: A 416 GLN cc_start: 0.8004 (mt0) cc_final: 0.7722 (tt0) REVERT: A 419 GLN cc_start: 0.7841 (tt0) cc_final: 0.7546 (tm-30) REVERT: B 151 GLU cc_start: 0.7188 (tt0) cc_final: 0.6923 (tt0) REVERT: B 357 MET cc_start: 0.9167 (mmt) cc_final: 0.8838 (mmt) REVERT: B 419 GLN cc_start: 0.7771 (tt0) cc_final: 0.7474 (tm-30) REVERT: B 474 MET cc_start: 0.8063 (mmp) cc_final: 0.7850 (mmm) REVERT: B 494 LYS cc_start: 0.7875 (mttt) cc_final: 0.7080 (mmtt) outliers start: 20 outliers final: 4 residues processed: 112 average time/residue: 1.1449 time to fit residues: 135.4104 Evaluate side-chains 96 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 271 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.096018 restraints weight = 8418.510| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.41 r_work: 0.2879 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7034 Z= 0.157 Angle : 0.502 6.254 9542 Z= 0.269 Chirality : 0.039 0.147 1124 Planarity : 0.003 0.034 1150 Dihedral : 4.449 37.962 920 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.06 % Allowed : 14.01 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.28), residues: 842 helix: 2.50 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.37 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 PHE 0.014 0.002 PHE A 408 TYR 0.025 0.002 TYR A 158 ARG 0.005 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 460) hydrogen bonds : angle 4.00392 ( 1290) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.58681 ( 4) covalent geometry : bond 0.00362 ( 7032) covalent geometry : angle 0.50172 ( 9538) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.927 Fit side-chains REVERT: A 24 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8277 (mm) REVERT: A 44 LYS cc_start: 0.7336 (tmtm) cc_final: 0.7052 (tttt) REVERT: A 270 LYS cc_start: 0.7876 (mmtm) cc_final: 0.7275 (mttt) REVERT: A 343 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8664 (mp) REVERT: A 419 GLN cc_start: 0.7923 (tt0) cc_final: 0.7622 (tm-30) REVERT: B 151 GLU cc_start: 0.7336 (tt0) cc_final: 0.7084 (tt0) REVERT: B 357 MET cc_start: 0.9152 (mmt) cc_final: 0.8827 (mmt) REVERT: B 415 ARG cc_start: 0.7931 (ptt-90) cc_final: 0.6464 (ttt-90) REVERT: B 419 GLN cc_start: 0.7838 (tt0) cc_final: 0.7561 (tm-30) REVERT: B 474 MET cc_start: 0.8116 (mmp) cc_final: 0.7912 (mmm) REVERT: B 494 LYS cc_start: 0.7972 (mttt) cc_final: 0.7219 (mmtt) outliers start: 16 outliers final: 6 residues processed: 105 average time/residue: 1.2726 time to fit residues: 140.7279 Evaluate side-chains 102 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 100 LEU 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 B residue 340 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 300 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.112912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.094689 restraints weight = 8464.324| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.42 r_work: 0.2862 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7034 Z= 0.173 Angle : 0.510 6.951 9542 Z= 0.273 Chirality : 0.040 0.153 1124 Planarity : 0.004 0.035 1150 Dihedral : 4.545 38.957 920 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.57 % Allowed : 14.27 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.28), residues: 842 helix: 2.50 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.39 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 PHE 0.014 0.002 PHE A 408 TYR 0.024 0.002 TYR A 158 ARG 0.005 0.001 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 460) hydrogen bonds : angle 3.97927 ( 1290) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.62304 ( 4) covalent geometry : bond 0.00403 ( 7032) covalent geometry : angle 0.50947 ( 9538) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.849 Fit side-chains REVERT: A 24 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8276 (mm) REVERT: A 44 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7075 (tttt) REVERT: A 270 LYS cc_start: 0.7837 (mmtm) cc_final: 0.7236 (mttt) REVERT: A 343 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8629 (mp) REVERT: A 419 GLN cc_start: 0.8008 (tt0) cc_final: 0.7713 (tm-30) REVERT: B 151 GLU cc_start: 0.7331 (tt0) cc_final: 0.7076 (tt0) REVERT: B 419 GLN cc_start: 0.7843 (tt0) cc_final: 0.7559 (tm-30) REVERT: B 474 MET cc_start: 0.8132 (mmp) cc_final: 0.7922 (mmm) REVERT: B 494 LYS cc_start: 0.8009 (mttt) cc_final: 0.7273 (mmtm) outliers start: 20 outliers final: 6 residues processed: 110 average time/residue: 1.1705 time to fit residues: 135.8347 Evaluate side-chains 106 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ** 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 = 0.3208 r_free = 0.3208 target = 0.112443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.094168 restraints weight = 8377.165| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.45 r_work: 0.2842 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7034 Z= 0.191 Angle : 0.526 7.287 9542 Z= 0.281 Chirality : 0.041 0.159 1124 Planarity : 0.004 0.036 1150 Dihedral : 4.642 39.964 920 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.31 % Allowed : 14.52 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.28), residues: 842 helix: 2.40 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.39 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 PHE 0.014 0.002 PHE A 408 TYR 0.024 0.002 TYR A 158 ARG 0.004 0.001 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 460) hydrogen bonds : angle 4.01533 ( 1290) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.76596 ( 4) covalent geometry : bond 0.00451 ( 7032) covalent geometry : angle 0.52603 ( 9538) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.822 Fit side-chains REVERT: A 24 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8268 (mm) REVERT: A 44 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7111 (tttt) REVERT: A 270 LYS cc_start: 0.7843 (mmtm) cc_final: 0.7241 (mttt) REVERT: A 343 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8634 (mp) REVERT: A 419 GLN cc_start: 0.8058 (tt0) cc_final: 0.7758 (tm-30) REVERT: B 151 GLU cc_start: 0.7350 (tt0) cc_final: 0.7095 (tt0) REVERT: B 419 GLN cc_start: 0.7966 (tt0) cc_final: 0.7570 (tm-30) REVERT: B 462 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7696 (t0) REVERT: B 494 LYS cc_start: 0.8010 (mttt) cc_final: 0.7252 (mmtm) outliers start: 18 outliers final: 7 residues processed: 110 average time/residue: 1.1737 time to fit residues: 136.1849 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 : 0.805 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 462 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3233 r_free = 0.3233 target = 0.114482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.096464 restraints weight = 8433.163| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.42 r_work: 0.2888 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1477 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= 0.128 Angle : 0.474 7.026 9542 Z= 0.254 Chirality : 0.038 0.145 1124 Planarity : 0.003 0.033 1150 Dihedral : 4.391 39.261 920 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.44 % Allowed : 14.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.29), residues: 842 helix: 2.65 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.005 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.019 0.002 TYR B 158 ARG 0.004 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 460) hydrogen bonds : angle 3.87383 ( 1290) SS BOND : bond 0.00039 ( 2) SS BOND : angle 0.50909 ( 4) covalent geometry : bond 0.00288 ( 7032) covalent geometry : angle 0.47412 ( 9538) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.780 Fit side-chains REVERT: A 24 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 270 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7266 (mttt) REVERT: A 343 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8645 (mp) REVERT: A 419 GLN cc_start: 0.8035 (tt0) cc_final: 0.7765 (tm-30) REVERT: B 69 MET cc_start: 0.9032 (mmt) cc_final: 0.8461 (mmt) REVERT: B 151 GLU cc_start: 0.7312 (tt0) cc_final: 0.7064 (tt0) REVERT: B 419 GLN cc_start: 0.7896 (tt0) cc_final: 0.7524 (tm-30) REVERT: B 462 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7685 (t0) REVERT: B 494 LYS cc_start: 0.7953 (mttt) cc_final: 0.7219 (mmtm) outliers start: 19 outliers final: 6 residues processed: 118 average time/residue: 1.1170 time to fit residues: 139.1403 Evaluate side-chains 109 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 B residue 340 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 462 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 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 = 0.3228 r_free = 0.3228 target = 0.113970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.095721 restraints weight = 8339.501| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.46 r_work: 0.2873 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1513 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= 0.143 Angle : 0.495 7.530 9542 Z= 0.264 Chirality : 0.039 0.146 1124 Planarity : 0.003 0.034 1150 Dihedral : 4.422 39.003 920 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.70 % Allowed : 14.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.29), residues: 842 helix: 2.62 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 PHE 0.013 0.001 PHE B 408 TYR 0.021 0.002 TYR B 158 ARG 0.004 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 460) hydrogen bonds : angle 3.87937 ( 1290) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.52067 ( 4) covalent geometry : bond 0.00328 ( 7032) covalent geometry : angle 0.49519 ( 9538) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.781 Fit side-chains REVERT: A 24 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8223 (mm) REVERT: A 44 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6951 (tptt) REVERT: A 270 LYS cc_start: 0.7833 (mmtm) cc_final: 0.7266 (mttt) REVERT: A 343 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 419 GLN cc_start: 0.8040 (tt0) cc_final: 0.7754 (tm-30) REVERT: B 151 GLU cc_start: 0.7327 (tt0) cc_final: 0.7086 (tt0) REVERT: B 419 GLN cc_start: 0.7874 (tt0) cc_final: 0.7498 (tm-30) REVERT: B 462 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7706 (t0) REVERT: B 494 LYS cc_start: 0.7952 (mttt) cc_final: 0.7200 (mmtm) outliers start: 21 outliers final: 8 residues processed: 117 average time/residue: 1.1574 time to fit residues: 143.0812 Evaluate side-chains 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 176 LEU 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 Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 462 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.0570 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 271 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 = 0.3269 r_free = 0.3269 target = 0.117128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.099005 restraints weight = 8347.079| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.46 r_work: 0.2918 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1695 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= 0.104 Angle : 0.461 7.555 9542 Z= 0.247 Chirality : 0.037 0.139 1124 Planarity : 0.003 0.032 1150 Dihedral : 4.193 38.075 920 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 15.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.29), residues: 842 helix: 2.77 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.25 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 232 HIS 0.005 0.001 HIS B 335 PHE 0.014 0.001 PHE A 408 TYR 0.018 0.002 TYR B 158 ARG 0.005 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 460) hydrogen bonds : angle 3.76167 ( 1290) SS BOND : bond 0.00039 ( 2) SS BOND : angle 0.41506 ( 4) covalent geometry : bond 0.00226 ( 7032) covalent geometry : angle 0.46133 ( 9538) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.869 Fit side-chains REVERT: A 24 LEU cc_start: 0.8464 (tp) cc_final: 0.8218 (mm) REVERT: A 44 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6767 (tptt) REVERT: A 270 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7215 (mttt) REVERT: A 343 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8596 (mp) REVERT: A 419 GLN cc_start: 0.8014 (tt0) cc_final: 0.7748 (tm-30) REVERT: B 69 MET cc_start: 0.9023 (mmt) cc_final: 0.8482 (mmt) REVERT: B 70 SER cc_start: 0.8668 (t) cc_final: 0.8372 (p) REVERT: B 151 GLU cc_start: 0.7224 (tt0) cc_final: 0.6992 (tt0) REVERT: B 294 LEU cc_start: 0.8731 (tp) cc_final: 0.8501 (tp) REVERT: B 419 GLN cc_start: 0.7762 (tt0) cc_final: 0.7436 (tm-30) REVERT: B 462 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7759 (t0) REVERT: B 494 LYS cc_start: 0.7812 (mttt) cc_final: 0.7052 (mmtm) outliers start: 16 outliers final: 5 residues processed: 115 average time/residue: 1.2349 time to fit residues: 149.4363 Evaluate side-chains 107 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 344 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 462 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 271 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 = 0.3220 r_free = 0.3220 target = 0.113436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.095198 restraints weight = 8492.910| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.43 r_work: 0.2863 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7034 Z= 0.161 Angle : 0.518 7.683 9542 Z= 0.276 Chirality : 0.039 0.146 1124 Planarity : 0.003 0.034 1150 Dihedral : 3.937 22.488 916 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 1.54 % Allowed : 16.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.29), residues: 842 helix: 2.64 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.006 0.001 HIS B 335 PHE 0.013 0.001 PHE B 408 TYR 0.021 0.002 TYR A 158 ARG 0.007 0.001 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 460) hydrogen bonds : angle 3.87307 ( 1290) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.60077 ( 4) covalent geometry : bond 0.00377 ( 7032) covalent geometry : angle 0.51800 ( 9538) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.728 Fit side-chains REVERT: A 24 LEU cc_start: 0.8497 (tp) cc_final: 0.8249 (mm) REVERT: A 270 LYS cc_start: 0.7803 (mmtm) cc_final: 0.7224 (mttt) REVERT: A 343 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 419 GLN cc_start: 0.8053 (tt0) cc_final: 0.7786 (tm-30) REVERT: A 474 MET cc_start: 0.7674 (mpp) cc_final: 0.7376 (mmm) REVERT: B 70 SER cc_start: 0.8715 (t) cc_final: 0.8422 (p) REVERT: B 151 GLU cc_start: 0.7329 (tt0) cc_final: 0.7088 (tt0) REVERT: B 294 LEU cc_start: 0.8762 (tp) cc_final: 0.8532 (tp) REVERT: B 419 GLN cc_start: 0.7842 (tt0) cc_final: 0.7500 (tm-30) REVERT: B 462 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7830 (t0) REVERT: B 494 LYS cc_start: 0.7877 (mttt) cc_final: 0.7093 (mmtm) outliers start: 12 outliers final: 7 residues processed: 110 average time/residue: 1.1864 time to fit residues: 137.5943 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 : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 400 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 462 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.0050 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 271 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.098038 restraints weight = 8479.108| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.48 r_work: 0.2898 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7034 Z= 0.113 Angle : 0.477 7.722 9542 Z= 0.255 Chirality : 0.038 0.141 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.748 19.124 916 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 1.41 % Allowed : 16.45 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.29), residues: 842 helix: 2.76 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.25 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.004 0.001 HIS A 335 PHE 0.014 0.001 PHE B 408 TYR 0.019 0.002 TYR B 158 ARG 0.007 0.001 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 460) hydrogen bonds : angle 3.78912 ( 1290) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.44269 ( 4) covalent geometry : bond 0.00249 ( 7032) covalent geometry : angle 0.47715 ( 9538) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.849 Fit side-chains REVERT: A 24 LEU cc_start: 0.8465 (tp) cc_final: 0.8219 (mm) REVERT: A 270 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7163 (mttt) REVERT: A 343 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8602 (mp) REVERT: A 419 GLN cc_start: 0.8023 (tt0) cc_final: 0.7774 (tm-30) REVERT: A 474 MET cc_start: 0.7664 (mpp) cc_final: 0.7368 (mmm) REVERT: B 70 SER cc_start: 0.8674 (t) cc_final: 0.8400 (p) REVERT: B 151 GLU cc_start: 0.7234 (tt0) cc_final: 0.6995 (tt0) REVERT: B 294 LEU cc_start: 0.8736 (tp) cc_final: 0.8508 (tp) REVERT: B 419 GLN cc_start: 0.7783 (tt0) cc_final: 0.7450 (tm-30) REVERT: B 420 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7824 (mtm180) REVERT: B 462 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7776 (t0) REVERT: B 494 LYS cc_start: 0.7723 (mttt) cc_final: 0.6987 (mmtm) outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 1.2773 time to fit residues: 148.0414 Evaluate side-chains 106 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 400 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 462 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 0.0170 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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 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 = 0.3256 r_free = 0.3256 target = 0.116300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.098263 restraints weight = 8428.688| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.43 r_work: 0.2915 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 0.025 7034 Z= 0.109 Angle : 0.476 7.575 9542 Z= 0.255 Chirality : 0.037 0.136 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.710 18.902 916 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 1.41 % Allowed : 16.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.29), residues: 842 helix: 2.82 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.24 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.005 0.001 HIS A 335 PHE 0.014 0.001 PHE A 408 TYR 0.018 0.001 TYR A 158 ARG 0.007 0.001 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 460) hydrogen bonds : angle 3.73700 ( 1290) SS BOND : bond 0.00018 ( 2) SS BOND : angle 0.41555 ( 4) covalent geometry : bond 0.00240 ( 7032) covalent geometry : angle 0.47651 ( 9538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4866.47 seconds wall clock time: 84 minutes 46.70 seconds (5086.70 seconds total)