Starting phenix.real_space_refine on Wed Sep 17 03:35:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdv_61399/09_2025/9jdv_61399_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdv_61399/09_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_61399/09_2025/9jdv_61399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdv_61399/09_2025/9jdv_61399.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdv_61399/09_2025/9jdv_61399_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdv_61399/09_2025/9jdv_61399_trim.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.96, per 1000 atoms: 0.29 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: 0.24 Conformation dependent library (CDL) restraints added in 79.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.12 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: 0.42 Time building geometry restraints manager: 0.30 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: 1.150 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.150 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.560 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 90 TYR 0.003 0.001 TYR A 152 PHE 0.023 0.001 PHE A 241 TRP 0.004 0.000 TRP A 30 HIS 0.001 0.000 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00646 ( 3397) covalent geometry : angle 0.70619 ( 4638) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.89919 ( 4) hydrogen bonds : bond 0.14107 ( 237) hydrogen bonds : angle 5.52250 ( 684) 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 : 0.124 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: 0.0670 time to fit residues: 8.6302 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 : 0.119 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 492 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.236961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.203445 restraints weight = 4326.568| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 3.34 r_work: 0.4333 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2427 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= 0.139 Angle : 0.625 7.802 4642 Z= 0.293 Chirality : 0.041 0.147 544 Planarity : 0.004 0.032 572 Dihedral : 4.952 51.959 464 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.77 % Allowed : 18.26 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.42), residues: 425 helix: 1.17 (0.31), residues: 292 sheet: -1.99 (1.45), residues: 10 loop : 0.36 (0.64), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.014 0.001 TYR A 152 PHE 0.023 0.002 PHE A 241 TRP 0.013 0.001 TRP A 50 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3397) covalent geometry : angle 0.62511 ( 4638) SS BOND : bond 0.00422 ( 2) SS BOND : angle 0.60259 ( 4) hydrogen bonds : bond 0.03514 ( 237) hydrogen bonds : angle 4.18415 ( 684) Misc. bond : bond 0.00798 ( 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 91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7700 (ttp) cc_final: 0.7291 (ttp) REVERT: A 96 TRP cc_start: 0.4683 (m100) cc_final: 0.4130 (m-10) REVERT: A 181 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7151 (tt) REVERT: A 343 MET cc_start: 0.2861 (tpt) cc_final: 0.2181 (tpt) outliers start: 13 outliers final: 7 residues processed: 86 average time/residue: 0.0376 time to fit residues: 4.4066 Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 486 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 38 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 382 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.223098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.186748 restraints weight = 4471.375| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 3.58 r_work: 0.4102 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3166 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= 0.141 Angle : 0.632 6.811 4642 Z= 0.299 Chirality : 0.041 0.121 544 Planarity : 0.004 0.031 572 Dihedral : 5.104 53.791 463 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.22 % Allowed : 18.84 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.43), residues: 425 helix: 1.63 (0.31), residues: 293 sheet: -1.66 (1.80), residues: 10 loop : 0.77 (0.66), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.012 0.001 TYR A 122 PHE 0.017 0.002 PHE A 241 TRP 0.024 0.001 TRP A 495 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3397) covalent geometry : angle 0.62962 ( 4638) SS BOND : bond 0.00724 ( 2) SS BOND : angle 1.78758 ( 4) hydrogen bonds : bond 0.03528 ( 237) hydrogen bonds : angle 3.99951 ( 684) Misc. bond : bond 0.00488 ( 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 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7490 (ttp) cc_final: 0.7135 (ttp) REVERT: A 96 TRP cc_start: 0.4645 (m100) cc_final: 0.4075 (m-10) REVERT: A 149 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: A 181 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7075 (tt) REVERT: A 215 MET cc_start: 0.7377 (tpp) cc_final: 0.7153 (tpp) REVERT: A 343 MET cc_start: 0.2799 (tpt) cc_final: 0.2187 (tpt) REVERT: A 372 GLN cc_start: 0.8232 (tp-100) cc_final: 0.7907 (tp-100) REVERT: A 413 LEU cc_start: 0.7440 (mt) cc_final: 0.7226 (tp) outliers start: 18 outliers final: 12 residues processed: 77 average time/residue: 0.0407 time to fit residues: 4.2628 Evaluate side-chains 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 149 GLN 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 424 THR Chi-restraints excluded: chain A residue 450 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4566 r_free = 0.4566 target = 0.219547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.184292 restraints weight = 4271.226| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 3.43 r_work: 0.4077 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3653 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= 0.134 Angle : 0.593 7.432 4642 Z= 0.284 Chirality : 0.040 0.134 544 Planarity : 0.004 0.031 572 Dihedral : 5.312 57.985 463 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.77 % Allowed : 23.19 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.43), residues: 425 helix: 1.79 (0.31), residues: 296 sheet: None (None), residues: 0 loop : 0.73 (0.63), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 48 TYR 0.013 0.002 TYR A 122 PHE 0.014 0.002 PHE A 241 TRP 0.011 0.001 TRP A 495 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3397) covalent geometry : angle 0.59167 ( 4638) SS BOND : bond 0.00437 ( 2) SS BOND : angle 1.68608 ( 4) hydrogen bonds : bond 0.03511 ( 237) hydrogen bonds : angle 3.97549 ( 684) Misc. bond : bond 0.00330 ( 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 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7602 (ttp) cc_final: 0.7392 (ttm) REVERT: A 96 TRP cc_start: 0.4506 (m100) cc_final: 0.3874 (m-10) REVERT: A 149 GLN cc_start: 0.8174 (mt0) cc_final: 0.7872 (mp10) REVERT: A 181 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7051 (tt) REVERT: A 215 MET cc_start: 0.7616 (tpp) cc_final: 0.7262 (tpp) REVERT: A 343 MET cc_start: 0.2768 (tpt) cc_final: 0.1417 (tpp) REVERT: A 413 LEU cc_start: 0.7544 (mt) cc_final: 0.7276 (tp) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.0413 time to fit residues: 4.0717 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.216532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.180758 restraints weight = 4308.829| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.46 r_work: 0.4043 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4007 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= 0.140 Angle : 0.592 7.050 4642 Z= 0.286 Chirality : 0.040 0.115 544 Planarity : 0.004 0.030 572 Dihedral : 5.038 50.873 463 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.22 % Allowed : 23.19 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.43), residues: 425 helix: 1.87 (0.31), residues: 295 sheet: None (None), residues: 0 loop : 0.92 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.012 0.001 TYR A 122 PHE 0.015 0.002 PHE A 241 TRP 0.019 0.001 TRP A 50 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3397) covalent geometry : angle 0.59056 ( 4638) SS BOND : bond 0.00518 ( 2) SS BOND : angle 1.50485 ( 4) hydrogen bonds : bond 0.03506 ( 237) hydrogen bonds : angle 4.00554 ( 684) Misc. bond : bond 0.00258 ( 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: 18 poor density : 70 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7662 (ttp) cc_final: 0.7451 (ttm) REVERT: A 96 TRP cc_start: 0.4560 (m100) cc_final: 0.3875 (m-10) REVERT: A 149 GLN cc_start: 0.8231 (mt0) cc_final: 0.7890 (mp10) REVERT: A 181 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7035 (tt) REVERT: A 215 MET cc_start: 0.7704 (tpp) cc_final: 0.7333 (tpp) REVERT: A 343 MET cc_start: 0.2831 (tpt) cc_final: 0.1430 (tpp) REVERT: A 372 GLN cc_start: 0.8391 (tp-100) cc_final: 0.7915 (tp-100) outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.0378 time to fit residues: 4.0191 Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 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 260 LEU 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 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 5 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.216466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.181917 restraints weight = 4332.958| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 3.43 r_work: 0.4045 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4218 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 7.061 4642 Z= 0.278 Chirality : 0.039 0.116 544 Planarity : 0.004 0.031 572 Dihedral : 4.742 46.729 463 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 6.09 % Allowed : 23.48 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.44), residues: 425 helix: 1.91 (0.31), residues: 295 sheet: None (None), residues: 0 loop : 0.82 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.010 0.001 TYR A 122 PHE 0.020 0.002 PHE A 358 TRP 0.014 0.001 TRP A 50 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3397) covalent geometry : angle 0.57292 ( 4638) SS BOND : bond 0.00334 ( 2) SS BOND : angle 1.24272 ( 4) hydrogen bonds : bond 0.03416 ( 237) hydrogen bonds : angle 3.96031 ( 684) Misc. bond : bond 0.00225 ( 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 96 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7653 (ttp) cc_final: 0.7440 (ttm) REVERT: A 96 TRP cc_start: 0.4446 (m100) cc_final: 0.3772 (m-10) REVERT: A 149 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: A 181 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6958 (tt) REVERT: A 215 MET cc_start: 0.7688 (tpp) cc_final: 0.7279 (tpp) REVERT: A 343 MET cc_start: 0.2818 (tpt) cc_final: 0.1423 (tpp) REVERT: A 372 GLN cc_start: 0.8392 (tp-100) cc_final: 0.7910 (tp-100) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 0.0372 time to fit residues: 4.3376 Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 149 GLN Chi-restraints excluded: chain A residue 180 TYR 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 260 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET 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 38 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.222218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.187832 restraints weight = 4459.723| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 3.36 r_work: 0.4189 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4391 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= 0.129 Angle : 0.592 8.287 4642 Z= 0.286 Chirality : 0.040 0.114 544 Planarity : 0.004 0.030 572 Dihedral : 4.613 44.175 463 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.51 % Allowed : 25.51 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.44), residues: 425 helix: 1.90 (0.31), residues: 295 sheet: None (None), residues: 0 loop : 0.89 (0.65), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.009 0.001 TYR A 122 PHE 0.016 0.002 PHE A 449 TRP 0.022 0.001 TRP A 50 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3397) covalent geometry : angle 0.59162 ( 4638) SS BOND : bond 0.00382 ( 2) SS BOND : angle 1.21718 ( 4) hydrogen bonds : bond 0.03428 ( 237) hydrogen bonds : angle 3.97886 ( 684) Misc. bond : bond 0.00214 ( 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 91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7836 (ttp) cc_final: 0.7617 (ttm) REVERT: A 77 ILE cc_start: 0.5597 (OUTLIER) cc_final: 0.5321 (mm) REVERT: A 96 TRP cc_start: 0.4485 (m100) cc_final: 0.3776 (m-10) REVERT: A 149 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: A 181 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7028 (tt) REVERT: A 215 MET cc_start: 0.7863 (tpp) cc_final: 0.7432 (tpp) REVERT: A 343 MET cc_start: 0.2908 (tpt) cc_final: 0.1514 (tpp) REVERT: A 372 GLN cc_start: 0.8499 (tp-100) cc_final: 0.8040 (tp-100) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.0427 time to fit residues: 4.6576 Evaluate side-chains 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 149 GLN 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 260 LEU 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 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 40 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.222569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.187215 restraints weight = 4517.296| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 3.43 r_work: 0.4182 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4520 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= 0.128 Angle : 0.588 7.912 4642 Z= 0.284 Chirality : 0.040 0.114 544 Planarity : 0.004 0.031 572 Dihedral : 4.502 42.383 463 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.51 % Allowed : 26.09 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.44), residues: 425 helix: 1.92 (0.31), residues: 295 sheet: None (None), residues: 0 loop : 0.92 (0.65), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.008 0.001 TYR A 122 PHE 0.015 0.002 PHE A 449 TRP 0.019 0.001 TRP A 50 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3397) covalent geometry : angle 0.58738 ( 4638) SS BOND : bond 0.00374 ( 2) SS BOND : angle 1.18009 ( 4) hydrogen bonds : bond 0.03430 ( 237) hydrogen bonds : angle 3.97088 ( 684) Misc. bond : bond 0.00201 ( 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 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7845 (ttp) cc_final: 0.7629 (ttm) REVERT: A 77 ILE cc_start: 0.5654 (OUTLIER) cc_final: 0.5373 (mm) REVERT: A 96 TRP cc_start: 0.4534 (m100) cc_final: 0.3796 (m-10) REVERT: A 149 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7715 (mp10) REVERT: A 181 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7021 (tt) REVERT: A 215 MET cc_start: 0.7844 (tpp) cc_final: 0.7416 (tpp) REVERT: A 343 MET cc_start: 0.2866 (tpt) cc_final: 0.1520 (tpp) REVERT: A 372 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8038 (tp-100) outliers start: 19 outliers final: 14 residues processed: 79 average time/residue: 0.0421 time to fit residues: 4.5365 Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 149 GLN 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 260 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 423 ASN 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 21 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.0070 chunk 22 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.221692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.186815 restraints weight = 4466.500| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 3.36 r_work: 0.4182 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4580 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= 0.131 Angle : 0.603 7.978 4642 Z= 0.292 Chirality : 0.040 0.115 544 Planarity : 0.004 0.031 572 Dihedral : 4.385 41.756 462 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.80 % Allowed : 25.22 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.43), residues: 425 helix: 1.90 (0.31), residues: 295 sheet: None (None), residues: 0 loop : 0.87 (0.65), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.008 0.001 TYR A 122 PHE 0.015 0.002 PHE A 449 TRP 0.016 0.001 TRP A 50 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3397) covalent geometry : angle 0.60188 ( 4638) SS BOND : bond 0.00382 ( 2) SS BOND : angle 1.18609 ( 4) hydrogen bonds : bond 0.03508 ( 237) hydrogen bonds : angle 4.03523 ( 684) Misc. bond : bond 0.00198 ( 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 91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7858 (ttp) cc_final: 0.7638 (ttm) REVERT: A 77 ILE cc_start: 0.5698 (OUTLIER) cc_final: 0.5424 (mm) REVERT: A 96 TRP cc_start: 0.4552 (m100) cc_final: 0.3820 (m-10) REVERT: A 149 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: A 181 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7020 (tt) REVERT: A 215 MET cc_start: 0.7861 (tpp) cc_final: 0.7432 (tpp) REVERT: A 343 MET cc_start: 0.2852 (tpt) cc_final: 0.1498 (tpp) REVERT: A 372 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8029 (tp-100) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 0.0442 time to fit residues: 4.7462 Evaluate side-chains 88 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 149 GLN 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 260 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET 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 7 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4615 r_free = 0.4615 target = 0.219676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.185362 restraints weight = 4373.671| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.28 r_work: 0.4170 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4756 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= 0.139 Angle : 0.628 10.276 4642 Z= 0.300 Chirality : 0.041 0.122 544 Planarity : 0.004 0.031 572 Dihedral : 4.427 41.326 462 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.44), residues: 425 helix: 1.89 (0.31), residues: 293 sheet: -2.10 (1.83), residues: 10 loop : 1.11 (0.68), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.010 0.001 TYR A 122 PHE 0.014 0.002 PHE A 241 TRP 0.015 0.001 TRP A 50 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3397) covalent geometry : angle 0.62688 ( 4638) SS BOND : bond 0.00456 ( 2) SS BOND : angle 1.39282 ( 4) hydrogen bonds : bond 0.03580 ( 237) hydrogen bonds : angle 4.13360 ( 684) Misc. bond : bond 0.00197 ( 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 92 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7801 (ttp) cc_final: 0.7577 (ttm) REVERT: A 77 ILE cc_start: 0.5819 (OUTLIER) cc_final: 0.5545 (mm) REVERT: A 96 TRP cc_start: 0.4673 (m100) cc_final: 0.3919 (m-10) REVERT: A 149 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: A 181 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7070 (tt) REVERT: A 215 MET cc_start: 0.7894 (tpp) cc_final: 0.7485 (tpp) REVERT: A 343 MET cc_start: 0.2800 (tpt) cc_final: 0.1464 (tpp) REVERT: A 372 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8040 (tp-100) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.0471 time to fit residues: 5.1397 Evaluate side-chains 88 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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 88 CYS Chi-restraints excluded: chain A residue 149 GLN 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 260 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET 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 9 optimal weight: 0.0070 chunk 42 optimal weight: 0.0270 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.0370 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- 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 = 0.223465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.188605 restraints weight = 4491.191| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 3.43 r_work: 0.4204 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.4771 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= 0.124 Angle : 0.621 10.396 4642 Z= 0.295 Chirality : 0.040 0.167 544 Planarity : 0.004 0.031 572 Dihedral : 4.193 42.003 461 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.48 % Allowed : 28.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.44), residues: 425 helix: 1.83 (0.31), residues: 300 sheet: -2.26 (1.82), residues: 10 loop : 1.11 (0.70), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 477 TYR 0.005 0.001 TYR A 152 PHE 0.015 0.002 PHE A 360 TRP 0.017 0.001 TRP A 50 HIS 0.002 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3397) covalent geometry : angle 0.62081 ( 4638) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.91567 ( 4) hydrogen bonds : bond 0.03433 ( 237) hydrogen bonds : angle 4.04862 ( 684) Misc. bond : bond 0.00182 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 870.14 seconds wall clock time: 15 minutes 37.13 seconds (937.13 seconds total)