Starting phenix.real_space_refine on Sat May 10 13:30:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lsk_63358/05_2025/9lsk_63358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lsk_63358/05_2025/9lsk_63358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lsk_63358/05_2025/9lsk_63358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lsk_63358/05_2025/9lsk_63358.map" model { file = "/net/cci-nas-00/data/ceres_data/9lsk_63358/05_2025/9lsk_63358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lsk_63358/05_2025/9lsk_63358.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 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 40 5.16 5 C 4256 2.51 5 N 1024 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6422 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3189 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 416} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3189 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 416} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'CIT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'CIT': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.42, per 1000 atoms: 0.69 Number of scatterers: 6422 At special positions: 0 Unit cell: (68.4584, 74.232, 107.224, 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 40 16.00 O 1102 8.00 N 1024 7.00 C 4256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.0 seconds 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 2 sheets defined 81.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 28 through 45 Processing helix chain 'A' and resid 50 through 72 removed outlier: 3.829A pdb=" N ILE A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 115 through 132 removed outlier: 4.489A pdb=" N VAL A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 167 removed outlier: 3.836A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 204 through 237 removed outlier: 4.257A pdb=" N TYR A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 288 removed outlier: 3.525A pdb=" N THR A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.612A pdb=" N GLY A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 359 through 385 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 419 through 446 Processing helix chain 'B' and resid 28 through 45 Processing helix chain 'B' and resid 50 through 72 removed outlier: 3.867A pdb=" N ILE B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 81 through 96 Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.660A pdb=" N LEU B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 167 removed outlier: 4.278A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 204 through 237 removed outlier: 3.998A pdb=" N TYR B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.795A pdb=" N SER B 241 " --> pdb=" O HIS B 237 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 242' Processing helix chain 'B' and resid 264 through 288 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.536A pdb=" N GLY B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 336 Processing helix chain 'B' and resid 336 through 348 Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 359 through 385 Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'B' and resid 419 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 23 518 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1973 1.34 - 1.46: 1044 1.46 - 1.58: 3458 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 6545 Sorted by residual: bond pdb=" N VAL A 410 " pdb=" CA VAL A 410 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.48e+00 bond pdb=" N GLY A 403 " pdb=" CA GLY A 403 " ideal model delta sigma weight residual 1.447 1.475 -0.028 1.09e-02 8.42e+03 6.64e+00 bond pdb=" N ASP A 407 " pdb=" CA ASP A 407 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.50e+00 bond pdb=" N SER A 412 " pdb=" CA SER A 412 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.30e+00 bond pdb=" N ASN A 401 " pdb=" CA ASN A 401 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.34e-02 5.57e+03 5.20e+00 ... (remaining 6540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 8728 2.19 - 4.38: 125 4.38 - 6.56: 23 6.56 - 8.75: 4 8.75 - 10.94: 3 Bond angle restraints: 8883 Sorted by residual: angle pdb=" N MET A 399 " pdb=" CA MET A 399 " pdb=" C MET A 399 " ideal model delta sigma weight residual 113.55 105.02 8.53 1.26e+00 6.30e-01 4.58e+01 angle pdb=" CA GLY A 403 " pdb=" C GLY A 403 " pdb=" O GLY A 403 " ideal model delta sigma weight residual 122.29 117.45 4.84 8.10e-01 1.52e+00 3.57e+01 angle pdb=" CA ASP A 407 " pdb=" CB ASP A 407 " pdb=" CG ASP A 407 " ideal model delta sigma weight residual 112.60 117.91 -5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" C ASP A 407 " pdb=" CA ASP A 407 " pdb=" CB ASP A 407 " ideal model delta sigma weight residual 110.85 119.66 -8.81 1.70e+00 3.46e-01 2.69e+01 angle pdb=" N ASP A 407 " pdb=" CA ASP A 407 " pdb=" C ASP A 407 " ideal model delta sigma weight residual 111.36 105.79 5.57 1.09e+00 8.42e-01 2.62e+01 ... (remaining 8878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3519 17.43 - 34.87: 240 34.87 - 52.30: 31 52.30 - 69.73: 6 69.73 - 87.17: 2 Dihedral angle restraints: 3798 sinusoidal: 1386 harmonic: 2412 Sorted by residual: dihedral pdb=" CA GLY A 396 " pdb=" C GLY A 396 " pdb=" N LEU A 397 " pdb=" CA LEU A 397 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" C ASP A 407 " pdb=" N ASP A 407 " pdb=" CA ASP A 407 " pdb=" CB ASP A 407 " ideal model delta harmonic sigma weight residual -122.60 -133.42 10.82 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" CA ARG B 402 " pdb=" C ARG B 402 " pdb=" N GLY B 403 " pdb=" CA GLY B 403 " ideal model delta harmonic sigma weight residual 180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 3795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 865 0.056 - 0.111: 193 0.111 - 0.167: 18 0.167 - 0.222: 2 0.222 - 0.278: 2 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA ASP A 407 " pdb=" N ASP A 407 " pdb=" C ASP A 407 " pdb=" CB ASP A 407 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU A 408 " pdb=" N LEU A 408 " pdb=" C LEU A 408 " pdb=" CB LEU A 408 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA MET A 399 " pdb=" N MET A 399 " pdb=" C MET A 399 " pdb=" CB MET A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.27e-01 ... (remaining 1077 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 332 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C PHE B 332 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE B 332 " -0.009 2.00e-02 2.50e+03 pdb=" N SER B 333 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 65 " -0.012 2.00e-02 2.50e+03 1.00e-02 1.77e+00 pdb=" CG PHE B 65 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 65 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 65 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 65 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 65 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 65 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 332 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C PHE A 332 " 0.022 2.00e-02 2.50e+03 pdb=" O PHE A 332 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 333 " -0.007 2.00e-02 2.50e+03 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 346 2.73 - 3.27: 7044 3.27 - 3.81: 11277 3.81 - 4.36: 12500 4.36 - 4.90: 22369 Nonbonded interactions: 53536 Sorted by model distance: nonbonded pdb=" O GLY A 127 " pdb=" OG SER A 131 " model vdw 2.185 3.040 nonbonded pdb=" O TYR A 144 " pdb=" OG1 THR A 147 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR B 264 " pdb=" OE1 GLU B 267 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A 204 " pdb=" OE1 GLU A 206 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASP B 171 " pdb=" N ARG B 172 " model vdw 2.239 3.120 ... (remaining 53531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 258 or (resid 259 and (name N or name CA or nam \ e C or name O or name CB )) or resid 260 through 446 or resid 501)) selection = (chain 'B' and (resid 18 through 248 or (resid 249 through 259 and (name N or na \ me CA or name C or name O or name CB )) or resid 260 through 446 or resid 501)) } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.110 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.004 0.040 6545 Z= 0.209 Angle : 0.681 10.939 8883 Z= 0.408 Chirality : 0.045 0.278 1080 Planarity : 0.003 0.024 1085 Dihedral : 11.950 87.168 2270 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.31 % Allowed : 0.31 % Favored : 99.39 % Cbeta Deviations : 0.13 % 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: 1.52 (0.30), residues: 854 helix: 1.78 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.01 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 303 HIS 0.003 0.000 HIS A 299 PHE 0.023 0.002 PHE B 65 TYR 0.016 0.001 TYR A 300 ARG 0.004 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.06246 ( 518) hydrogen bonds : angle 4.64799 ( 1548) covalent geometry : bond 0.00409 ( 6545) covalent geometry : angle 0.68077 ( 8883) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.639 Fit side-chains REVERT: B 231 ASP cc_start: 0.9021 (t70) cc_final: 0.8368 (t0) REVERT: B 350 ASP cc_start: 0.7845 (t0) cc_final: 0.7643 (t0) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 1.0525 time to fit residues: 111.7145 Evaluate side-chains 68 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.062650 restraints weight = 12710.570| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.94 r_work: 0.2700 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6545 Z= 0.158 Angle : 0.586 12.320 8883 Z= 0.302 Chirality : 0.041 0.138 1080 Planarity : 0.004 0.029 1085 Dihedral : 6.002 51.218 934 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.22 % Allowed : 11.16 % Favored : 87.61 % 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: 1.79 (0.29), residues: 854 helix: 2.06 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 239 HIS 0.003 0.000 HIS A 299 PHE 0.021 0.001 PHE B 87 TYR 0.019 0.001 TYR A 31 ARG 0.005 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 518) hydrogen bonds : angle 4.37620 ( 1548) covalent geometry : bond 0.00365 ( 6545) covalent geometry : angle 0.58566 ( 8883) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.642 Fit side-chains REVERT: A 131 SER cc_start: 0.8760 (m) cc_final: 0.8473 (m) REVERT: A 171 ASP cc_start: 0.8594 (t0) cc_final: 0.8394 (t0) REVERT: A 389 ILE cc_start: 0.9098 (mt) cc_final: 0.8885 (mp) REVERT: B 103 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8676 (mt-10) REVERT: B 231 ASP cc_start: 0.8972 (t70) cc_final: 0.8411 (t70) REVERT: B 304 MET cc_start: 0.8818 (ttt) cc_final: 0.8469 (ttm) REVERT: B 350 ASP cc_start: 0.8251 (t0) cc_final: 0.7725 (t0) outliers start: 8 outliers final: 2 residues processed: 75 average time/residue: 0.9756 time to fit residues: 78.1416 Evaluate side-chains 70 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 170 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN A 362 ASN B 352 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.062605 restraints weight = 12881.212| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.91 r_work: 0.2730 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6545 Z= 0.132 Angle : 0.547 11.044 8883 Z= 0.281 Chirality : 0.040 0.135 1080 Planarity : 0.003 0.033 1085 Dihedral : 5.691 47.654 932 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.22 % Allowed : 13.15 % Favored : 85.63 % 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: 1.85 (0.30), residues: 854 helix: 2.13 (0.21), residues: 658 sheet: None (None), residues: 0 loop : -2.08 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 239 HIS 0.002 0.000 HIS A 299 PHE 0.017 0.001 PHE B 65 TYR 0.017 0.001 TYR A 31 ARG 0.005 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 518) hydrogen bonds : angle 4.24373 ( 1548) covalent geometry : bond 0.00293 ( 6545) covalent geometry : angle 0.54741 ( 8883) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.697 Fit side-chains REVERT: A 131 SER cc_start: 0.8853 (m) cc_final: 0.8559 (m) REVERT: A 350 ASP cc_start: 0.7886 (t0) cc_final: 0.6852 (t0) REVERT: B 103 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8659 (mt-10) REVERT: B 231 ASP cc_start: 0.9030 (t70) cc_final: 0.8418 (t70) REVERT: B 304 MET cc_start: 0.8810 (ttt) cc_final: 0.8453 (ttm) outliers start: 8 outliers final: 2 residues processed: 78 average time/residue: 0.8849 time to fit residues: 73.9976 Evaluate side-chains 69 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.085470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.062638 restraints weight = 13067.713| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.98 r_work: 0.2744 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6545 Z= 0.134 Angle : 0.539 11.385 8883 Z= 0.276 Chirality : 0.040 0.135 1080 Planarity : 0.003 0.034 1085 Dihedral : 5.543 45.357 932 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.60 % Allowed : 14.68 % Favored : 82.72 % 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: 1.96 (0.30), residues: 854 helix: 2.29 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -2.10 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 239 HIS 0.002 0.000 HIS A 299 PHE 0.016 0.001 PHE B 65 TYR 0.017 0.001 TYR A 31 ARG 0.003 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 518) hydrogen bonds : angle 4.14887 ( 1548) covalent geometry : bond 0.00301 ( 6545) covalent geometry : angle 0.53895 ( 8883) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.684 Fit side-chains REVERT: A 131 SER cc_start: 0.8870 (m) cc_final: 0.8576 (m) REVERT: B 103 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8664 (mt-10) REVERT: B 231 ASP cc_start: 0.9041 (t70) cc_final: 0.8431 (t70) REVERT: B 304 MET cc_start: 0.8797 (ttt) cc_final: 0.8450 (ttm) REVERT: B 350 ASP cc_start: 0.8405 (t0) cc_final: 0.7893 (t0) outliers start: 17 outliers final: 5 residues processed: 80 average time/residue: 0.9207 time to fit residues: 79.0981 Evaluate side-chains 75 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** 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 = 0.3278 r_free = 0.3278 target = 0.085117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.062853 restraints weight = 12977.147| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.90 r_work: 0.2732 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6545 Z= 0.131 Angle : 0.538 11.136 8883 Z= 0.275 Chirality : 0.039 0.131 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.444 45.111 932 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.45 % Allowed : 16.21 % Favored : 81.35 % 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: 1.99 (0.30), residues: 854 helix: 2.31 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -2.09 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 239 HIS 0.002 0.000 HIS A 299 PHE 0.015 0.001 PHE B 65 TYR 0.017 0.001 TYR A 31 ARG 0.003 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 518) hydrogen bonds : angle 4.13314 ( 1548) covalent geometry : bond 0.00295 ( 6545) covalent geometry : angle 0.53766 ( 8883) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.674 Fit side-chains REVERT: A 131 SER cc_start: 0.8840 (m) cc_final: 0.8542 (m) REVERT: B 103 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8634 (mt-10) REVERT: B 141 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8482 (mp) REVERT: B 231 ASP cc_start: 0.9031 (t70) cc_final: 0.8405 (t0) REVERT: B 304 MET cc_start: 0.8801 (ttt) cc_final: 0.8429 (ttm) REVERT: B 350 ASP cc_start: 0.8422 (t0) cc_final: 0.7909 (t0) outliers start: 16 outliers final: 7 residues processed: 78 average time/residue: 0.8343 time to fit residues: 69.9336 Evaluate side-chains 78 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 384 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** 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 = 0.3295 r_free = 0.3295 target = 0.086185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.063717 restraints weight = 12894.552| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.93 r_work: 0.2740 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6545 Z= 0.129 Angle : 0.535 11.155 8883 Z= 0.272 Chirality : 0.040 0.145 1080 Planarity : 0.003 0.036 1085 Dihedral : 5.317 45.337 932 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.52 % Allowed : 15.75 % Favored : 80.73 % 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: 2.08 (0.30), residues: 854 helix: 2.36 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -2.01 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 239 HIS 0.002 0.000 HIS A 299 PHE 0.015 0.001 PHE B 65 TYR 0.017 0.001 TYR B 31 ARG 0.003 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 518) hydrogen bonds : angle 4.10855 ( 1548) covalent geometry : bond 0.00286 ( 6545) covalent geometry : angle 0.53451 ( 8883) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.727 Fit side-chains REVERT: A 417 MET cc_start: 0.8879 (tpt) cc_final: 0.8517 (mmm) REVERT: B 103 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8632 (mt-10) REVERT: B 141 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8463 (mp) REVERT: B 231 ASP cc_start: 0.9035 (t70) cc_final: 0.8359 (t0) REVERT: B 304 MET cc_start: 0.8782 (ttt) cc_final: 0.8412 (ttm) REVERT: B 350 ASP cc_start: 0.8438 (t0) cc_final: 0.7934 (t0) outliers start: 23 outliers final: 13 residues processed: 85 average time/residue: 0.8490 time to fit residues: 77.6544 Evaluate side-chains 83 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 384 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** 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 = 0.3292 r_free = 0.3292 target = 0.085491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.062848 restraints weight = 12841.043| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.92 r_work: 0.2732 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6545 Z= 0.139 Angle : 0.555 11.171 8883 Z= 0.283 Chirality : 0.040 0.134 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.252 46.184 932 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.67 % Allowed : 16.06 % Favored : 80.28 % 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 (0.29), residues: 854 helix: 2.27 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.84 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 239 HIS 0.002 0.000 HIS A 299 PHE 0.015 0.001 PHE B 65 TYR 0.017 0.001 TYR A 31 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 518) hydrogen bonds : angle 4.12175 ( 1548) covalent geometry : bond 0.00314 ( 6545) covalent geometry : angle 0.55451 ( 8883) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.691 Fit side-chains REVERT: A 417 MET cc_start: 0.8934 (tpt) cc_final: 0.8562 (mmm) REVERT: B 103 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8657 (mt-10) REVERT: B 141 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 231 ASP cc_start: 0.9050 (t70) cc_final: 0.8392 (t0) REVERT: B 350 ASP cc_start: 0.8418 (t0) cc_final: 0.7918 (t0) outliers start: 24 outliers final: 13 residues processed: 81 average time/residue: 0.8399 time to fit residues: 73.1693 Evaluate side-chains 80 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 384 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 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 = 0.3274 r_free = 0.3274 target = 0.084705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.062285 restraints weight = 12884.025| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.90 r_work: 0.2721 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6545 Z= 0.146 Angle : 0.553 11.763 8883 Z= 0.284 Chirality : 0.040 0.133 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.237 46.712 932 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.06 % Allowed : 17.13 % Favored : 79.82 % 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 (0.29), residues: 854 helix: 2.28 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.81 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 239 HIS 0.002 0.000 HIS A 299 PHE 0.016 0.001 PHE A 226 TYR 0.017 0.001 TYR A 31 ARG 0.002 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 518) hydrogen bonds : angle 4.14580 ( 1548) covalent geometry : bond 0.00335 ( 6545) covalent geometry : angle 0.55293 ( 8883) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.676 Fit side-chains REVERT: A 175 MET cc_start: 0.9067 (mmm) cc_final: 0.8818 (mtm) REVERT: A 417 MET cc_start: 0.8924 (tpt) cc_final: 0.8555 (mmm) REVERT: B 103 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8653 (mt-10) REVERT: B 141 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 231 ASP cc_start: 0.9068 (t70) cc_final: 0.8389 (t0) REVERT: B 304 MET cc_start: 0.8817 (ttt) cc_final: 0.8485 (ttm) REVERT: B 350 ASP cc_start: 0.8461 (t0) cc_final: 0.7955 (t0) outliers start: 20 outliers final: 11 residues processed: 79 average time/residue: 0.8149 time to fit residues: 69.2790 Evaluate side-chains 79 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 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 = 0.3293 r_free = 0.3293 target = 0.085586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.062740 restraints weight = 12954.886| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.93 r_work: 0.2743 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6545 Z= 0.138 Angle : 0.551 12.177 8883 Z= 0.282 Chirality : 0.040 0.130 1080 Planarity : 0.003 0.034 1085 Dihedral : 5.188 46.607 932 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.60 % Allowed : 17.74 % Favored : 79.66 % 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 (0.29), residues: 854 helix: 2.30 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.78 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 239 HIS 0.002 0.000 HIS A 299 PHE 0.019 0.001 PHE A 226 TYR 0.017 0.001 TYR A 31 ARG 0.003 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 518) hydrogen bonds : angle 4.13413 ( 1548) covalent geometry : bond 0.00311 ( 6545) covalent geometry : angle 0.55052 ( 8883) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.707 Fit side-chains REVERT: A 417 MET cc_start: 0.8967 (tpt) cc_final: 0.8595 (mmm) REVERT: B 103 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8661 (mt-10) REVERT: B 141 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8486 (mp) REVERT: B 231 ASP cc_start: 0.9083 (t70) cc_final: 0.8425 (t0) REVERT: B 304 MET cc_start: 0.8812 (ttt) cc_final: 0.8498 (ttm) REVERT: B 350 ASP cc_start: 0.8466 (t0) cc_final: 0.7948 (t0) outliers start: 17 outliers final: 11 residues processed: 74 average time/residue: 0.9197 time to fit residues: 72.7821 Evaluate side-chains 79 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 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 = 0.3300 r_free = 0.3300 target = 0.086416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.063921 restraints weight = 13063.211| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.95 r_work: 0.2741 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6545 Z= 0.130 Angle : 0.554 12.579 8883 Z= 0.283 Chirality : 0.040 0.136 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.129 45.817 932 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.29 % Allowed : 18.04 % Favored : 79.66 % 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: 2.17 (0.29), residues: 854 helix: 2.30 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.76 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 239 HIS 0.002 0.000 HIS A 299 PHE 0.019 0.001 PHE A 226 TYR 0.017 0.001 TYR A 31 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 518) hydrogen bonds : angle 4.10218 ( 1548) covalent geometry : bond 0.00287 ( 6545) covalent geometry : angle 0.55417 ( 8883) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.674 Fit side-chains REVERT: A 352 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8811 (mm-40) REVERT: A 417 MET cc_start: 0.8926 (tpt) cc_final: 0.8542 (mmm) REVERT: B 103 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8635 (mt-10) REVERT: B 141 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 231 ASP cc_start: 0.9038 (t70) cc_final: 0.8376 (t0) REVERT: B 304 MET cc_start: 0.8741 (ttt) cc_final: 0.8446 (ttm) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.9618 time to fit residues: 79.0945 Evaluate side-chains 78 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 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 = 0.3303 r_free = 0.3303 target = 0.086169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.063235 restraints weight = 13124.097| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.97 r_work: 0.2753 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6545 Z= 0.136 Angle : 0.560 12.483 8883 Z= 0.285 Chirality : 0.040 0.130 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.117 46.208 932 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.60 % Allowed : 18.35 % Favored : 79.05 % 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: 2.21 (0.29), residues: 854 helix: 2.35 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.78 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 239 HIS 0.002 0.000 HIS A 299 PHE 0.017 0.001 PHE A 226 TYR 0.017 0.001 TYR A 31 ARG 0.003 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 518) hydrogen bonds : angle 4.09996 ( 1548) covalent geometry : bond 0.00305 ( 6545) covalent geometry : angle 0.56040 ( 8883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3377.13 seconds wall clock time: 59 minutes 17.34 seconds (3557.34 seconds total)