Starting phenix.real_space_refine on Mon Mar 11 15:53:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jej_36190/03_2024/8jej_36190_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jej_36190/03_2024/8jej_36190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jej_36190/03_2024/8jej_36190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jej_36190/03_2024/8jej_36190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jej_36190/03_2024/8jej_36190_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jej_36190/03_2024/8jej_36190_updated.pdb" } resolution = 2.5 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= 0.047 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: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5421 2.51 5 N 1490 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 468": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "C GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8604 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4167 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 52.668 65.790 36.133 1.00 17.16 S ATOM 1738 SG CYS A 222 53.574 70.572 32.001 1.00 21.97 S ATOM 1698 SG CYS A 216 52.124 65.227 29.426 1.00 25.68 S Time building chain proxies: 7.52, per 1000 atoms: 0.87 Number of scatterers: 8604 At special positions: 0 Unit cell: (103.53, 109.62, 76.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1639 8.00 N 1490 7.00 C 5421 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 - 3.50 Amino acid : False - 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 7 sheets defined 35.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 107 through 110 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 139 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 356 through 359 removed outlier: 3.614A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 441 through 461 removed outlier: 3.752A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 523 through 541 Processing helix chain 'B' and resid 49 through 62 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.883A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 52 through 56' Processing helix chain 'C' and resid 96 through 104 Processing helix chain 'C' and resid 120 through 125 removed outlier: 5.411A pdb=" N ARG C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 186 through 196 Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.660A pdb=" N HIS C 205 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 246 through 255 Processing helix chain 'C' and resid 266 through 273 Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 280 through 292 removed outlier: 3.739A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.915A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 374 through 382 Processing helix chain 'C' and resid 409 through 422 Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 446 through 450 Processing sheet with id= A, first strand: chain 'A' and resid 506 through 508 removed outlier: 6.427A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LYS A 247 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'A' and resid 198 through 200 Processing sheet with id= D, first strand: chain 'A' and resid 277 through 281 removed outlier: 3.731A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 326 through 332 removed outlier: 4.832A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 70 through 73 Processing sheet with id= G, first strand: chain 'C' and resid 384 through 388 252 hydrogen bonds defined for protein. 708 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: 2.36 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8745 1.76 - 2.30: 90 2.30 - 2.85: 0 2.85 - 3.39: 0 3.39 - 3.93: 3 Bond restraints: 8838 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.928 -1.628 2.00e-02 2.50e+03 6.63e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.816 -1.558 2.00e-02 2.50e+03 6.06e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.786 -1.553 2.00e-02 2.50e+03 6.03e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 8833 not shown) Histogram of bond angle deviations from ideal: 39.35 - 67.47: 5 67.47 - 95.59: 19 95.59 - 123.71: 11669 123.71 - 151.84: 383 151.84 - 179.96: 6 Bond angle restraints: 12082 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.25 47.50 3.00e+00 1.11e-01 2.51e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 67.92 44.67 3.00e+00 1.11e-01 2.22e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 68.73 34.53 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.25 69.61 33.64 3.00e+00 1.11e-01 1.26e+02 angle pdb="FE1 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 72.09 39.35 32.74 3.00e+00 1.11e-01 1.19e+02 ... (remaining 12077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 4991 35.83 - 71.65: 215 71.65 - 107.47: 18 107.47 - 143.30: 1 143.30 - 179.12: 1 Dihedral angle restraints: 5226 sinusoidal: 2074 harmonic: 3152 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -105.59 -74.41 0 5.00e+00 4.00e-02 2.21e+02 dihedral pdb=" C27 U10 C 504 " pdb=" C28 U10 C 504 " pdb=" C29 U10 C 504 " pdb=" C31 U10 C 504 " ideal model delta sinusoidal sigma weight residual 181.72 2.59 179.12 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2C HEC C 501 " pdb=" C3C HEC C 501 " pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -11.17 71.17 2 1.00e+01 1.00e-02 4.30e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.460: 1276 3.460 - 6.920: 0 6.920 - 10.380: 0 10.380 - 13.840: 0 13.840 - 17.300: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.53 17.30 2.00e-01 2.50e+01 7.48e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA PRO B 160 " pdb=" N PRO B 160 " pdb=" C PRO B 160 " pdb=" CB PRO B 160 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1274 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " 0.013 2.00e-02 2.50e+03 1.00e-01 1.75e+02 pdb=" C1M U10 C 504 " -0.117 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " 0.092 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " 0.053 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " -0.184 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.046 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 80 " 0.125 5.00e-02 4.00e+02 1.92e-01 5.92e+01 pdb=" N PRO A 81 " -0.333 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.032 2.00e-02 2.50e+03 6.75e-02 4.56e+01 pdb=" CGD HEC C 501 " 0.117 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.042 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.043 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 311 2.71 - 3.26: 8661 3.26 - 3.81: 15361 3.81 - 4.35: 20599 4.35 - 4.90: 32191 Nonbonded interactions: 77123 Sorted by model distance: nonbonded pdb=" N GLU C 129 " pdb=" OE1 GLU C 129 " model vdw 2.165 2.520 nonbonded pdb=" OH TYR A 139 " pdb=" O PRO A 168 " model vdw 2.243 2.440 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.259 2.688 nonbonded pdb=" S3 F3S A 602 " pdb="FE3 F3S A 602 " model vdw 2.261 2.688 nonbonded pdb=" S1 F3S A 602 " pdb="FE1 F3S A 602 " model vdw 2.262 2.688 ... (remaining 77118 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: 0.010 Normalize map: mean=0, sd=1: 1.590 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: 6.650 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 33.980 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:15.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.030 1.628 8838 Z= 1.548 Angle : 1.336 47.497 12082 Z= 0.502 Chirality : 0.486 17.300 1277 Planarity : 0.008 0.192 1569 Dihedral : 18.651 179.124 3214 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 16.70 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1083 helix: 1.15 (0.27), residues: 379 sheet: 0.08 (0.54), residues: 92 loop : -0.60 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 338 HIS 0.005 0.001 HIS A 76 PHE 0.019 0.001 PHE A 270 TYR 0.023 0.001 TYR A 443 ARG 0.002 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: B 164 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6242 (m-70) REVERT: C 187 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6888 (m-30) outliers start: 23 outliers final: 21 residues processed: 123 average time/residue: 1.2061 time to fit residues: 158.3673 Evaluate side-chains 127 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 501 HIS B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.179 8838 Z= 0.344 Angle : 1.472 84.363 12082 Z= 0.541 Chirality : 0.088 2.638 1277 Planarity : 0.006 0.137 1569 Dihedral : 12.252 129.880 1322 Min Nonbonded Distance : 1.502 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 2.93 % Allowed : 15.80 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1083 helix: 1.08 (0.27), residues: 382 sheet: 0.07 (0.53), residues: 93 loop : -0.61 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 338 HIS 0.007 0.001 HIS A 76 PHE 0.020 0.002 PHE A 270 TYR 0.016 0.002 TYR A 443 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 1.077 Fit side-chains REVERT: B 164 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.6661 (m-70) REVERT: C 118 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.6967 (tpt) REVERT: C 187 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: C 302 THR cc_start: 0.7240 (OUTLIER) cc_final: 0.6969 (t) outliers start: 26 outliers final: 17 residues processed: 123 average time/residue: 1.3502 time to fit residues: 176.4412 Evaluate side-chains 124 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 0.0570 chunk 87 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 501 HIS B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 8838 Z= 0.225 Angle : 1.221 73.892 12082 Z= 0.452 Chirality : 0.052 0.941 1277 Planarity : 0.005 0.102 1569 Dihedral : 11.244 90.218 1303 Min Nonbonded Distance : 1.530 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 3.05 % Allowed : 16.70 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1083 helix: 1.33 (0.27), residues: 384 sheet: 0.45 (0.57), residues: 84 loop : -0.45 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.017 0.001 PHE A 270 TYR 0.016 0.001 TYR A 443 ARG 0.001 0.000 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 0.937 Fit side-chains REVERT: A 152 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7961 (tp30) REVERT: A 276 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.6942 (tp40) REVERT: A 389 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7721 (mttt) REVERT: A 468 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: B 154 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7846 (mtt180) REVERT: B 164 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.6342 (m-70) REVERT: C 187 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.6941 (m-30) REVERT: C 302 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.7034 (t) outliers start: 27 outliers final: 14 residues processed: 125 average time/residue: 1.3384 time to fit residues: 177.6269 Evaluate side-chains 131 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 501 HIS B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.166 8838 Z= 0.329 Angle : 1.317 79.176 12082 Z= 0.493 Chirality : 0.051 0.474 1277 Planarity : 0.006 0.098 1569 Dihedral : 11.390 85.396 1298 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 3.27 % Allowed : 16.82 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1083 helix: 1.18 (0.27), residues: 376 sheet: 0.03 (0.54), residues: 92 loop : -0.51 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 338 HIS 0.007 0.001 HIS A 76 PHE 0.023 0.002 PHE A 80 TYR 0.013 0.002 TYR A 443 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 1.063 Fit side-chains REVERT: A 152 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: A 276 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7054 (tp40) REVERT: C 64 PHE cc_start: 0.6363 (OUTLIER) cc_final: 0.5263 (p90) REVERT: C 110 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7304 (p0) REVERT: C 118 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7038 (tpt) REVERT: C 129 GLU cc_start: 0.7545 (mp0) cc_final: 0.7292 (mp0) REVERT: C 187 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7075 (t0) REVERT: C 302 THR cc_start: 0.7243 (OUTLIER) cc_final: 0.6978 (t) REVERT: C 395 MET cc_start: 0.9240 (ttt) cc_final: 0.8858 (ttt) outliers start: 29 outliers final: 19 residues processed: 124 average time/residue: 1.3354 time to fit residues: 175.7418 Evaluate side-chains 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.0010 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.167 8838 Z= 0.172 Angle : 1.243 78.778 12082 Z= 0.451 Chirality : 0.045 0.451 1277 Planarity : 0.005 0.079 1569 Dihedral : 10.323 84.972 1298 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.58 % Rotamer: Outliers : 2.71 % Allowed : 17.83 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1083 helix: 1.45 (0.27), residues: 386 sheet: 0.61 (0.58), residues: 82 loop : -0.41 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.015 0.001 TYR A 443 ARG 0.001 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: A 468 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: B 116 PRO cc_start: 0.8114 (Cg_exo) cc_final: 0.7820 (Cg_endo) REVERT: B 154 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7837 (mtt180) REVERT: B 164 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.6160 (m-70) REVERT: C 110 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7628 (p0) REVERT: C 129 GLU cc_start: 0.7541 (mp0) cc_final: 0.7288 (mp0) REVERT: C 187 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7076 (t0) outliers start: 24 outliers final: 10 residues processed: 129 average time/residue: 1.3570 time to fit residues: 186.2769 Evaluate side-chains 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 8838 Z= 0.327 Angle : 1.309 79.170 12082 Z= 0.493 Chirality : 0.051 0.443 1277 Planarity : 0.006 0.088 1569 Dihedral : 11.097 85.233 1297 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 3.72 % Allowed : 17.38 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1083 helix: 1.26 (0.27), residues: 377 sheet: 0.54 (0.59), residues: 82 loop : -0.47 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 338 HIS 0.007 0.001 HIS A 76 PHE 0.024 0.002 PHE A 80 TYR 0.012 0.002 TYR A 232 ARG 0.003 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7873 (tp30) REVERT: A 276 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7043 (tp40) REVERT: A 468 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: B 135 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: C 64 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.5206 (p90) REVERT: C 110 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7561 (p0) REVERT: C 118 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.6966 (tpt) REVERT: C 129 GLU cc_start: 0.7551 (mp0) cc_final: 0.7276 (mp0) REVERT: C 187 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6994 (t0) REVERT: C 302 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6987 (t) REVERT: C 329 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.6018 (pp) outliers start: 33 outliers final: 16 residues processed: 121 average time/residue: 1.4554 time to fit residues: 186.3394 Evaluate side-chains 123 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.0020 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.166 8838 Z= 0.194 Angle : 1.256 78.705 12082 Z= 0.460 Chirality : 0.047 0.445 1277 Planarity : 0.005 0.078 1569 Dihedral : 10.439 88.016 1297 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 2.60 % Allowed : 18.17 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1083 helix: 1.48 (0.27), residues: 378 sheet: 0.50 (0.57), residues: 84 loop : -0.38 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.017 0.001 PHE A 270 TYR 0.014 0.001 TYR A 443 ARG 0.007 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7955 (tp30) REVERT: A 468 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: B 116 PRO cc_start: 0.8123 (Cg_exo) cc_final: 0.7856 (Cg_endo) REVERT: B 154 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7814 (mtt180) REVERT: B 164 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.6465 (m-70) REVERT: C 129 GLU cc_start: 0.7540 (mp0) cc_final: 0.7267 (mp0) REVERT: C 187 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6995 (t0) outliers start: 23 outliers final: 11 residues processed: 125 average time/residue: 1.3628 time to fit residues: 180.7798 Evaluate side-chains 126 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 8838 Z= 0.195 Angle : 1.246 77.504 12082 Z= 0.456 Chirality : 0.048 0.534 1277 Planarity : 0.005 0.075 1569 Dihedral : 10.273 86.466 1295 Min Nonbonded Distance : 1.555 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 2.82 % Allowed : 18.06 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1083 helix: 1.58 (0.27), residues: 378 sheet: 0.48 (0.57), residues: 84 loop : -0.37 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.017 0.001 PHE A 270 TYR 0.013 0.001 TYR A 443 ARG 0.008 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: A 468 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: B 116 PRO cc_start: 0.8128 (Cg_exo) cc_final: 0.7868 (Cg_endo) REVERT: B 154 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7822 (mtt180) REVERT: B 164 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.6365 (m-70) REVERT: C 129 GLU cc_start: 0.7569 (mp0) cc_final: 0.7295 (mp0) REVERT: C 187 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7015 (t0) outliers start: 25 outliers final: 11 residues processed: 123 average time/residue: 1.2608 time to fit residues: 165.2683 Evaluate side-chains 125 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 8838 Z= 0.266 Angle : 1.273 77.207 12082 Z= 0.473 Chirality : 0.050 0.596 1277 Planarity : 0.005 0.079 1569 Dihedral : 10.634 89.064 1294 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 2.48 % Allowed : 18.40 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1083 helix: 1.49 (0.27), residues: 376 sheet: 0.47 (0.58), residues: 84 loop : -0.41 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 338 HIS 0.005 0.001 HIS A 76 PHE 0.020 0.002 PHE A 270 TYR 0.012 0.002 TYR A 232 ARG 0.008 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: A 468 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: B 116 PRO cc_start: 0.8118 (Cg_exo) cc_final: 0.7859 (Cg_endo) REVERT: B 135 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: B 154 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7836 (mtt180) REVERT: B 164 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.6343 (m-70) REVERT: C 129 GLU cc_start: 0.7570 (mp0) cc_final: 0.7292 (mp0) REVERT: C 187 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7031 (t0) outliers start: 22 outliers final: 12 residues processed: 124 average time/residue: 1.4302 time to fit residues: 188.0934 Evaluate side-chains 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 0.2980 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 8838 Z= 0.266 Angle : 1.086 56.807 12082 Z= 0.410 Chirality : 0.074 2.084 1277 Planarity : 0.006 0.115 1569 Dihedral : 10.155 84.224 1294 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.14 % Allowed : 18.85 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1083 helix: 1.64 (0.27), residues: 379 sheet: 0.44 (0.58), residues: 84 loop : -0.34 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.005 0.001 HIS A 110 PHE 0.016 0.001 PHE C 210 TYR 0.012 0.001 TYR A 443 ARG 0.008 0.000 ARG B 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: A 189 GLU cc_start: 0.7124 (pt0) cc_final: 0.6778 (mt-10) REVERT: B 116 PRO cc_start: 0.8150 (Cg_exo) cc_final: 0.7890 (Cg_endo) REVERT: B 135 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7084 (m-30) REVERT: B 154 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7808 (mtt180) REVERT: B 164 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.6302 (m-70) REVERT: C 129 GLU cc_start: 0.7561 (mp0) cc_final: 0.7282 (mp0) outliers start: 19 outliers final: 11 residues processed: 125 average time/residue: 1.3667 time to fit residues: 181.4541 Evaluate side-chains 127 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 351 ASN B 138 ASN ** C 124 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 = 0.3455 r_free = 0.3455 target = 0.129617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105382 restraints weight = 9121.527| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.33 r_work: 0.3135 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 8838 Z= 0.204 Angle : 1.074 82.639 12082 Z= 0.404 Chirality : 0.060 1.415 1277 Planarity : 0.005 0.113 1569 Dihedral : 10.080 86.552 1292 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.92 % Allowed : 19.19 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1083 helix: 1.66 (0.27), residues: 380 sheet: 0.44 (0.58), residues: 84 loop : -0.33 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.017 0.001 PHE A 270 TYR 0.012 0.001 TYR A 443 ARG 0.009 0.000 ARG B 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3597.57 seconds wall clock time: 65 minutes 13.02 seconds (3913.02 seconds total)