Starting phenix.real_space_refine on Fri May 9 17:14:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdv_61399/05_2025/9jdv_61399_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdv_61399/05_2025/9jdv_61399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jdv_61399/05_2025/9jdv_61399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdv_61399/05_2025/9jdv_61399.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdv_61399/05_2025/9jdv_61399_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdv_61399/05_2025/9jdv_61399_trim.cif" } resolution = 3.32 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= 0.003 sd= 0.060 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 28 5.16 5 C 2164 2.51 5 N 558 2.21 5 O 561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3311 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3298 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 26, 'TRANS': 408} Chain breaks: 4 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.80, per 1000 atoms: 0.85 Number of scatterers: 3311 At special positions: 0 Unit cell: (94.17, 51.1, 66.43, 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 28 16.00 O 561 8.00 N 558 7.00 C 2164 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 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 375.8 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 82.3% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 removed outlier: 4.267A pdb=" N GLU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 171 removed outlier: 4.069A pdb=" N GLY A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 191 Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.801A pdb=" N ALA A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 273 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.858A pdb=" N ARG A 342 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 343 " --> pdb=" O LEU A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.601A pdb=" N LEU A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Proline residue: A 391 - end of helix removed outlier: 4.255A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 removed outlier: 3.515A pdb=" N THR A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 460 removed outlier: 4.070A pdb=" N SER A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 465 No H-bonds generated for 'chain 'A' and resid 464 through 465' Processing helix chain 'A' and resid 467 through 467 No H-bonds generated for 'chain 'A' and resid 467 through 467' Processing helix chain 'A' and resid 468 through 487 Proline residue: A 484 - end of helix removed outlier: 3.548A pdb=" N ARG A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.573A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 Proline residue: A 505 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.723A pdb=" N ARG A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 684 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: 0.94 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 499 1.30 - 1.43: 900 1.43 - 1.55: 1954 1.55 - 1.68: 0 1.68 - 1.81: 44 Bond restraints: 3397 Sorted by residual: bond pdb=" CA SER A 242 " pdb=" C SER A 242 " ideal model delta sigma weight residual 1.523 1.438 0.086 1.34e-02 5.57e+03 4.08e+01 bond pdb=" C4 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 1.352 1.465 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" N PHE A 241 " pdb=" CA PHE A 241 " ideal model delta sigma weight residual 1.457 1.387 0.070 1.29e-02 6.01e+03 2.97e+01 bond pdb=" C4 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.352 1.456 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C2 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.376 1.478 -0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 3392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 4555 2.10 - 4.20: 55 4.20 - 6.30: 20 6.30 - 8.40: 6 8.40 - 10.50: 2 Bond angle restraints: 4638 Sorted by residual: angle pdb=" N ARG A 477 " pdb=" CA ARG A 477 " pdb=" C ARG A 477 " ideal model delta sigma weight residual 111.14 104.52 6.62 1.08e+00 8.57e-01 3.76e+01 angle pdb=" C ALA A 476 " pdb=" N ARG A 477 " pdb=" CA ARG A 477 " ideal model delta sigma weight residual 120.44 115.34 5.10 1.36e+00 5.41e-01 1.41e+01 angle pdb=" N PHE A 241 " pdb=" CA PHE A 241 " pdb=" C PHE A 241 " ideal model delta sigma weight residual 110.80 103.28 7.52 2.13e+00 2.20e-01 1.25e+01 angle pdb=" C2 URC A 601 " pdb=" N1 URC A 601 " pdb=" C6 URC A 601 " ideal model delta sigma weight residual 129.31 118.81 10.50 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C SER A 266 " pdb=" N VAL A 267 " pdb=" CA VAL A 267 " ideal model delta sigma weight residual 120.24 122.31 -2.07 6.30e-01 2.52e+00 1.08e+01 ... (remaining 4633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 1775 17.81 - 35.63: 156 35.63 - 53.44: 32 53.44 - 71.25: 5 71.25 - 89.07: 3 Dihedral angle restraints: 1971 sinusoidal: 735 harmonic: 1236 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 -140.99 54.99 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 127.97 -34.97 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" C SER A 242 " pdb=" N SER A 242 " pdb=" CA SER A 242 " pdb=" CB SER A 242 " ideal model delta harmonic sigma weight residual -122.60 -114.32 -8.28 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 1968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 347 0.027 - 0.054: 129 0.054 - 0.081: 43 0.081 - 0.108: 23 0.108 - 0.135: 2 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA VAL A 426 " pdb=" N VAL A 426 " pdb=" C VAL A 426 " pdb=" CB VAL A 426 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA PRO A 407 " pdb=" N PRO A 407 " pdb=" C PRO A 407 " pdb=" CB PRO A 407 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.94e-01 chirality pdb=" CA PRO A 268 " pdb=" N PRO A 268 " pdb=" C PRO A 268 " pdb=" CB PRO A 268 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 541 not shown) Planarity restraints: 572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 239 " 0.027 2.00e-02 2.50e+03 5.59e-02 3.13e+01 pdb=" C LEU A 239 " -0.097 2.00e-02 2.50e+03 pdb=" O LEU A 239 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY A 240 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 241 " -0.005 2.00e-02 2.50e+03 1.09e-02 2.08e+00 pdb=" CG PHE A 241 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 241 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 241 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 241 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 241 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 241 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 267 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 268 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " -0.016 5.00e-02 4.00e+02 ... (remaining 569 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 77 2.70 - 3.25: 3402 3.25 - 3.80: 5480 3.80 - 4.35: 6879 4.35 - 4.90: 11201 Nonbonded interactions: 27039 Sorted by model distance: nonbonded pdb=" O GLY A 240 " pdb=" C PHE A 241 " model vdw 2.150 3.270 nonbonded pdb=" CE2 PHE A 241 " pdb=" O13 URC A 601 " model vdw 2.168 2.672 nonbonded pdb=" O PHE A 241 " pdb=" C SER A 242 " model vdw 2.240 3.270 nonbonded pdb=" O SER A 242 " pdb=" N HIS A 245 " model vdw 2.262 3.120 nonbonded pdb=" O GLY A 240 " pdb=" N PHE A 243 " model vdw 2.272 3.120 ... (remaining 27034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.770 Find NCS groups from input model: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 : 0.013 0.687 3400 Z= 1.237 Angle : 0.706 10.503 4642 Z= 0.385 Chirality : 0.035 0.135 544 Planarity : 0.004 0.056 572 Dihedral : 13.991 89.067 1167 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.03 % Allowed : 9.28 % Favored : 88.70 % 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: -0.41 (0.40), residues: 425 helix: 0.02 (0.29), residues: 289 sheet: -2.23 (1.36), residues: 10 loop : -0.44 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 30 HIS 0.001 0.000 HIS A 428 PHE 0.023 0.001 PHE A 241 TYR 0.003 0.001 TYR A 152 ARG 0.001 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.14107 ( 237) hydrogen bonds : angle 5.52250 ( 684) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.89919 ( 4) covalent geometry : bond 0.00646 ( 3397) covalent geometry : angle 0.70619 ( 4638) Misc. bond : bond 0.68682 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.337 Fit side-chains REVERT: A 29 MET cc_start: 0.7581 (ttp) cc_final: 0.7280 (ttp) REVERT: A 96 TRP cc_start: 0.4546 (m100) cc_final: 0.4252 (m-10) REVERT: A 343 MET cc_start: 0.2977 (tpt) cc_final: 0.1234 (tpp) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.1582 time to fit residues: 20.2440 Evaluate side-chains 74 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 424 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 39 ASN A 382 GLN A 492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.226216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.192196 restraints weight = 4352.070| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.26 r_work: 0.4234 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3400 Z= 0.202 Angle : 0.696 7.486 4642 Z= 0.334 Chirality : 0.045 0.146 544 Planarity : 0.005 0.027 572 Dihedral : 5.434 55.606 464 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.64 % Allowed : 19.71 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.43), residues: 425 helix: 0.94 (0.31), residues: 297 sheet: -1.89 (1.53), residues: 10 loop : 0.63 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.007 0.001 HIS A 47 PHE 0.022 0.003 PHE A 40 TYR 0.022 0.002 TYR A 122 ARG 0.004 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 237) hydrogen bonds : angle 4.43608 ( 684) SS BOND : bond 0.00834 ( 2) SS BOND : angle 1.16059 ( 4) covalent geometry : bond 0.00453 ( 3397) covalent geometry : angle 0.69502 ( 4638) Misc. bond : bond 0.00623 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.4820 (m100) cc_final: 0.4197 (m-10) REVERT: A 181 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7257 (tt) REVERT: A 234 MET cc_start: 0.6536 (tpp) cc_final: 0.6253 (tpp) REVERT: A 343 MET cc_start: 0.2930 (tpt) cc_final: 0.1487 (tpp) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 0.0991 time to fit residues: 11.4507 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.225803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.192166 restraints weight = 4281.711| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 3.30 r_work: 0.4243 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3400 Z= 0.130 Angle : 0.614 7.460 4642 Z= 0.291 Chirality : 0.040 0.131 544 Planarity : 0.004 0.030 572 Dihedral : 5.287 53.989 463 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.19 % Allowed : 24.06 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.43), residues: 425 helix: 1.47 (0.31), residues: 296 sheet: -2.17 (1.67), residues: 10 loop : 1.09 (0.67), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 495 HIS 0.002 0.001 HIS A 492 PHE 0.019 0.002 PHE A 358 TYR 0.007 0.001 TYR A 122 ARG 0.003 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 237) hydrogen bonds : angle 4.16606 ( 684) SS BOND : bond 0.00396 ( 2) SS BOND : angle 2.03002 ( 4) covalent geometry : bond 0.00289 ( 3397) covalent geometry : angle 0.61113 ( 4638) Misc. bond : bond 0.00525 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.4664 (m100) cc_final: 0.4077 (m-10) REVERT: A 149 GLN cc_start: 0.7909 (mt0) cc_final: 0.7661 (mp10) REVERT: A 181 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7136 (tt) REVERT: A 343 MET cc_start: 0.2853 (tpt) cc_final: 0.1424 (tpp) outliers start: 11 outliers final: 8 residues processed: 78 average time/residue: 0.0999 time to fit residues: 10.4301 Evaluate side-chains 77 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.225469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.190667 restraints weight = 4418.608| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 3.42 r_work: 0.4219 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3400 Z= 0.129 Angle : 0.598 7.366 4642 Z= 0.284 Chirality : 0.040 0.129 544 Planarity : 0.004 0.031 572 Dihedral : 4.716 40.637 463 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.77 % Allowed : 24.35 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.44), residues: 425 helix: 1.66 (0.31), residues: 297 sheet: -2.18 (1.89), residues: 10 loop : 0.91 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 50 HIS 0.002 0.001 HIS A 47 PHE 0.017 0.002 PHE A 358 TYR 0.014 0.001 TYR A 152 ARG 0.003 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 237) hydrogen bonds : angle 4.10002 ( 684) SS BOND : bond 0.00156 ( 2) SS BOND : angle 1.32885 ( 4) covalent geometry : bond 0.00288 ( 3397) covalent geometry : angle 0.59711 ( 4638) Misc. bond : bond 0.00358 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.4519 (m100) cc_final: 0.3892 (m-10) REVERT: A 149 GLN cc_start: 0.7979 (mt0) cc_final: 0.7752 (mp10) REVERT: A 181 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7113 (tt) REVERT: A 215 MET cc_start: 0.7591 (tpp) cc_final: 0.7311 (tpp) REVERT: A 343 MET cc_start: 0.2853 (tpt) cc_final: 0.1457 (tpp) REVERT: A 358 PHE cc_start: 0.8216 (t80) cc_final: 0.7985 (t80) REVERT: A 372 GLN cc_start: 0.8389 (tp-100) cc_final: 0.7991 (tp-100) REVERT: A 421 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8000 (mp) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.1050 time to fit residues: 10.6589 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.223757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.190559 restraints weight = 4359.078| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.32 r_work: 0.4224 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.125 Angle : 0.574 7.414 4642 Z= 0.276 Chirality : 0.039 0.123 544 Planarity : 0.004 0.031 572 Dihedral : 4.425 44.006 462 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.77 % Allowed : 25.22 % Favored : 71.01 % 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: 2.16 (0.44), residues: 425 helix: 1.79 (0.31), residues: 296 sheet: -2.21 (1.86), residues: 10 loop : 1.08 (0.69), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 50 HIS 0.002 0.001 HIS A 492 PHE 0.015 0.002 PHE A 358 TYR 0.014 0.001 TYR A 152 ARG 0.001 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 237) hydrogen bonds : angle 4.04645 ( 684) SS BOND : bond 0.00210 ( 2) SS BOND : angle 0.97761 ( 4) covalent geometry : bond 0.00278 ( 3397) covalent geometry : angle 0.57323 ( 4638) Misc. bond : bond 0.00289 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7734 (ttm) cc_final: 0.7398 (ttp) REVERT: A 96 TRP cc_start: 0.4538 (m100) cc_final: 0.3889 (m-10) REVERT: A 149 GLN cc_start: 0.7968 (mt0) cc_final: 0.7726 (mp10) REVERT: A 181 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7050 (tt) REVERT: A 215 MET cc_start: 0.7680 (tpp) cc_final: 0.7350 (tpp) REVERT: A 343 MET cc_start: 0.2840 (tpt) cc_final: 0.1441 (tpp) REVERT: A 372 GLN cc_start: 0.8343 (tp-100) cc_final: 0.7912 (tp-100) REVERT: A 421 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7929 (mp) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 0.1031 time to fit residues: 11.4138 Evaluate side-chains 75 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4648 r_free = 0.4648 target = 0.222493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.187290 restraints weight = 4446.099| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 3.46 r_work: 0.4188 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3400 Z= 0.134 Angle : 0.593 8.204 4642 Z= 0.286 Chirality : 0.041 0.120 544 Planarity : 0.004 0.035 572 Dihedral : 4.385 47.050 461 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.51 % Allowed : 25.80 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.44), residues: 425 helix: 1.76 (0.31), residues: 296 sheet: -2.25 (1.78), residues: 10 loop : 1.06 (0.68), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 50 HIS 0.003 0.001 HIS A 245 PHE 0.015 0.002 PHE A 241 TYR 0.012 0.001 TYR A 122 ARG 0.002 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 237) hydrogen bonds : angle 4.11053 ( 684) SS BOND : bond 0.00285 ( 2) SS BOND : angle 1.09382 ( 4) covalent geometry : bond 0.00304 ( 3397) covalent geometry : angle 0.59237 ( 4638) Misc. bond : bond 0.00260 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7776 (ttm) cc_final: 0.7469 (ttp) REVERT: A 77 ILE cc_start: 0.5585 (OUTLIER) cc_final: 0.5315 (mm) REVERT: A 96 TRP cc_start: 0.4534 (m100) cc_final: 0.3884 (m-10) REVERT: A 149 GLN cc_start: 0.7963 (mt0) cc_final: 0.7702 (mp10) REVERT: A 181 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7070 (tt) REVERT: A 215 MET cc_start: 0.7835 (tpp) cc_final: 0.7514 (tpp) REVERT: A 343 MET cc_start: 0.2834 (tpt) cc_final: 0.1417 (tpp) REVERT: A 372 GLN cc_start: 0.8445 (tp-100) cc_final: 0.8006 (tp-100) REVERT: A 421 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7979 (mp) outliers start: 19 outliers final: 12 residues processed: 82 average time/residue: 0.0975 time to fit residues: 10.7510 Evaluate side-chains 84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.0770 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4658 r_free = 0.4658 target = 0.221526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.187621 restraints weight = 4398.046| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 3.41 r_work: 0.4195 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.126 Angle : 0.591 7.984 4642 Z= 0.284 Chirality : 0.040 0.120 544 Planarity : 0.004 0.035 572 Dihedral : 4.408 49.749 461 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.93 % Allowed : 26.96 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.44), residues: 425 helix: 1.79 (0.31), residues: 295 sheet: -2.24 (1.82), residues: 10 loop : 1.07 (0.68), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 50 HIS 0.002 0.001 HIS A 86 PHE 0.014 0.002 PHE A 241 TYR 0.012 0.001 TYR A 152 ARG 0.001 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 237) hydrogen bonds : angle 4.06318 ( 684) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.93374 ( 4) covalent geometry : bond 0.00279 ( 3397) covalent geometry : angle 0.59063 ( 4638) Misc. bond : bond 0.00241 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ILE cc_start: 0.5653 (OUTLIER) cc_final: 0.5391 (mm) REVERT: A 96 TRP cc_start: 0.4572 (m100) cc_final: 0.3905 (m-10) REVERT: A 149 GLN cc_start: 0.7988 (mt0) cc_final: 0.7702 (mp10) REVERT: A 181 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7061 (tt) REVERT: A 215 MET cc_start: 0.7842 (tpp) cc_final: 0.7478 (tpp) REVERT: A 343 MET cc_start: 0.2880 (tpt) cc_final: 0.1469 (tpp) REVERT: A 372 GLN cc_start: 0.8440 (tp-100) cc_final: 0.7996 (tp-100) outliers start: 17 outliers final: 12 residues processed: 80 average time/residue: 0.0990 time to fit residues: 10.5870 Evaluate side-chains 83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4659 r_free = 0.4659 target = 0.221249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.187086 restraints weight = 4391.560| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 3.42 r_work: 0.4187 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3400 Z= 0.127 Angle : 0.604 8.062 4642 Z= 0.288 Chirality : 0.041 0.153 544 Planarity : 0.004 0.036 572 Dihedral : 4.440 50.936 461 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.22 % Allowed : 27.83 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.44), residues: 425 helix: 1.79 (0.31), residues: 296 sheet: -2.18 (1.85), residues: 10 loop : 1.13 (0.68), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 50 HIS 0.002 0.001 HIS A 245 PHE 0.017 0.002 PHE A 360 TYR 0.012 0.001 TYR A 152 ARG 0.001 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 237) hydrogen bonds : angle 4.07193 ( 684) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.93636 ( 4) covalent geometry : bond 0.00282 ( 3397) covalent geometry : angle 0.60352 ( 4638) Misc. bond : bond 0.00222 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7735 (ttm) cc_final: 0.7469 (ttp) REVERT: A 77 ILE cc_start: 0.5714 (OUTLIER) cc_final: 0.5452 (mm) REVERT: A 96 TRP cc_start: 0.4503 (m100) cc_final: 0.3812 (m-10) REVERT: A 149 GLN cc_start: 0.8010 (mt0) cc_final: 0.7737 (mp10) REVERT: A 181 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7018 (tt) REVERT: A 215 MET cc_start: 0.7880 (tpp) cc_final: 0.7514 (tpp) REVERT: A 267 VAL cc_start: 0.8397 (t) cc_final: 0.8151 (m) REVERT: A 343 MET cc_start: 0.2875 (tpt) cc_final: 0.1485 (tpp) REVERT: A 372 GLN cc_start: 0.8438 (tp-100) cc_final: 0.7990 (tp-100) outliers start: 18 outliers final: 13 residues processed: 83 average time/residue: 0.1110 time to fit residues: 12.0201 Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.220954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.185801 restraints weight = 4405.311| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 3.38 r_work: 0.4175 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3400 Z= 0.134 Angle : 0.610 8.050 4642 Z= 0.293 Chirality : 0.041 0.117 544 Planarity : 0.004 0.036 572 Dihedral : 4.476 52.020 461 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.64 % Allowed : 28.41 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.44), residues: 425 helix: 1.77 (0.31), residues: 296 sheet: -2.26 (1.84), residues: 10 loop : 1.08 (0.68), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.002 0.001 HIS A 86 PHE 0.015 0.002 PHE A 449 TYR 0.012 0.001 TYR A 152 ARG 0.002 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 237) hydrogen bonds : angle 4.10208 ( 684) SS BOND : bond 0.00326 ( 2) SS BOND : angle 1.00213 ( 4) covalent geometry : bond 0.00303 ( 3397) covalent geometry : angle 0.60974 ( 4638) Misc. bond : bond 0.00217 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7774 (ttm) cc_final: 0.7509 (ttp) REVERT: A 77 ILE cc_start: 0.5772 (OUTLIER) cc_final: 0.5481 (mm) REVERT: A 96 TRP cc_start: 0.4534 (m100) cc_final: 0.3813 (m-10) REVERT: A 149 GLN cc_start: 0.8016 (mt0) cc_final: 0.7744 (mp10) REVERT: A 181 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7065 (tt) REVERT: A 215 MET cc_start: 0.7881 (tpp) cc_final: 0.7511 (tpp) REVERT: A 267 VAL cc_start: 0.8456 (t) cc_final: 0.8200 (m) REVERT: A 343 MET cc_start: 0.2861 (tpt) cc_final: 0.1445 (tpp) REVERT: A 372 GLN cc_start: 0.8475 (tp-100) cc_final: 0.8033 (tp-100) outliers start: 16 outliers final: 13 residues processed: 81 average time/residue: 0.1122 time to fit residues: 11.7728 Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4633 r_free = 0.4633 target = 0.220942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.185507 restraints weight = 4387.342| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 3.44 r_work: 0.4169 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3400 Z= 0.130 Angle : 0.610 8.208 4642 Z= 0.291 Chirality : 0.041 0.118 544 Planarity : 0.004 0.034 572 Dihedral : 4.520 53.904 461 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.35 % Allowed : 28.70 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.44), residues: 425 helix: 1.76 (0.31), residues: 296 sheet: -2.26 (1.84), residues: 10 loop : 1.05 (0.68), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 50 HIS 0.002 0.000 HIS A 86 PHE 0.015 0.002 PHE A 241 TYR 0.012 0.001 TYR A 152 ARG 0.001 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 237) hydrogen bonds : angle 4.09365 ( 684) SS BOND : bond 0.00234 ( 2) SS BOND : angle 1.01538 ( 4) covalent geometry : bond 0.00294 ( 3397) covalent geometry : angle 0.60975 ( 4638) Misc. bond : bond 0.00204 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.5312 (tpp) cc_final: 0.4855 (tpp) REVERT: A 29 MET cc_start: 0.7777 (ttm) cc_final: 0.7528 (ttp) REVERT: A 77 ILE cc_start: 0.5816 (OUTLIER) cc_final: 0.5533 (mm) REVERT: A 96 TRP cc_start: 0.4589 (m100) cc_final: 0.3846 (m-10) REVERT: A 149 GLN cc_start: 0.8032 (mt0) cc_final: 0.7745 (mp10) REVERT: A 181 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7078 (tt) REVERT: A 215 MET cc_start: 0.7932 (tpp) cc_final: 0.7535 (tpp) REVERT: A 343 MET cc_start: 0.2791 (tpt) cc_final: 0.1425 (tpp) REVERT: A 372 GLN cc_start: 0.8486 (tp-100) cc_final: 0.8047 (tp-100) outliers start: 15 outliers final: 12 residues processed: 80 average time/residue: 0.1110 time to fit residues: 11.5113 Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4625 r_free = 0.4625 target = 0.220669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.185240 restraints weight = 4443.090| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 3.40 r_work: 0.4168 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.132 Angle : 0.613 8.206 4642 Z= 0.295 Chirality : 0.042 0.122 544 Planarity : 0.004 0.034 572 Dihedral : 4.527 54.422 461 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.35 % Allowed : 29.28 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.44), residues: 425 helix: 1.73 (0.31), residues: 299 sheet: -2.27 (1.89), residues: 10 loop : 1.21 (0.70), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.002 0.001 HIS A 86 PHE 0.014 0.002 PHE A 241 TYR 0.013 0.001 TYR A 152 ARG 0.001 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 237) hydrogen bonds : angle 4.08855 ( 684) SS BOND : bond 0.00264 ( 2) SS BOND : angle 1.00971 ( 4) covalent geometry : bond 0.00299 ( 3397) covalent geometry : angle 0.61291 ( 4638) Misc. bond : bond 0.00197 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1723.37 seconds wall clock time: 30 minutes 36.65 seconds (1836.65 seconds total)