Starting phenix.real_space_refine on Fri Dec 27 11:52:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bvt_16271/12_2024/8bvt_16271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bvt_16271/12_2024/8bvt_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_16271/12_2024/8bvt_16271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bvt_16271/12_2024/8bvt_16271.map" model { file = "/net/cci-nas-00/data/ceres_data/8bvt_16271/12_2024/8bvt_16271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bvt_16271/12_2024/8bvt_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.32, per 1000 atoms: 0.74 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: 1.39 Conformation dependent library (CDL) restraints added in 628.4 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: 0.44 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: 1.21 Time building geometry restraints manager: 1.39 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: 1.670 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.040 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- 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 4613 Z= 0.522 Angle : 1.221 43.365 6292 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 *********************** 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 : 0.524 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: 0.1078 time to fit residues: 14.2149 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 : 0.573 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 4613 Z= 0.193 Angle : 0.747 13.985 6292 Z= 0.350 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 *********************** 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 : 0.531 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8820 (tpt) cc_final: 0.8378 (tpt) REVERT: A 122 THR cc_start: 0.9395 (p) cc_final: 0.9137 (t) REVERT: A 142 MET cc_start: 0.9590 (tpp) cc_final: 0.9249 (tpp) REVERT: A 168 ASN cc_start: 0.7975 (m-40) cc_final: 0.7545 (m110) REVERT: A 482 TYR cc_start: 0.7562 (t80) cc_final: 0.7127 (t80) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.1144 time to fit residues: 17.6861 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 : 1.118 ------------------------------------------------------------------------------- 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 30 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4613 Z= 0.196 Angle : 0.695 9.880 6292 Z= 0.320 Chirality : 0.041 0.159 742 Planarity : 0.004 0.046 799 Dihedral : 4.965 29.819 686 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.73 % Allowed : 39.16 % 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: 0.69 (0.35), residues: 615 helix: 1.35 (0.27), residues: 362 sheet: 0.91 (0.82), residues: 49 loop : -1.29 (0.45), 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 0.012 0.001 PHE A 347 TYR 0.013 0.001 TYR A 354 ARG 0.003 0.000 ARG A 273 *********************** 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 112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.462 Fit side-chains REVERT: A 23 MET cc_start: 0.8841 (tpt) cc_final: 0.8425 (tpt) REVERT: A 76 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 122 THR cc_start: 0.9433 (p) cc_final: 0.9155 (t) REVERT: A 394 ARG cc_start: 0.7766 (mtm180) cc_final: 0.6981 (mtm180) REVERT: A 482 TYR cc_start: 0.7584 (t80) cc_final: 0.7000 (t80) REVERT: A 485 MET cc_start: 0.9192 (tmm) cc_final: 0.8721 (tpt) outliers start: 16 outliers final: 14 residues processed: 105 average time/residue: 0.1277 time to fit residues: 18.5028 Evaluate side-chains 109 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 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 41 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- 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 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4613 Z= 0.260 Angle : 0.707 10.108 6292 Z= 0.332 Chirality : 0.042 0.170 742 Planarity : 0.004 0.046 799 Dihedral : 4.825 31.423 686 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % 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: 0.68 (0.35), residues: 615 helix: 1.37 (0.27), residues: 359 sheet: 0.97 (0.81), 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 0.003 0.001 HIS A 47 PHE 0.014 0.001 PHE A 262 TYR 0.010 0.001 TYR A 169 ARG 0.003 0.000 ARG A 273 *********************** 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 126 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.516 Fit side-chains REVERT: A 23 MET cc_start: 0.8906 (tpt) cc_final: 0.8508 (tpt) REVERT: A 76 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 122 THR cc_start: 0.9465 (p) cc_final: 0.9216 (t) REVERT: A 359 ASP cc_start: 0.9029 (t0) cc_final: 0.8823 (t0) REVERT: A 482 TYR cc_start: 0.7575 (t80) cc_final: 0.6928 (t80) outliers start: 29 outliers final: 21 residues processed: 115 average time/residue: 0.1066 time to fit residues: 17.3738 Evaluate side-chains 118 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 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 177 THR Chi-restraints excluded: chain A residue 199 LEU 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 339 PHE 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 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 33 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 50.0000 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4613 Z= 0.226 Angle : 0.735 14.919 6292 Z= 0.335 Chirality : 0.042 0.133 742 Planarity : 0.005 0.052 799 Dihedral : 4.774 32.060 686 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.29 % Allowed : 38.00 % 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: 0.68 (0.35), residues: 615 helix: 1.39 (0.27), residues: 359 sheet: 0.78 (0.81), residues: 50 loop : -1.31 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.010 0.001 TYR A 354 ARG 0.002 0.000 ARG A 273 *********************** 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 127 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.529 Fit side-chains REVERT: A 7 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9227 (tp) REVERT: A 76 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 122 THR cc_start: 0.9459 (p) cc_final: 0.9209 (t) REVERT: A 359 ASP cc_start: 0.9090 (t0) cc_final: 0.8868 (t0) REVERT: A 482 TYR cc_start: 0.7592 (t80) cc_final: 0.6910 (t80) REVERT: A 485 MET cc_start: 0.9175 (tmm) cc_final: 0.8722 (tpt) outliers start: 27 outliers final: 21 residues processed: 119 average time/residue: 0.0982 time to fit residues: 16.6798 Evaluate side-chains 119 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 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 11 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4613 Z= 0.191 Angle : 0.742 15.406 6292 Z= 0.332 Chirality : 0.041 0.169 742 Planarity : 0.004 0.051 799 Dihedral : 4.675 32.189 686 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 6.06 % Allowed : 39.86 % Favored : 54.08 % 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: 0.77 (0.35), residues: 615 helix: 1.47 (0.27), residues: 359 sheet: 1.01 (0.82), residues: 49 loop : -1.34 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.002 0.000 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.010 0.001 TYR A 354 ARG 0.002 0.000 ARG A 394 *********************** 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 125 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.536 Fit side-chains REVERT: A 76 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 122 THR cc_start: 0.9438 (p) cc_final: 0.9186 (t) REVERT: A 234 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A 359 ASP cc_start: 0.9142 (t0) cc_final: 0.8917 (t0) REVERT: A 482 TYR cc_start: 0.7598 (t80) cc_final: 0.6922 (t80) outliers start: 26 outliers final: 22 residues processed: 116 average time/residue: 0.1167 time to fit residues: 19.1985 Evaluate side-chains 119 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 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 426 LEU Chi-restraints excluded: chain A residue 449 TYR 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 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.0060 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 0.0470 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.0470 overall best weight: 0.2992 ------------------------------------------------------------------------------- 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** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 0.035 4613 Z= 0.185 Angle : 0.775 15.309 6292 Z= 0.343 Chirality : 0.042 0.218 742 Planarity : 0.004 0.050 799 Dihedral : 4.658 32.500 686 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.53 % Allowed : 39.16 % Favored : 54.31 % 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: 1.47 (0.28), residues: 357 sheet: 1.09 (0.84), residues: 49 loop : -1.36 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.001 0.000 HIS A 47 PHE 0.016 0.001 PHE A 347 TYR 0.019 0.001 TYR A 354 ARG 0.002 0.000 ARG A 273 *********************** 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 124 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.561 Fit side-chains REVERT: A 76 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 234 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 359 ASP cc_start: 0.9170 (t0) cc_final: 0.8826 (t0) REVERT: A 482 TYR cc_start: 0.7610 (t80) cc_final: 0.6913 (t80) REVERT: A 485 MET cc_start: 0.9144 (tmm) cc_final: 0.8610 (tpt) outliers start: 28 outliers final: 19 residues processed: 115 average time/residue: 0.1168 time to fit residues: 18.5961 Evaluate side-chains 115 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 187 VAL 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 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 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 0.0970 chunk 51 optimal weight: 50.0000 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4613 Z= 0.198 Angle : 0.801 15.792 6292 Z= 0.349 Chirality : 0.042 0.224 742 Planarity : 0.004 0.048 799 Dihedral : 4.537 32.789 686 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.13 % Allowed : 39.16 % 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: 0.71 (0.35), residues: 615 helix: 1.43 (0.27), residues: 357 sheet: 1.14 (0.83), residues: 50 loop : -1.42 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 109 HIS 0.002 0.000 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.008 0.001 TYR A 354 ARG 0.003 0.000 ARG A 162 *********************** 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 119 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.9573 (tpp) cc_final: 0.9318 (tpp) REVERT: A 234 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7645 (tm-30) REVERT: A 344 MET cc_start: 0.8751 (tmm) cc_final: 0.8548 (tmm) REVERT: A 359 ASP cc_start: 0.9196 (t0) cc_final: 0.8872 (t0) REVERT: A 482 TYR cc_start: 0.7611 (t80) cc_final: 0.6900 (t80) REVERT: A 485 MET cc_start: 0.9134 (tmm) cc_final: 0.8639 (tpt) outliers start: 22 outliers final: 20 residues processed: 112 average time/residue: 0.1145 time to fit residues: 17.7412 Evaluate side-chains 110 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 493 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 51 optimal weight: 50.0000 chunk 54 optimal weight: 0.0370 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4613 Z= 0.253 Angle : 0.807 16.001 6292 Z= 0.358 Chirality : 0.043 0.214 742 Planarity : 0.005 0.047 799 Dihedral : 4.508 33.632 686 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.36 % Allowed : 39.16 % 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: 0.57 (0.35), residues: 615 helix: 1.26 (0.27), residues: 364 sheet: 1.17 (0.85), residues: 49 loop : -1.46 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 109 HIS 0.003 0.001 HIS A 47 PHE 0.014 0.001 PHE A 347 TYR 0.008 0.001 TYR A 354 ARG 0.007 0.000 ARG A 273 *********************** 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 117 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.493 Fit side-chains REVERT: A 23 MET cc_start: 0.8919 (tpt) cc_final: 0.8473 (tpt) REVERT: A 76 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8047 (mm-30) REVERT: A 122 THR cc_start: 0.9463 (p) cc_final: 0.9226 (t) REVERT: A 234 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 359 ASP cc_start: 0.9243 (t0) cc_final: 0.8972 (t0) REVERT: A 482 TYR cc_start: 0.7634 (t80) cc_final: 0.6907 (t80) REVERT: A 485 MET cc_start: 0.9159 (tmm) cc_final: 0.8651 (tpt) outliers start: 23 outliers final: 22 residues processed: 110 average time/residue: 0.1123 time to fit residues: 17.1033 Evaluate side-chains 116 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 145 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 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 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 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 55 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 40.0000 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4613 Z= 0.204 Angle : 0.828 15.865 6292 Z= 0.358 Chirality : 0.043 0.212 742 Planarity : 0.005 0.048 799 Dihedral : 4.407 31.283 686 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.13 % Allowed : 39.16 % 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: 0.62 (0.35), residues: 615 helix: 1.31 (0.27), residues: 364 sheet: 1.10 (0.84), residues: 50 loop : -1.45 (0.44), residues: 201 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 0.013 0.001 PHE A 347 TYR 0.008 0.001 TYR A 354 ARG 0.006 0.000 ARG A 273 ********************** 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 116 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.536 Fit side-chains REVERT: A 23 MET cc_start: 0.8893 (tpt) cc_final: 0.8454 (tpt) REVERT: A 76 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8036 (mm-30) REVERT: A 142 MET cc_start: 0.9557 (tpp) cc_final: 0.9344 (tpp) REVERT: A 234 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7697 (tm-30) REVERT: A 359 ASP cc_start: 0.9237 (t0) cc_final: 0.8996 (t0) REVERT: A 482 TYR cc_start: 0.7670 (t80) cc_final: 0.6923 (t80) REVERT: A 485 MET cc_start: 0.9133 (tmm) cc_final: 0.8682 (tpt) outliers start: 22 outliers final: 22 residues processed: 110 average time/residue: 0.1029 time to fit residues: 16.1754 Evaluate side-chains 115 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.0020 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.127457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105809 restraints weight = 12312.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.108806 restraints weight = 6357.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.110828 restraints weight = 4123.243| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4613 Z= 0.202 Angle : 0.816 16.032 6292 Z= 0.353 Chirality : 0.042 0.212 742 Planarity : 0.005 0.048 799 Dihedral : 4.351 31.273 686 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: 1.30 (0.27), residues: 362 sheet: 1.07 (0.83), residues: 50 loop : -1.40 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.003 0.001 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.008 0.001 TYR A 354 ARG 0.005 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1260.05 seconds wall clock time: 23 minutes 56.40 seconds (1436.40 seconds total)