Starting phenix.real_space_refine on Sun Apr 27 04:52:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bvt_16271/04_2025/8bvt_16271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bvt_16271/04_2025/8bvt_16271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bvt_16271/04_2025/8bvt_16271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bvt_16271/04_2025/8bvt_16271.map" model { file = "/net/cci-nas-00/data/ceres_data/8bvt_16271/04_2025/8bvt_16271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bvt_16271/04_2025/8bvt_16271.cif" } resolution = 3.94 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= 0.002 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 2907 2.51 5 N 776 2.21 5 O 801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4517 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3933 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 28, 'TRANS': 479} Chain breaks: 2 Chain: "B" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 565 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 216 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'RTO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.44, per 1000 atoms: 1.20 Number of scatterers: 4517 At special positions: 0 Unit cell: (115.648, 70.72, 82.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 801 8.00 N 776 7.00 C 2907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " 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: 1.47 Conformation dependent library (CDL) restraints added in 614.5 milliseconds 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1146 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 64.0% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.611A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 removed outlier: 4.283A pdb=" N VAL A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 132 through 160 removed outlier: 3.687A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 181 Processing helix chain 'A' and resid 184 through 214 removed outlier: 3.746A pdb=" N SER A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 244 Processing helix chain 'A' and resid 246 through 266 Proline residue: A 257 - end of helix removed outlier: 4.009A pdb=" N ILE A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.255A pdb=" N LYS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.508A pdb=" N LEU A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 332 removed outlier: 3.531A pdb=" N CYS A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 359 removed outlier: 3.981A pdb=" N ASP A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 removed outlier: 3.974A pdb=" N GLY A 364 " --> pdb=" O GLN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 392 removed outlier: 3.733A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 420 through 449 Processing helix chain 'A' and resid 453 through 478 Proline residue: A 473 - end of helix removed outlier: 4.010A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 502 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.101A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.802A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 22 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.607A pdb=" N ARG B 59 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 843 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: 1.40 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 1 1.17 - 1.33: 1150 1.33 - 1.49: 1534 1.49 - 1.66: 1875 1.66 - 1.82: 53 Bond restraints: 4613 Sorted by residual: bond pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " ideal model delta sigma weight residual 1.492 1.011 0.481 5.00e-02 4.00e+02 9.25e+01 bond pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 1.503 1.217 0.286 3.40e-02 8.65e+02 7.06e+01 bond pdb=" N PRO A 88 " pdb=" CA PRO A 88 " ideal model delta sigma weight residual 1.465 1.566 -0.101 2.03e-02 2.43e+03 2.49e+01 bond pdb=" N04 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.625 1.711 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C11 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.776 1.817 -0.041 2.00e-02 2.50e+03 4.10e+00 ... (remaining 4608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.67: 6278 8.67 - 17.35: 10 17.35 - 26.02: 1 26.02 - 34.69: 1 34.69 - 43.37: 2 Bond angle restraints: 6292 Sorted by residual: angle pdb=" CA PRO A 88 " pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " ideal model delta sigma weight residual 104.50 66.53 37.97 1.90e+00 2.77e-01 3.99e+02 angle pdb=" N PRO A 88 " pdb=" CD PRO A 88 " pdb=" CG PRO A 88 " ideal model delta sigma weight residual 103.20 74.08 29.12 1.50e+00 4.44e-01 3.77e+02 angle pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 106.10 149.47 -43.37 3.20e+00 9.77e-02 1.84e+02 angle pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 112.00 99.99 12.01 1.40e+00 5.10e-01 7.36e+01 angle pdb=" CA PRO A 494 " pdb=" N PRO A 494 " pdb=" CD PRO A 494 " ideal model delta sigma weight residual 112.00 102.70 9.30 1.40e+00 5.10e-01 4.41e+01 ... (remaining 6287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2318 17.69 - 35.37: 314 35.37 - 53.06: 74 53.06 - 70.75: 12 70.75 - 88.44: 10 Dihedral angle restraints: 2728 sinusoidal: 944 harmonic: 1784 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual 93.00 27.55 65.45 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" N PRO A 88 " pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " pdb=" CB PRO A 88 " ideal model delta sinusoidal sigma weight residual 30.00 107.54 -77.54 1 1.50e+01 4.44e-03 3.35e+01 dihedral pdb=" CA PRO A 88 " pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sinusoidal sigma weight residual 38.00 123.96 -85.96 1 2.00e+01 2.50e-03 2.23e+01 ... (remaining 2725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 564 0.048 - 0.095: 138 0.095 - 0.143: 31 0.143 - 0.190: 6 0.190 - 0.238: 3 Chirality restraints: 742 Sorted by residual: chirality pdb=" CA PRO A 494 " pdb=" N PRO A 494 " pdb=" C PRO A 494 " pdb=" CB PRO A 494 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" C PRO A 88 " pdb=" CB PRO A 88 " both_signs ideal model delta sigma weight residual False 2.72 2.93 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO A 257 " pdb=" N PRO A 257 " pdb=" C PRO A 257 " pdb=" CB PRO A 257 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 739 not shown) Planarity restraints: 799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " 0.052 2.00e-02 2.50e+03 9.66e-02 9.34e+01 pdb=" C SER B 114 " -0.167 2.00e-02 2.50e+03 pdb=" O SER B 114 " 0.061 2.00e-02 2.50e+03 pdb=" N ALA B 115 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 493 " 0.070 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A 494 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 87 " 0.046 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 88 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.035 5.00e-02 4.00e+02 ... (remaining 796 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 164 2.71 - 3.25: 4839 3.25 - 3.80: 7722 3.80 - 4.35: 8493 4.35 - 4.90: 14395 Nonbonded interactions: 35613 Sorted by model distance: nonbonded pdb=" OG1 THR A 172 " pdb=" OG SER A 198 " model vdw 2.157 3.040 nonbonded pdb=" OD1 ASP A 70 " pdb=" N GLN A 74 " model vdw 2.257 3.120 nonbonded pdb=" OG SER A 401 " pdb=" O CYS A 433 " model vdw 2.267 3.040 nonbonded pdb=" NH1 ARG A 394 " pdb=" OG1 THR A 507 " model vdw 2.276 3.120 nonbonded pdb=" ND2 ASN A 39 " pdb=" O MET A 358 " model vdw 2.285 3.120 ... (remaining 35608 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 3.110 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.420 Find NCS groups from input model: 0.050 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.009 0.481 4615 Z= 0.268 Angle : 1.221 43.365 6296 Z= 0.576 Chirality : 0.046 0.238 742 Planarity : 0.007 0.100 799 Dihedral : 17.639 88.436 1576 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.23 % Allowed : 44.99 % Favored : 54.78 % 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: 0.33 (0.34), residues: 615 helix: 1.09 (0.27), residues: 357 sheet: 0.48 (0.82), residues: 48 loop : -1.34 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 109 HIS 0.002 0.001 HIS A 47 PHE 0.025 0.002 PHE A 262 TYR 0.016 0.001 TYR A 482 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.13470 ( 289) hydrogen bonds : angle 5.71807 ( 843) SS BOND : bond 0.00474 ( 2) SS BOND : angle 1.43776 ( 4) covalent geometry : bond 0.00929 ( 4613) covalent geometry : angle 1.22064 ( 6292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 482 TYR cc_start: 0.7709 (t80) cc_final: 0.7377 (t80) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1046 time to fit residues: 13.9355 Evaluate side-chains 92 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 50.0000 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** 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 = 0.3954 r_free = 0.3954 target = 0.126964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.106152 restraints weight = 12205.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109132 restraints weight = 6208.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.110996 restraints weight = 3960.443| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4615 Z= 0.140 Angle : 0.749 13.987 6296 Z= 0.351 Chirality : 0.041 0.149 742 Planarity : 0.004 0.036 799 Dihedral : 5.035 29.273 686 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.03 % Allowed : 39.86 % Favored : 57.11 % 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: 0.61 (0.35), residues: 615 helix: 1.27 (0.27), residues: 362 sheet: 0.86 (0.81), residues: 49 loop : -1.29 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 109 HIS 0.002 0.000 HIS A 47 PHE 0.014 0.001 PHE A 347 TYR 0.017 0.001 TYR A 354 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 289) hydrogen bonds : angle 4.83909 ( 843) SS BOND : bond 0.00684 ( 2) SS BOND : angle 1.98728 ( 4) covalent geometry : bond 0.00299 ( 4613) covalent geometry : angle 0.74725 ( 6292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8705 (tpt) cc_final: 0.8261 (tpt) REVERT: A 122 THR cc_start: 0.9381 (p) cc_final: 0.9077 (t) REVERT: A 142 MET cc_start: 0.9578 (tpp) cc_final: 0.9257 (tpp) REVERT: A 168 ASN cc_start: 0.7960 (m-40) cc_final: 0.7547 (m110) REVERT: A 482 TYR cc_start: 0.7562 (t80) cc_final: 0.7146 (t80) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.1143 time to fit residues: 17.5495 Evaluate side-chains 103 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 40.0000 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** 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 = 0.3921 r_free = 0.3921 target = 0.125149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.103513 restraints weight = 12447.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106512 restraints weight = 6342.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.108514 restraints weight = 4076.711| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4615 Z= 0.165 Angle : 0.706 10.074 6296 Z= 0.330 Chirality : 0.041 0.156 742 Planarity : 0.005 0.045 799 Dihedral : 5.006 30.253 686 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.90 % Allowed : 38.93 % Favored : 56.18 % 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: 0.69 (0.35), residues: 615 helix: 1.38 (0.27), residues: 359 sheet: 0.86 (0.81), residues: 49 loop : -1.30 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.002 0.001 HIS A 47 PHE 0.014 0.001 PHE A 262 TYR 0.013 0.001 TYR A 354 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 289) hydrogen bonds : angle 4.74057 ( 843) SS BOND : bond 0.00652 ( 2) SS BOND : angle 2.03340 ( 4) covalent geometry : bond 0.00372 ( 4613) covalent geometry : angle 0.70428 ( 6292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.455 Fit side-chains REVERT: A 23 MET cc_start: 0.8806 (tpt) cc_final: 0.8392 (tpt) REVERT: A 76 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 122 THR cc_start: 0.9434 (p) cc_final: 0.9135 (t) REVERT: A 361 GLN cc_start: 0.7680 (mm110) cc_final: 0.7476 (mm110) REVERT: A 394 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7015 (mtm180) REVERT: A 482 TYR cc_start: 0.7556 (t80) cc_final: 0.6998 (t80) REVERT: A 485 MET cc_start: 0.9198 (tmm) cc_final: 0.8736 (tpt) outliers start: 21 outliers final: 16 residues processed: 110 average time/residue: 0.1068 time to fit residues: 16.4553 Evaluate side-chains 115 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 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 38 GLN ** 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 = 0.3942 r_free = 0.3942 target = 0.126583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.105016 restraints weight = 12473.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.108038 restraints weight = 6315.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.110133 restraints weight = 4047.575| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4615 Z= 0.133 Angle : 0.697 11.063 6296 Z= 0.320 Chirality : 0.041 0.165 742 Planarity : 0.004 0.046 799 Dihedral : 4.818 30.606 686 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.59 % Allowed : 39.86 % Favored : 54.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.35), residues: 615 helix: 1.40 (0.27), residues: 362 sheet: 0.96 (0.81), residues: 49 loop : -1.31 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.002 0.000 HIS A 47 PHE 0.014 0.001 PHE A 347 TYR 0.010 0.001 TYR A 354 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 289) hydrogen bonds : angle 4.60289 ( 843) SS BOND : bond 0.00546 ( 2) SS BOND : angle 1.82964 ( 4) covalent geometry : bond 0.00296 ( 4613) covalent geometry : angle 0.69614 ( 6292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.802 Fit side-chains REVERT: A 76 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 122 THR cc_start: 0.9434 (p) cc_final: 0.9136 (t) REVERT: A 394 ARG cc_start: 0.7728 (mtm180) cc_final: 0.6963 (mtm180) REVERT: A 482 TYR cc_start: 0.7591 (t80) cc_final: 0.6962 (t80) outliers start: 24 outliers final: 18 residues processed: 112 average time/residue: 0.1169 time to fit residues: 18.4471 Evaluate side-chains 112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 40.0000 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** 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 = 0.3940 r_free = 0.3940 target = 0.126567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104784 restraints weight = 12563.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107818 restraints weight = 6369.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.109881 restraints weight = 4090.707| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4615 Z= 0.140 Angle : 0.724 15.837 6296 Z= 0.328 Chirality : 0.041 0.166 742 Planarity : 0.004 0.050 799 Dihedral : 4.750 31.439 686 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 6.06 % Allowed : 38.46 % Favored : 55.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.35), residues: 615 helix: 1.43 (0.27), residues: 359 sheet: 0.81 (0.82), residues: 50 loop : -1.29 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 274 HIS 0.002 0.000 HIS A 47 PHE 0.014 0.001 PHE A 347 TYR 0.010 0.001 TYR A 354 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 289) hydrogen bonds : angle 4.57964 ( 843) SS BOND : bond 0.00532 ( 2) SS BOND : angle 1.79262 ( 4) covalent geometry : bond 0.00317 ( 4613) covalent geometry : angle 0.72330 ( 6292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.482 Fit side-chains REVERT: A 7 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9224 (tp) REVERT: A 23 MET cc_start: 0.8766 (tpt) cc_final: 0.8424 (tpt) REVERT: A 76 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 122 THR cc_start: 0.9438 (p) cc_final: 0.9147 (t) REVERT: A 361 GLN cc_start: 0.7619 (mm110) cc_final: 0.7375 (mm110) REVERT: A 482 TYR cc_start: 0.7584 (t80) cc_final: 0.6923 (t80) REVERT: A 485 MET cc_start: 0.9172 (tmm) cc_final: 0.8717 (tpt) outliers start: 26 outliers final: 20 residues processed: 112 average time/residue: 0.1011 time to fit residues: 16.1591 Evaluate side-chains 117 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 0.0040 chunk 29 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 51 optimal weight: 50.0000 chunk 60 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.125766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.103950 restraints weight = 12533.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.106990 restraints weight = 6377.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.109050 restraints weight = 4099.908| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4615 Z= 0.144 Angle : 0.734 15.182 6296 Z= 0.332 Chirality : 0.041 0.148 742 Planarity : 0.004 0.049 799 Dihedral : 4.698 32.507 686 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 6.76 % Allowed : 38.23 % Favored : 55.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.35), residues: 615 helix: 1.43 (0.27), residues: 359 sheet: 0.90 (0.83), residues: 50 loop : -1.31 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 274 HIS 0.003 0.000 HIS A 47 PHE 0.014 0.001 PHE A 347 TYR 0.010 0.001 TYR A 354 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 289) hydrogen bonds : angle 4.56643 ( 843) SS BOND : bond 0.00720 ( 2) SS BOND : angle 1.73158 ( 4) covalent geometry : bond 0.00325 ( 4613) covalent geometry : angle 0.73284 ( 6292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.482 Fit side-chains REVERT: A 76 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 122 THR cc_start: 0.9441 (p) cc_final: 0.9163 (t) REVERT: A 359 ASP cc_start: 0.9048 (t0) cc_final: 0.8831 (t0) REVERT: A 361 GLN cc_start: 0.7704 (mm110) cc_final: 0.7438 (mm110) REVERT: A 482 TYR cc_start: 0.7588 (t80) cc_final: 0.6934 (t80) outliers start: 29 outliers final: 24 residues processed: 115 average time/residue: 0.1026 time to fit residues: 16.8680 Evaluate side-chains 118 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.126462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.104066 restraints weight = 12451.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.107108 restraints weight = 6464.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.109167 restraints weight = 4204.336| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4615 Z= 0.145 Angle : 0.748 15.462 6296 Z= 0.335 Chirality : 0.041 0.179 742 Planarity : 0.004 0.050 799 Dihedral : 4.641 33.244 686 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 6.76 % Allowed : 38.23 % Favored : 55.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.35), residues: 615 helix: 1.44 (0.27), residues: 359 sheet: 1.12 (0.84), residues: 49 loop : -1.33 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 274 HIS 0.002 0.000 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.009 0.001 TYR A 354 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 289) hydrogen bonds : angle 4.58686 ( 843) SS BOND : bond 0.00634 ( 2) SS BOND : angle 1.50175 ( 4) covalent geometry : bond 0.00330 ( 4613) covalent geometry : angle 0.74700 ( 6292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.525 Fit side-chains REVERT: A 76 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7927 (mm-30) REVERT: A 122 THR cc_start: 0.9444 (p) cc_final: 0.9163 (t) REVERT: A 359 ASP cc_start: 0.9132 (t0) cc_final: 0.8834 (t0) REVERT: A 361 GLN cc_start: 0.7755 (mm110) cc_final: 0.7526 (mm110) REVERT: A 367 MET cc_start: 0.8403 (mmt) cc_final: 0.8183 (mmt) REVERT: A 482 TYR cc_start: 0.7597 (t80) cc_final: 0.6919 (t80) REVERT: A 485 MET cc_start: 0.9162 (tmm) cc_final: 0.8652 (tpt) outliers start: 29 outliers final: 23 residues processed: 117 average time/residue: 0.1030 time to fit residues: 17.1838 Evaluate side-chains 118 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 40.0000 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.125711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.103892 restraints weight = 12466.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.106857 restraints weight = 6416.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.108907 restraints weight = 4160.599| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4615 Z= 0.149 Angle : 0.802 16.198 6296 Z= 0.354 Chirality : 0.042 0.179 742 Planarity : 0.004 0.048 799 Dihedral : 4.608 33.674 686 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 6.53 % Allowed : 38.23 % Favored : 55.24 % 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: 0.67 (0.35), residues: 615 helix: 1.34 (0.27), residues: 359 sheet: 1.16 (0.85), residues: 49 loop : -1.34 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 274 HIS 0.002 0.001 HIS A 47 PHE 0.017 0.001 PHE A 347 TYR 0.020 0.001 TYR A 354 ARG 0.002 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 289) hydrogen bonds : angle 4.60596 ( 843) SS BOND : bond 0.00716 ( 2) SS BOND : angle 2.88389 ( 4) covalent geometry : bond 0.00341 ( 4613) covalent geometry : angle 0.79888 ( 6292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.536 Fit side-chains REVERT: A 7 LEU cc_start: 0.9524 (tp) cc_final: 0.9308 (tp) REVERT: A 76 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 122 THR cc_start: 0.9446 (p) cc_final: 0.9166 (t) REVERT: A 359 ASP cc_start: 0.9126 (t0) cc_final: 0.8834 (t0) REVERT: A 361 GLN cc_start: 0.7778 (mm110) cc_final: 0.7539 (mm110) REVERT: A 464 MET cc_start: 0.8020 (ttt) cc_final: 0.7633 (ttp) REVERT: A 482 TYR cc_start: 0.7606 (t80) cc_final: 0.6933 (t80) REVERT: A 485 MET cc_start: 0.9153 (tmm) cc_final: 0.8657 (tpt) outliers start: 28 outliers final: 26 residues processed: 115 average time/residue: 0.1183 time to fit residues: 18.7295 Evaluate side-chains 118 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.0000 chunk 52 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 39 ASN ** 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 = 0.3947 r_free = 0.3947 target = 0.126794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105357 restraints weight = 12412.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.108323 restraints weight = 6406.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.110371 restraints weight = 4149.873| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4615 Z= 0.136 Angle : 0.829 16.173 6296 Z= 0.359 Chirality : 0.042 0.200 742 Planarity : 0.005 0.048 799 Dihedral : 4.559 33.589 686 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.83 % Allowed : 38.46 % Favored : 55.71 % 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: 0.70 (0.35), residues: 615 helix: 1.39 (0.27), residues: 358 sheet: 1.16 (0.86), residues: 49 loop : -1.37 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 86 HIS 0.002 0.000 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.009 0.001 TYR A 354 ARG 0.007 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 289) hydrogen bonds : angle 4.60386 ( 843) SS BOND : bond 0.00581 ( 2) SS BOND : angle 2.35169 ( 4) covalent geometry : bond 0.00305 ( 4613) covalent geometry : angle 0.82732 ( 6292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.495 Fit side-chains REVERT: A 76 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8073 (mm-30) REVERT: A 359 ASP cc_start: 0.9146 (t0) cc_final: 0.8819 (t0) REVERT: A 361 GLN cc_start: 0.7621 (mm110) cc_final: 0.7397 (mm110) REVERT: A 482 TYR cc_start: 0.7621 (t80) cc_final: 0.6934 (t80) REVERT: A 485 MET cc_start: 0.9136 (tmm) cc_final: 0.8670 (tpt) outliers start: 25 outliers final: 23 residues processed: 111 average time/residue: 0.1122 time to fit residues: 17.4687 Evaluate side-chains 112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 51 optimal weight: 40.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.126500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.105083 restraints weight = 12465.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.108028 restraints weight = 6402.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110069 restraints weight = 4146.666| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4615 Z= 0.139 Angle : 0.831 16.126 6296 Z= 0.361 Chirality : 0.042 0.186 742 Planarity : 0.005 0.048 799 Dihedral : 4.571 33.507 686 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.83 % Allowed : 38.23 % Favored : 55.94 % 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: 0.55 (0.35), residues: 615 helix: 1.25 (0.27), residues: 364 sheet: 1.13 (0.84), residues: 50 loop : -1.49 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.003 0.001 HIS A 47 PHE 0.015 0.001 PHE A 347 TYR 0.009 0.001 TYR A 444 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 289) hydrogen bonds : angle 4.58975 ( 843) SS BOND : bond 0.00585 ( 2) SS BOND : angle 2.12117 ( 4) covalent geometry : bond 0.00315 ( 4613) covalent geometry : angle 0.82911 ( 6292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.518 Fit side-chains REVERT: A 76 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8092 (mm-30) REVERT: A 359 ASP cc_start: 0.9136 (t0) cc_final: 0.8830 (t0) REVERT: A 464 MET cc_start: 0.8018 (ttt) cc_final: 0.7672 (ttp) REVERT: A 482 TYR cc_start: 0.7654 (t80) cc_final: 0.6930 (t80) REVERT: A 485 MET cc_start: 0.9148 (tmm) cc_final: 0.8695 (tpt) outliers start: 25 outliers final: 23 residues processed: 111 average time/residue: 0.1083 time to fit residues: 17.0042 Evaluate side-chains 114 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 0.3980 chunk 57 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 30.0000 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** 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 = 0.3954 r_free = 0.3954 target = 0.127480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105921 restraints weight = 12418.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.108914 restraints weight = 6376.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110968 restraints weight = 4118.777| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4615 Z= 0.134 Angle : 0.836 16.250 6296 Z= 0.360 Chirality : 0.042 0.192 742 Planarity : 0.005 0.048 799 Dihedral : 4.379 30.790 686 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.59 % Allowed : 38.46 % Favored : 55.94 % 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: 0.62 (0.35), residues: 615 helix: 1.29 (0.27), residues: 363 sheet: 0.92 (0.80), residues: 56 loop : -1.41 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.001 0.000 HIS A 48 PHE 0.014 0.001 PHE A 347 TYR 0.007 0.001 TYR A 169 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 289) hydrogen bonds : angle 4.53444 ( 843) SS BOND : bond 0.00815 ( 2) SS BOND : angle 2.08936 ( 4) covalent geometry : bond 0.00299 ( 4613) covalent geometry : angle 0.83456 ( 6292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.85 seconds wall clock time: 32 minutes 24.16 seconds (1944.16 seconds total)