Starting phenix.real_space_refine on Tue Feb 11 07:03:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bvt_16271/02_2025/8bvt_16271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bvt_16271/02_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_16271/02_2025/8bvt_16271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bvt_16271/02_2025/8bvt_16271.map" model { file = "/net/cci-nas-00/data/ceres_data/8bvt_16271/02_2025/8bvt_16271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bvt_16271/02_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-5592/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: 3.60, per 1000 atoms: 0.80 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: 1.17 Conformation dependent library (CDL) restraints added in 560.5 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: 0.39 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: 1.00 Time building geometry restraints manager: 1.35 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: 1.030 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.910 Find NCS groups from input model: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.920 ------------------------------------------------------------------------------- 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 : 0.450 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: 0.1031 time to fit residues: 13.5976 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 : 0.485 ------------------------------------------------------------------------------- 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 = 0.126954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.106136 restraints weight = 12212.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109135 restraints weight = 6215.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.111180 restraints weight = 3963.450| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.514 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8693 (tpt) cc_final: 0.8255 (tpt) REVERT: A 122 THR cc_start: 0.9379 (p) cc_final: 0.9072 (t) REVERT: A 142 MET cc_start: 0.9572 (tpp) cc_final: 0.9247 (tpp) REVERT: A 168 ASN cc_start: 0.7952 (m-40) cc_final: 0.7538 (m110) REVERT: A 482 TYR cc_start: 0.7562 (t80) cc_final: 0.7152 (t80) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.1065 time to fit residues: 16.3715 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 : 0.587 ------------------------------------------------------------------------------- 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: 3.9990 chunk 50 optimal weight: 40.0000 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.123118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.101470 restraints weight = 12519.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.104311 restraints weight = 6449.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.106226 restraints weight = 4198.951| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4613 Z= 0.336 Angle : 0.741 10.162 6292 Z= 0.356 Chirality : 0.043 0.167 742 Planarity : 0.005 0.045 799 Dihedral : 5.108 31.022 686 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.53 % Allowed : 37.06 % Favored : 56.41 % 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 (0.34), residues: 615 helix: 1.27 (0.27), residues: 359 sheet: 0.70 (0.81), residues: 45 loop : -1.29 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.004 0.001 HIS A 337 PHE 0.016 0.002 PHE A 262 TYR 0.014 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 125 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.634 Fit side-chains REVERT: A 76 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 122 THR cc_start: 0.9452 (p) cc_final: 0.9167 (t) REVERT: A 482 TYR cc_start: 0.7584 (t80) cc_final: 0.7034 (t80) REVERT: A 485 MET cc_start: 0.9217 (tmm) cc_final: 0.8774 (tpt) outliers start: 28 outliers final: 23 residues processed: 115 average time/residue: 0.1152 time to fit residues: 19.2149 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 : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP 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 177 THR Chi-restraints excluded: chain A residue 199 LEU 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 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 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 475 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: 7.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 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** ** 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 = 0.3919 r_free = 0.3919 target = 0.125031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103292 restraints weight = 12470.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.106277 restraints weight = 6323.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108330 restraints weight = 4062.471| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1181 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= 0.209 Angle : 0.696 10.806 6292 Z= 0.323 Chirality : 0.042 0.150 742 Planarity : 0.005 0.047 799 Dihedral : 4.882 30.565 686 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: 0.72 (0.35), residues: 615 helix: 1.42 (0.27), residues: 359 sheet: 0.72 (0.81), residues: 50 loop : -1.28 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 274 HIS 0.002 0.000 HIS A 47 PHE 0.014 0.001 PHE A 347 TYR 0.008 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 123 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.506 Fit side-chains REVERT: A 23 MET cc_start: 0.8765 (tpt) cc_final: 0.8413 (tpt) REVERT: A 76 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7927 (mm-30) REVERT: A 122 THR cc_start: 0.9442 (p) cc_final: 0.9147 (t) REVERT: A 482 TYR cc_start: 0.7573 (t80) cc_final: 0.6942 (t80) outliers start: 27 outliers final: 20 residues processed: 114 average time/residue: 0.1106 time to fit residues: 17.4714 Evaluate side-chains 115 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 165 LEU 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 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 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: 0.9980 chunk 36 optimal weight: 0.0270 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.0020 overall best weight: 0.6046 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.126463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.104895 restraints weight = 12534.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.107962 restraints weight = 6316.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.109886 restraints weight = 4031.057| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1310 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= 0.188 Angle : 0.728 15.143 6292 Z= 0.327 Chirality : 0.041 0.148 742 Planarity : 0.004 0.050 799 Dihedral : 4.760 30.587 686 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.83 % Allowed : 39.39 % 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: 0.73 (0.35), residues: 615 helix: 1.45 (0.27), residues: 358 sheet: 0.68 (0.81), residues: 50 loop : -1.29 (0.45), residues: 207 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 0.010 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 124 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.558 Fit side-chains REVERT: A 23 MET cc_start: 0.8762 (tpt) cc_final: 0.8402 (tpt) REVERT: A 76 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7908 (mm-30) REVERT: A 122 THR cc_start: 0.9439 (p) cc_final: 0.9140 (t) REVERT: A 394 ARG cc_start: 0.7587 (mtm180) cc_final: 0.6754 (mtm180) REVERT: A 482 TYR cc_start: 0.7575 (t80) cc_final: 0.6895 (t80) REVERT: A 485 MET cc_start: 0.9173 (tmm) cc_final: 0.8698 (tpt) outliers start: 25 outliers final: 20 residues processed: 116 average time/residue: 0.1133 time to fit residues: 18.4754 Evaluate side-chains 115 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 51 optimal weight: 50.0000 chunk 60 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.124357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.102472 restraints weight = 12579.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.105427 restraints weight = 6409.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.107423 restraints weight = 4146.775| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4613 Z= 0.255 Angle : 0.755 14.963 6292 Z= 0.344 Chirality : 0.042 0.173 742 Planarity : 0.005 0.049 799 Dihedral : 4.790 33.192 686 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.76 % Allowed : 38.69 % 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: 0.69 (0.35), residues: 615 helix: 1.39 (0.27), residues: 359 sheet: 0.95 (0.81), residues: 49 loop : -1.32 (0.44), residues: 207 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 0.010 0.001 TYR A 354 ARG 0.002 0.000 ARG A 273 *********************** 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 126 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.496 Fit side-chains REVERT: A 23 MET cc_start: 0.8831 (tpt) cc_final: 0.8490 (tpt) REVERT: A 76 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7948 (mm-30) REVERT: A 79 LEU cc_start: 0.8583 (tp) cc_final: 0.8365 (tp) REVERT: A 122 THR cc_start: 0.9462 (p) cc_final: 0.9171 (t) REVERT: A 359 ASP cc_start: 0.9117 (t0) cc_final: 0.8824 (t0) REVERT: A 482 TYR cc_start: 0.7588 (t80) cc_final: 0.6933 (t80) outliers start: 29 outliers final: 26 residues processed: 116 average time/residue: 0.1060 time to fit residues: 17.4860 Evaluate side-chains 123 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 165 LEU 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 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 471 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: 0.1980 chunk 10 optimal weight: 0.0170 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.126622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104799 restraints weight = 12350.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107805 restraints weight = 6316.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.109864 restraints weight = 4086.980| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1520 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= 0.189 Angle : 0.772 16.092 6292 Z= 0.340 Chirality : 0.041 0.165 742 Planarity : 0.004 0.049 799 Dihedral : 4.662 32.541 686 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 6.06 % Allowed : 40.09 % Favored : 53.85 % 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: 1.42 (0.27), residues: 358 sheet: 1.08 (0.83), residues: 49 loop : -1.32 (0.44), residues: 208 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 0.009 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 121 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.528 Fit side-chains REVERT: A 76 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 359 ASP cc_start: 0.9144 (t0) cc_final: 0.8873 (t0) REVERT: A 464 MET cc_start: 0.7955 (ttt) cc_final: 0.7551 (ttp) REVERT: A 482 TYR cc_start: 0.7595 (t80) cc_final: 0.6918 (t80) REVERT: A 485 MET cc_start: 0.9164 (tmm) cc_final: 0.8639 (tpt) outliers start: 26 outliers final: 21 residues processed: 113 average time/residue: 0.1127 time to fit residues: 17.7945 Evaluate side-chains 113 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 493 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 40.0000 chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.127126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.105544 restraints weight = 12415.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.108508 restraints weight = 6345.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.110607 restraints weight = 4121.722| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4613 Z= 0.197 Angle : 0.802 15.766 6292 Z= 0.350 Chirality : 0.042 0.180 742 Planarity : 0.005 0.048 799 Dihedral : 4.584 33.062 686 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 6.29 % Allowed : 39.16 % 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: 1.41 (0.27), residues: 357 sheet: 1.13 (0.85), residues: 49 loop : -1.32 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.002 0.000 HIS A 47 PHE 0.015 0.001 PHE A 347 TYR 0.020 0.001 TYR A 354 ARG 0.006 0.000 ARG A 273 *********************** 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 122 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.472 Fit side-chains REVERT: A 76 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7962 (mm-30) REVERT: A 162 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7700 (ttt-90) REVERT: A 359 ASP cc_start: 0.9174 (t0) cc_final: 0.8908 (t0) REVERT: A 482 TYR cc_start: 0.7612 (t80) cc_final: 0.6904 (t80) REVERT: A 485 MET cc_start: 0.9157 (tmm) cc_final: 0.8667 (tpt) outliers start: 27 outliers final: 20 residues processed: 113 average time/residue: 0.1086 time to fit residues: 17.1177 Evaluate side-chains 112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 14 optimal weight: 0.0060 chunk 60 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 30.0000 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.127406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.105959 restraints weight = 12389.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.108935 restraints weight = 6380.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.111005 restraints weight = 4126.773| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4613 Z= 0.202 Angle : 0.819 15.496 6292 Z= 0.356 Chirality : 0.043 0.201 742 Planarity : 0.005 0.047 799 Dihedral : 4.566 33.493 686 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.13 % Allowed : 39.63 % 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: 0.70 (0.35), residues: 615 helix: 1.39 (0.27), residues: 357 sheet: 1.03 (0.83), residues: 50 loop : -1.31 (0.44), residues: 208 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 0.005 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 118 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.480 Fit side-chains REVERT: A 76 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8086 (mm-30) REVERT: A 162 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7695 (ttt-90) REVERT: A 359 ASP cc_start: 0.9197 (t0) cc_final: 0.8787 (t0) REVERT: A 464 MET cc_start: 0.8007 (ttt) cc_final: 0.7651 (ttp) REVERT: A 482 TYR cc_start: 0.7631 (t80) cc_final: 0.6919 (t80) REVERT: A 485 MET cc_start: 0.9137 (tmm) cc_final: 0.8678 (tpt) outliers start: 22 outliers final: 20 residues processed: 112 average time/residue: 0.1066 time to fit residues: 16.8074 Evaluate side-chains 111 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 56 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 40.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.123888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.102125 restraints weight = 12522.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.104971 restraints weight = 6536.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.107009 restraints weight = 4298.207| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1820 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= 0.262 Angle : 0.847 16.683 6292 Z= 0.373 Chirality : 0.044 0.181 742 Planarity : 0.005 0.046 799 Dihedral : 4.668 34.148 686 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % 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: 0.58 (0.34), residues: 615 helix: 1.25 (0.27), residues: 360 sheet: 1.09 (0.84), residues: 49 loop : -1.35 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 266 HIS 0.003 0.001 HIS A 47 PHE 0.015 0.001 PHE A 347 TYR 0.009 0.001 TYR A 169 ARG 0.005 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 118 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.481 Fit side-chains REVERT: A 76 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8134 (mm-30) REVERT: A 122 THR cc_start: 0.9469 (p) cc_final: 0.9171 (t) REVERT: A 359 ASP cc_start: 0.9162 (t0) cc_final: 0.8864 (t0) REVERT: A 482 TYR cc_start: 0.7682 (t80) cc_final: 0.6976 (t80) REVERT: A 485 MET cc_start: 0.9167 (tmm) cc_final: 0.8761 (tpt) outliers start: 24 outliers final: 23 residues processed: 112 average time/residue: 0.1003 time to fit residues: 16.0505 Evaluate side-chains 116 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 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 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 30.0000 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.125317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103838 restraints weight = 12511.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.106810 restraints weight = 6531.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.108774 restraints weight = 4281.735| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1898 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= 0.214 Angle : 0.852 16.532 6292 Z= 0.367 Chirality : 0.044 0.190 742 Planarity : 0.005 0.047 799 Dihedral : 4.520 31.124 686 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 0.63 (0.35), residues: 615 helix: 1.31 (0.27), residues: 360 sheet: 1.01 (0.82), residues: 50 loop : -1.34 (0.44), residues: 205 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 0.007 0.001 TYR A 353 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: 1563.97 seconds wall clock time: 28 minutes 50.71 seconds (1730.71 seconds total)