Starting phenix.real_space_refine on Thu Jun 5 22:02:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9n_37376/06_2025/8w9n_37376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9n_37376/06_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_37376/06_2025/8w9n_37376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9n_37376/06_2025/8w9n_37376.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9n_37376/06_2025/8w9n_37376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9n_37376/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 4.43, per 1000 atoms: 0.65 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: 1.59 Conformation dependent library (CDL) restraints added in 901.0 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: 0.64 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: 1.99 Time building geometry restraints manager: 1.92 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.240 ------------------------------------------------------------------------------- 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 : 0.716 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: 1.2024 time to fit residues: 136.9350 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 : 0.718 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.116768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.098568 restraints weight = 8233.545| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.40 r_work: 0.2925 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7034 Z= 0.121 Angle : 0.478 6.312 9542 Z= 0.262 Chirality : 0.038 0.136 1124 Planarity : 0.003 0.028 1150 Dihedral : 4.748 49.845 924 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.49 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 0.015 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 0.03756 ( 460) hydrogen bonds : angle 4.12976 ( 1290) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.25242 ( 4) covalent geometry : bond 0.00260 ( 7032) covalent geometry : angle 0.47763 ( 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 117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.784 Fit side-chains REVERT: A 270 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7235 (mttt) REVERT: A 343 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8643 (mp) REVERT: A 357 MET cc_start: 0.9182 (mmt) cc_final: 0.8980 (mmt) REVERT: A 416 GLN cc_start: 0.8004 (mt0) cc_final: 0.7734 (tt0) REVERT: A 419 GLN cc_start: 0.7864 (tt0) cc_final: 0.7575 (tm-30) REVERT: B 151 GLU cc_start: 0.7247 (tt0) cc_final: 0.6976 (tt0) REVERT: B 357 MET cc_start: 0.9174 (mmt) cc_final: 0.8839 (mmt) REVERT: B 419 GLN cc_start: 0.7796 (tt0) cc_final: 0.7507 (tm-30) REVERT: B 474 MET cc_start: 0.8101 (mmp) cc_final: 0.7892 (mmm) REVERT: B 494 LYS cc_start: 0.7893 (mttt) cc_final: 0.7074 (mmtt) outliers start: 20 outliers final: 4 residues processed: 111 average time/residue: 1.1811 time to fit residues: 138.5245 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 : 0.698 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.114411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.096298 restraints weight = 8420.609| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.42 r_work: 0.2884 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1237 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= 0.150 Angle : 0.491 6.216 9542 Z= 0.265 Chirality : 0.039 0.143 1124 Planarity : 0.003 0.031 1150 Dihedral : 4.419 38.005 920 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.31 % Allowed : 13.62 % Favored : 84.06 % 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: 2.50 (0.28), residues: 842 helix: 2.58 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 270 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 0.001 PHE A 408 TYR 0.025 0.002 TYR A 158 ARG 0.004 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 460) hydrogen bonds : angle 3.98882 ( 1290) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.57167 ( 4) covalent geometry : bond 0.00343 ( 7032) covalent geometry : angle 0.49075 ( 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 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.693 Fit side-chains REVERT: A 24 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8274 (mm) REVERT: A 44 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7048 (tttt) REVERT: A 270 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7272 (mttt) REVERT: A 343 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 419 GLN cc_start: 0.7880 (tt0) cc_final: 0.7623 (tm-30) REVERT: B 151 GLU cc_start: 0.7338 (tt0) cc_final: 0.7088 (tt0) REVERT: B 415 ARG cc_start: 0.7923 (ptt-90) cc_final: 0.6464 (ttt-90) REVERT: B 419 GLN cc_start: 0.7812 (tt0) cc_final: 0.7543 (tm-30) REVERT: B 474 MET cc_start: 0.8117 (mmp) cc_final: 0.7912 (mmm) REVERT: B 494 LYS cc_start: 0.7970 (mttt) cc_final: 0.7214 (mmtt) outliers start: 18 outliers final: 6 residues processed: 106 average time/residue: 1.2916 time to fit residues: 144.2315 Evaluate side-chains 101 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 49 optimal weight: 2.9990 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: 3.9990 chunk 2 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 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 = 0.3223 r_free = 0.3223 target = 0.113691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.095369 restraints weight = 8459.649| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.46 r_work: 0.2867 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7034 Z= 0.159 Angle : 0.495 6.530 9542 Z= 0.266 Chirality : 0.039 0.150 1124 Planarity : 0.003 0.033 1150 Dihedral : 4.477 38.714 920 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.35 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: 2.52 (0.28), residues: 842 helix: 2.57 (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 0.014 0.001 PHE A 408 TYR 0.024 0.002 TYR A 158 ARG 0.004 0.001 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 460) hydrogen bonds : angle 3.94705 ( 1290) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.58286 ( 4) covalent geometry : bond 0.00368 ( 7032) covalent geometry : angle 0.49461 ( 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 117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.717 Fit side-chains REVERT: A 24 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8260 (mm) REVERT: A 270 LYS cc_start: 0.7832 (mmtm) cc_final: 0.7228 (mttt) REVERT: A 343 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8645 (mp) REVERT: A 419 GLN cc_start: 0.7974 (tt0) cc_final: 0.7674 (tm-30) REVERT: B 151 GLU cc_start: 0.7317 (tt0) cc_final: 0.7065 (tt0) REVERT: B 419 GLN cc_start: 0.7819 (tt0) cc_final: 0.7557 (tm-30) REVERT: B 474 MET cc_start: 0.8108 (mmp) cc_final: 0.7895 (mmm) REVERT: B 494 LYS cc_start: 0.7986 (mttt) cc_final: 0.7245 (mmtm) outliers start: 20 outliers final: 6 residues processed: 110 average time/residue: 1.2024 time to fit residues: 139.5535 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 : 0.724 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.114249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.096209 restraints weight = 8347.300| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.41 r_work: 0.2887 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7034 Z= 0.144 Angle : 0.486 7.637 9542 Z= 0.260 Chirality : 0.038 0.147 1124 Planarity : 0.003 0.034 1150 Dihedral : 4.417 38.385 920 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.31 % Allowed : 14.40 % 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: 2.59 (0.28), residues: 842 helix: 2.62 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.34 (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 0.022 0.002 TYR A 158 ARG 0.004 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 460) hydrogen bonds : angle 3.89435 ( 1290) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.53335 ( 4) covalent geometry : bond 0.00330 ( 7032) covalent geometry : angle 0.48636 ( 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 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.710 Fit side-chains REVERT: A 24 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 44 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6874 (tptt) REVERT: A 270 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7228 (mttt) REVERT: A 343 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8643 (mp) REVERT: A 419 GLN cc_start: 0.8035 (tt0) cc_final: 0.7768 (tm-30) REVERT: B 151 GLU cc_start: 0.7310 (tt0) cc_final: 0.7069 (tt0) REVERT: B 419 GLN cc_start: 0.7912 (tt0) cc_final: 0.7567 (tm-30) REVERT: B 494 LYS cc_start: 0.7974 (mttt) cc_final: 0.7241 (mmtm) outliers start: 18 outliers final: 7 residues processed: 114 average time/residue: 1.1924 time to fit residues: 143.5344 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 : 0.722 ------------------------------------------------------------------------------- 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 336 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 340 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 64 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 17 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 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 = 0.3259 r_free = 0.3259 target = 0.116453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098281 restraints weight = 8397.738| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.47 r_work: 0.2911 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1573 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= 0.108 Angle : 0.451 7.603 9542 Z= 0.243 Chirality : 0.037 0.139 1124 Planarity : 0.003 0.033 1150 Dihedral : 4.205 36.982 920 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 14.91 % 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 (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: 2.80 (0.29), residues: 842 helix: 2.82 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.32 (0.40), 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 0.014 0.001 PHE A 408 TYR 0.019 0.002 TYR A 158 ARG 0.004 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 460) hydrogen bonds : angle 3.77785 ( 1290) SS BOND : bond 0.00007 ( 2) SS BOND : angle 0.42267 ( 4) covalent geometry : bond 0.00236 ( 7032) covalent geometry : angle 0.45059 ( 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 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.768 Fit side-chains REVERT: A 24 LEU cc_start: 0.8460 (tp) cc_final: 0.8211 (mm) REVERT: A 270 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7225 (mttt) REVERT: A 343 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8596 (mp) REVERT: A 419 GLN cc_start: 0.7984 (tt0) cc_final: 0.7731 (tm-30) REVERT: B 70 SER cc_start: 0.8694 (t) cc_final: 0.8395 (p) REVERT: B 151 GLU cc_start: 0.7228 (tt0) cc_final: 0.6992 (tt0) REVERT: B 294 LEU cc_start: 0.8739 (tp) cc_final: 0.8507 (tp) REVERT: B 419 GLN cc_start: 0.7856 (tt0) cc_final: 0.7506 (tm-30) REVERT: B 494 LYS cc_start: 0.7898 (mttt) cc_final: 0.7152 (mmtm) outliers start: 16 outliers final: 5 residues processed: 114 average time/residue: 1.1957 time to fit residues: 143.9525 Evaluate side-chains 105 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 B residue 365 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 chunk 47 optimal weight: 0.0010 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.099077 restraints weight = 8304.671| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.46 r_work: 0.2915 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7034 Z= 0.105 Angle : 0.451 7.564 9542 Z= 0.242 Chirality : 0.037 0.132 1124 Planarity : 0.003 0.033 1150 Dihedral : 3.650 18.712 916 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 2.19 % Allowed : 15.17 % 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 (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: 2.89 (0.29), residues: 842 helix: 2.89 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.30 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 232 HIS 0.004 0.001 HIS A 335 PHE 0.014 0.001 PHE A 408 TYR 0.018 0.002 TYR B 158 ARG 0.004 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 460) hydrogen bonds : angle 3.72163 ( 1290) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.37623 ( 4) covalent geometry : bond 0.00230 ( 7032) covalent geometry : angle 0.45100 ( 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 121 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.785 Fit side-chains REVERT: A 24 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8224 (mm) REVERT: A 270 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7184 (mttt) REVERT: A 343 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 419 GLN cc_start: 0.7977 (tt0) cc_final: 0.7753 (tm-30) REVERT: B 70 SER cc_start: 0.8671 (t) cc_final: 0.8417 (p) REVERT: B 151 GLU cc_start: 0.7215 (tt0) cc_final: 0.6987 (tt0) REVERT: B 294 LEU cc_start: 0.8731 (tp) cc_final: 0.8495 (tp) REVERT: B 419 GLN cc_start: 0.7817 (tt0) cc_final: 0.7499 (tm-30) REVERT: B 494 LYS cc_start: 0.7811 (mttt) cc_final: 0.7053 (mmtm) outliers start: 17 outliers final: 6 residues processed: 117 average time/residue: 1.2116 time to fit residues: 149.5966 Evaluate side-chains 109 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 B residue 365 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.097882 restraints weight = 8384.871| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.42 r_work: 0.2902 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1702 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= 0.117 Angle : 0.468 7.570 9542 Z= 0.251 Chirality : 0.038 0.129 1124 Planarity : 0.003 0.032 1150 Dihedral : 3.697 19.729 916 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 2.06 % Allowed : 16.07 % Favored : 81.88 % 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: 2.86 (0.29), residues: 842 helix: 2.83 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.26 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 232 HIS 0.005 0.001 HIS A 335 PHE 0.013 0.001 PHE A 408 TYR 0.020 0.002 TYR A 158 ARG 0.005 0.001 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 460) hydrogen bonds : angle 3.73110 ( 1290) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.44151 ( 4) covalent geometry : bond 0.00262 ( 7032) covalent geometry : angle 0.46831 ( 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 117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.609 Fit side-chains REVERT: A 24 LEU cc_start: 0.8491 (tp) cc_final: 0.8248 (mm) REVERT: A 270 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7221 (mttt) REVERT: A 343 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8599 (mp) REVERT: A 419 GLN cc_start: 0.8023 (tt0) cc_final: 0.7781 (tm-30) REVERT: A 474 MET cc_start: 0.7650 (mpp) cc_final: 0.7397 (mmm) REVERT: B 42 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 70 SER cc_start: 0.8676 (t) cc_final: 0.8443 (p) REVERT: B 151 GLU cc_start: 0.7223 (tt0) cc_final: 0.6993 (tt0) REVERT: B 294 LEU cc_start: 0.8752 (tp) cc_final: 0.8518 (tp) REVERT: B 419 GLN cc_start: 0.7845 (tt0) cc_final: 0.7536 (tm-30) REVERT: B 494 LYS cc_start: 0.7822 (mttt) cc_final: 0.7047 (mmtm) outliers start: 16 outliers final: 7 residues processed: 114 average time/residue: 1.2669 time to fit residues: 153.5549 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 : 0.708 ------------------------------------------------------------------------------- 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 42 ILE Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.113401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094924 restraints weight = 8496.075| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.48 r_work: 0.2854 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7034 Z= 0.164 Angle : 0.514 7.398 9542 Z= 0.275 Chirality : 0.040 0.142 1124 Planarity : 0.003 0.033 1150 Dihedral : 3.964 23.044 916 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 1.93 % Allowed : 16.20 % Favored : 81.88 % 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: 2.64 (0.29), residues: 842 helix: 2.67 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.32 (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 A 335 PHE 0.013 0.002 PHE A 408 TYR 0.021 0.002 TYR A 158 ARG 0.005 0.001 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 460) hydrogen bonds : angle 3.86497 ( 1290) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.67511 ( 4) covalent geometry : bond 0.00383 ( 7032) covalent geometry : angle 0.51440 ( 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 118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.789 Fit side-chains REVERT: A 24 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8224 (mm) REVERT: A 270 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7208 (mttt) REVERT: A 343 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8589 (mp) REVERT: A 419 GLN cc_start: 0.8019 (tt0) cc_final: 0.7768 (tm-30) REVERT: B 42 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 70 SER cc_start: 0.8710 (t) cc_final: 0.8404 (p) REVERT: B 151 GLU cc_start: 0.7321 (tt0) cc_final: 0.7073 (tt0) REVERT: B 294 LEU cc_start: 0.8718 (tp) cc_final: 0.8492 (tp) REVERT: B 419 GLN cc_start: 0.7861 (tt0) cc_final: 0.7493 (tm-30) REVERT: B 494 LYS cc_start: 0.7861 (mttt) cc_final: 0.7069 (mmtm) outliers start: 15 outliers final: 8 residues processed: 114 average time/residue: 1.2345 time to fit residues: 148.4366 Evaluate side-chains 114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 400 LEU 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 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.0000 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.116626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098516 restraints weight = 8484.599| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.44 r_work: 0.2914 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7034 Z= 0.106 Angle : 0.470 7.625 9542 Z= 0.252 Chirality : 0.037 0.132 1124 Planarity : 0.003 0.031 1150 Dihedral : 3.715 18.905 916 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Rotamer: Outliers : 1.29 % Allowed : 17.22 % Favored : 81.49 % 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: 2.87 (0.29), residues: 842 helix: 2.82 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.21 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 232 HIS 0.004 0.001 HIS A 335 PHE 0.014 0.001 PHE A 408 TYR 0.018 0.002 TYR B 158 ARG 0.007 0.001 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03091 ( 460) hydrogen bonds : angle 3.75092 ( 1290) SS BOND : bond 0.00040 ( 2) SS BOND : angle 0.42898 ( 4) covalent geometry : bond 0.00232 ( 7032) covalent geometry : angle 0.47019 ( 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 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.812 Fit side-chains REVERT: A 24 LEU cc_start: 0.8490 (tp) cc_final: 0.8250 (mm) REVERT: A 270 LYS cc_start: 0.7766 (mmtm) cc_final: 0.7232 (mttt) REVERT: A 343 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 419 GLN cc_start: 0.8044 (tt0) cc_final: 0.7819 (tm-30) REVERT: A 474 MET cc_start: 0.7692 (mpp) cc_final: 0.7415 (mmm) REVERT: B 70 SER cc_start: 0.8665 (t) cc_final: 0.8420 (p) REVERT: B 151 GLU cc_start: 0.7225 (tt0) cc_final: 0.6989 (tt0) REVERT: B 248 PHE cc_start: 0.8572 (m-80) cc_final: 0.8332 (m-80) REVERT: B 294 LEU cc_start: 0.8753 (tp) cc_final: 0.8525 (tp) REVERT: B 419 GLN cc_start: 0.7818 (tt0) cc_final: 0.7499 (tm-30) REVERT: B 494 LYS cc_start: 0.7716 (mttt) cc_final: 0.7132 (mmtm) outliers start: 10 outliers final: 7 residues processed: 111 average time/residue: 1.2412 time to fit residues: 145.3901 Evaluate side-chains 111 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 3.9990 chunk 59 optimal weight: 0.0050 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.117064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098829 restraints weight = 8416.323| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.47 r_work: 0.2911 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1763 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 : 0.475 7.534 9542 Z= 0.254 Chirality : 0.037 0.131 1124 Planarity : 0.003 0.031 1150 Dihedral : 3.692 19.007 916 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 1.41 % Allowed : 16.97 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.87 (0.29), residues: 842 helix: 2.83 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.21 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 232 HIS 0.005 0.001 HIS A 335 PHE 0.013 0.001 PHE A 408 TYR 0.018 0.002 TYR B 158 ARG 0.006 0.001 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 460) hydrogen bonds : angle 3.71399 ( 1290) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.42077 ( 4) covalent geometry : bond 0.00241 ( 7032) covalent geometry : angle 0.47493 ( 9538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4819.65 seconds wall clock time: 83 minutes 8.17 seconds (4988.17 seconds total)