Starting phenix.real_space_refine on Tue Feb 13 07:24:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/02_2024/7cko_30389_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/02_2024/7cko_30389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/02_2024/7cko_30389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/02_2024/7cko_30389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/02_2024/7cko_30389_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/02_2024/7cko_30389_updated.pdb" } resolution = 2.95 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= 0.004 sd= 0.070 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 25 5.16 5 C 2624 2.51 5 N 681 2.21 5 O 699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B GLU 218": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4029 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2846 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 17, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1160 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 543 Unresolved non-hydrogen angles: 696 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 289 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'G5L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.83, per 1000 atoms: 0.70 Number of scatterers: 4029 At special positions: 0 Unit cell: (103.726, 58.1877, 116.375, 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 25 16.00 O 699 8.00 N 681 7.00 C 2624 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=0, symmetry=0 Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 895.7 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 4 sheets defined 59.4% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 Proline residue: A 37 - end of helix Processing helix chain 'A' and resid 41 through 51 removed outlier: 4.919A pdb=" N LYS A 45 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 83 removed outlier: 4.143A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 86 through 105 removed outlier: 4.366A pdb=" N PHE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 138 Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 143 through 171 removed outlier: 4.018A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 174 through 193 removed outlier: 4.000A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 193 " --> pdb=" O CYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 279 through 291 removed outlier: 5.729A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N SER A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 320 removed outlier: 4.013A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 323 through 328 Proline residue: A 327 - end of helix No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 331 through 346 removed outlier: 4.186A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 382 removed outlier: 3.912A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 removed outlier: 3.590A pdb=" N THR A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 414 Proline residue: A 406 - end of helix removed outlier: 4.011A pdb=" N ARG A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 448 removed outlier: 3.970A pdb=" N VAL A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 207 through 237 Proline residue: B 211 - end of helix removed outlier: 3.652A pdb=" N THR B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 25 through 33 Processing sheet with id= B, first strand: chain 'B' and resid 95 through 100 removed outlier: 4.067A pdb=" N GLY B 95 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 113 through 117 removed outlier: 8.601A pdb=" N GLU B 114 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR B 199 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE B 116 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG B 201 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 122 through 127 removed outlier: 3.501A pdb=" N ARG B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 804 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: 1.16 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 635 1.29 - 1.42: 1108 1.42 - 1.55: 2307 1.55 - 1.68: 30 1.68 - 1.81: 38 Bond restraints: 4118 Sorted by residual: bond pdb=" C18 G5L A 601 " pdb=" O20 G5L A 601 " ideal model delta sigma weight residual 1.204 1.396 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" C1 G5L A 601 " pdb=" C2 G5L A 601 " ideal model delta sigma weight residual 1.388 1.526 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C3 G5L A 601 " pdb=" C4 G5L A 601 " ideal model delta sigma weight residual 1.388 1.523 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C5 G5L A 601 " pdb=" C6 G5L A 601 " ideal model delta sigma weight residual 1.391 1.524 -0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" C TYR A 113 " pdb=" O TYR A 113 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.19e-02 7.06e+03 4.05e+01 ... (remaining 4113 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.20: 79 105.20 - 112.42: 1959 112.42 - 119.64: 1464 119.64 - 126.86: 2071 126.86 - 134.07: 51 Bond angle restraints: 5624 Sorted by residual: angle pdb=" CA PRO B 91 " pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 111.50 97.98 13.52 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA PRO B 93 " pdb=" N PRO B 93 " pdb=" CD PRO B 93 " ideal model delta sigma weight residual 111.50 99.06 12.44 1.40e+00 5.10e-01 7.90e+01 angle pdb=" CA TYR A 113 " pdb=" C TYR A 113 " pdb=" O TYR A 113 " ideal model delta sigma weight residual 120.42 113.85 6.57 1.06e+00 8.90e-01 3.84e+01 angle pdb=" C TYR A 113 " pdb=" CA TYR A 113 " pdb=" CB TYR A 113 " ideal model delta sigma weight residual 110.85 101.67 9.18 1.70e+00 3.46e-01 2.91e+01 angle pdb=" N ILE B 142 " pdb=" CA ILE B 142 " pdb=" C ILE B 142 " ideal model delta sigma weight residual 108.12 114.95 -6.83 1.34e+00 5.57e-01 2.60e+01 ... (remaining 5619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 2048 15.71 - 31.42: 187 31.42 - 47.13: 74 47.13 - 62.84: 28 62.84 - 78.55: 4 Dihedral angle restraints: 2341 sinusoidal: 679 harmonic: 1662 Sorted by residual: dihedral pdb=" C VAL B 50 " pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual -122.00 -139.05 17.05 0 2.50e+00 1.60e-01 4.65e+01 dihedral pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual 123.40 139.10 -15.70 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" CA ALA A 347 " pdb=" C ALA A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta harmonic sigma weight residual 180.00 149.79 30.21 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 2338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.365: 652 0.365 - 0.730: 7 0.730 - 1.095: 0 1.095 - 1.461: 0 1.461 - 1.826: 2 Chirality restraints: 661 Sorted by residual: chirality pdb=" CG LEU A 374 " pdb=" CB LEU A 374 " pdb=" CD1 LEU A 374 " pdb=" CD2 LEU A 374 " both_signs ideal model delta sigma weight residual False -2.59 -0.76 -1.83 2.00e-01 2.50e+01 8.33e+01 chirality pdb=" CG LEU A 66 " pdb=" CB LEU A 66 " pdb=" CD1 LEU A 66 " pdb=" CD2 LEU A 66 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.60e+01 chirality pdb=" CA GLU B 172 " pdb=" N GLU B 172 " pdb=" C GLU B 172 " pdb=" CB GLU B 172 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.91e+00 ... (remaining 658 not shown) Planarity restraints: 721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 90 " -0.081 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO B 91 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 113 " 0.032 2.00e-02 2.50e+03 2.84e-02 1.61e+01 pdb=" CG TYR A 113 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR A 113 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 113 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 113 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 113 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 113 " -0.040 2.00e-02 2.50e+03 pdb=" OH TYR A 113 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 406 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO A 407 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " 0.030 5.00e-02 4.00e+02 ... (remaining 718 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 31 2.55 - 3.14: 3376 3.14 - 3.73: 6096 3.73 - 4.31: 8379 4.31 - 4.90: 13862 Nonbonded interactions: 31744 Sorted by model distance: nonbonded pdb=" NH1 ARG A 196 " pdb=" O PRO A 197 " model vdw 1.964 2.520 nonbonded pdb=" O TYR A 293 " pdb=" OG SER A 294 " model vdw 2.083 2.440 nonbonded pdb=" O ASN A 107 " pdb=" OG1 THR A 108 " model vdw 2.150 2.440 nonbonded pdb=" O TYR A 140 " pdb=" NH2 ARG A 143 " model vdw 2.215 2.520 nonbonded pdb=" O LEU B 209 " pdb=" N PHE B 212 " model vdw 2.225 2.520 ... (remaining 31739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 3.670 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.450 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 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 : 0.012 0.192 4118 Z= 0.849 Angle : 1.322 13.517 5624 Z= 0.844 Chirality : 0.133 1.826 661 Planarity : 0.007 0.112 721 Dihedral : 16.623 78.549 1285 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.06 % Favored : 90.77 % Rotamer: Outliers : 12.88 % Allowed : 19.02 % Favored : 68.10 % Cbeta Deviations : 1.89 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.69 (0.32), residues: 585 helix: -1.47 (0.26), residues: 348 sheet: 0.29 (0.53), residues: 94 loop : -3.68 (0.39), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 18 HIS 0.005 0.001 HIS A 260 PHE 0.017 0.002 PHE A 332 TYR 0.056 0.003 TYR A 113 ARG 0.006 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 55 time to evaluate : 0.431 Fit side-chains REVERT: A 80 VAL cc_start: 0.8184 (p) cc_final: 0.7946 (m) REVERT: A 87 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7146 (mt) REVERT: A 94 CYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6182 (m) REVERT: A 105 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.6191 (m-10) REVERT: A 107 ASN cc_start: 0.5961 (p0) cc_final: 0.5755 (p0) REVERT: A 137 LYS cc_start: 0.5748 (OUTLIER) cc_final: 0.5019 (tptt) REVERT: A 139 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.5804 (m-10) REVERT: A 273 MET cc_start: 0.6638 (ppp) cc_final: 0.6314 (ppp) REVERT: A 398 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: A 446 ARG cc_start: 0.3800 (OUTLIER) cc_final: 0.3466 (mmp80) outliers start: 42 outliers final: 10 residues processed: 85 average time/residue: 0.8449 time to fit residues: 75.4172 Evaluate side-chains 66 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 49 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 223 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 127 ASN A 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4118 Z= 0.271 Angle : 0.699 7.656 5624 Z= 0.364 Chirality : 0.044 0.152 661 Planarity : 0.007 0.064 721 Dihedral : 8.510 58.988 666 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 9.20 % Allowed : 21.78 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.55 (0.34), residues: 585 helix: -0.58 (0.27), residues: 355 sheet: 0.44 (0.48), residues: 111 loop : -3.48 (0.44), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 424 HIS 0.003 0.001 HIS B 205 PHE 0.013 0.001 PHE A 27 TYR 0.021 0.002 TYR A 445 ARG 0.005 0.001 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 74 time to evaluate : 0.432 Fit side-chains REVERT: A 94 CYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6382 (m) REVERT: A 105 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.6103 (m-10) REVERT: A 139 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.5553 (m-10) REVERT: A 391 VAL cc_start: 0.7882 (p) cc_final: 0.7618 (t) REVERT: A 398 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: B 209 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6286 (pt) outliers start: 30 outliers final: 9 residues processed: 92 average time/residue: 0.6108 time to fit residues: 59.7532 Evaluate side-chains 86 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 30.0000 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 50.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4118 Z= 0.287 Angle : 0.711 7.609 5624 Z= 0.367 Chirality : 0.045 0.154 661 Planarity : 0.006 0.067 721 Dihedral : 8.343 57.620 647 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 10.43 % Allowed : 20.55 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.29 (0.34), residues: 585 helix: -0.30 (0.28), residues: 349 sheet: 0.40 (0.49), residues: 111 loop : -3.39 (0.44), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 424 HIS 0.003 0.001 HIS A 292 PHE 0.013 0.001 PHE B 227 TYR 0.022 0.002 TYR A 445 ARG 0.006 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8211 (t) cc_final: 0.7994 (m) REVERT: A 105 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6272 (m-10) REVERT: A 138 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: A 139 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.5866 (m-80) REVERT: A 141 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5666 (ptpt) REVERT: A 274 PHE cc_start: 0.7067 (m-80) cc_final: 0.6836 (m-80) REVERT: A 302 LEU cc_start: 0.8043 (mt) cc_final: 0.7828 (mm) REVERT: A 313 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7454 (ttt-90) REVERT: A 379 MET cc_start: 0.7776 (tpt) cc_final: 0.7477 (tpt) REVERT: A 391 VAL cc_start: 0.8069 (p) cc_final: 0.7752 (t) REVERT: A 393 LEU cc_start: 0.8033 (mt) cc_final: 0.7811 (mp) REVERT: A 398 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: A 414 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6956 (t0) REVERT: B 206 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6529 (mp) REVERT: B 209 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6406 (pt) REVERT: B 222 LEU cc_start: 0.5677 (OUTLIER) cc_final: 0.5082 (mm) REVERT: B 226 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.5879 (mp) outliers start: 34 outliers final: 12 residues processed: 104 average time/residue: 0.5654 time to fit residues: 62.6839 Evaluate side-chains 104 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4118 Z= 0.224 Angle : 0.661 7.549 5624 Z= 0.334 Chirality : 0.043 0.160 661 Planarity : 0.006 0.066 721 Dihedral : 7.961 57.035 647 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 9.51 % Allowed : 22.09 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.35), residues: 585 helix: 0.25 (0.29), residues: 344 sheet: 0.62 (0.49), residues: 111 loop : -2.80 (0.45), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 PHE 0.019 0.001 PHE A 27 TYR 0.015 0.001 TYR A 445 ARG 0.003 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 82 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 94 CYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6422 (m) REVERT: A 105 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6365 (m-10) REVERT: A 138 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: A 139 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.5954 (m-10) REVERT: A 302 LEU cc_start: 0.7910 (mt) cc_final: 0.7689 (mm) REVERT: A 379 MET cc_start: 0.7738 (tpt) cc_final: 0.7359 (tpt) REVERT: A 391 VAL cc_start: 0.7995 (p) cc_final: 0.7660 (t) REVERT: A 398 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: A 414 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6435 (t0) REVERT: B 206 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6813 (pp) outliers start: 31 outliers final: 12 residues processed: 100 average time/residue: 0.6167 time to fit residues: 65.5292 Evaluate side-chains 99 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 206 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 38 optimal weight: 30.0000 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4118 Z= 0.248 Angle : 0.693 8.882 5624 Z= 0.350 Chirality : 0.044 0.183 661 Planarity : 0.006 0.066 721 Dihedral : 7.997 59.852 647 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 9.20 % Allowed : 21.78 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.35), residues: 585 helix: 0.16 (0.29), residues: 353 sheet: 0.67 (0.50), residues: 111 loop : -2.66 (0.48), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.002 0.001 HIS A 344 PHE 0.011 0.001 PHE A 332 TYR 0.018 0.002 TYR A 445 ARG 0.005 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8165 (t) cc_final: 0.7965 (m) REVERT: A 94 CYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6454 (m) REVERT: A 105 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6373 (m-10) REVERT: A 126 PHE cc_start: 0.6804 (m-10) cc_final: 0.6476 (m-10) REVERT: A 138 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: A 139 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.6077 (m-80) REVERT: A 302 LEU cc_start: 0.8016 (mt) cc_final: 0.7784 (mm) REVERT: A 356 PHE cc_start: 0.6972 (m-80) cc_final: 0.6669 (m-80) REVERT: A 391 VAL cc_start: 0.7996 (p) cc_final: 0.7673 (t) REVERT: A 393 LEU cc_start: 0.8240 (mt) cc_final: 0.7998 (mp) REVERT: A 398 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6225 (mp0) REVERT: A 414 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6609 (t0) REVERT: B 206 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6888 (pp) outliers start: 30 outliers final: 12 residues processed: 105 average time/residue: 0.5824 time to fit residues: 65.0842 Evaluate side-chains 104 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 206 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4118 Z= 0.194 Angle : 0.672 11.800 5624 Z= 0.330 Chirality : 0.042 0.153 661 Planarity : 0.005 0.066 721 Dihedral : 7.379 58.705 647 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.75 % Allowed : 26.99 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.36), residues: 585 helix: 0.50 (0.29), residues: 349 sheet: 0.91 (0.50), residues: 111 loop : -2.40 (0.48), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 174 HIS 0.002 0.000 HIS A 292 PHE 0.020 0.001 PHE A 27 TYR 0.010 0.001 TYR A 445 ARG 0.002 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6432 (m-10) REVERT: A 126 PHE cc_start: 0.6666 (m-10) cc_final: 0.6419 (m-10) REVERT: A 138 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: A 139 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: A 302 LEU cc_start: 0.7873 (mt) cc_final: 0.7653 (mm) REVERT: A 356 PHE cc_start: 0.6894 (m-80) cc_final: 0.6554 (m-80) REVERT: A 391 VAL cc_start: 0.7935 (p) cc_final: 0.7585 (t) REVERT: A 393 LEU cc_start: 0.8191 (mt) cc_final: 0.7944 (mp) REVERT: A 398 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: B 206 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6724 (pp) outliers start: 22 outliers final: 8 residues processed: 99 average time/residue: 0.6291 time to fit residues: 66.0601 Evaluate side-chains 91 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 206 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4118 Z= 0.249 Angle : 0.712 10.118 5624 Z= 0.356 Chirality : 0.045 0.225 661 Planarity : 0.006 0.067 721 Dihedral : 7.075 59.533 642 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.13 % Allowed : 29.45 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.35), residues: 585 helix: 0.25 (0.28), residues: 351 sheet: 0.84 (0.51), residues: 111 loop : -2.49 (0.48), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 174 HIS 0.003 0.001 HIS A 344 PHE 0.010 0.001 PHE A 332 TYR 0.018 0.002 TYR A 445 ARG 0.005 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8182 (t) cc_final: 0.7957 (m) REVERT: A 105 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6474 (m-10) REVERT: A 126 PHE cc_start: 0.6642 (m-10) cc_final: 0.6407 (m-10) REVERT: A 138 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.6991 (m-80) REVERT: A 139 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.6028 (m-80) REVERT: A 302 LEU cc_start: 0.7972 (mt) cc_final: 0.7755 (mm) REVERT: A 356 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: A 391 VAL cc_start: 0.7946 (p) cc_final: 0.7606 (t) REVERT: A 398 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: B 206 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6586 (pp) outliers start: 20 outliers final: 5 residues processed: 92 average time/residue: 0.6418 time to fit residues: 62.6394 Evaluate side-chains 89 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain B residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.0030 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 4118 Z= 0.379 Angle : 0.824 11.971 5624 Z= 0.419 Chirality : 0.049 0.211 661 Planarity : 0.006 0.066 721 Dihedral : 7.613 57.844 642 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 6.44 % Allowed : 31.60 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.93 (0.34), residues: 585 helix: -0.29 (0.28), residues: 349 sheet: 0.85 (0.54), residues: 100 loop : -2.35 (0.46), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 174 HIS 0.005 0.001 HIS A 344 PHE 0.019 0.002 PHE B 227 TYR 0.024 0.002 TYR A 445 ARG 0.006 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.437 Fit side-chains REVERT: A 80 VAL cc_start: 0.8249 (p) cc_final: 0.7846 (m) REVERT: A 105 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6532 (m-10) REVERT: A 126 PHE cc_start: 0.6774 (m-10) cc_final: 0.6501 (m-10) REVERT: A 138 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: A 139 PHE cc_start: 0.6689 (OUTLIER) cc_final: 0.6324 (m-80) REVERT: A 302 LEU cc_start: 0.8010 (mt) cc_final: 0.7807 (mm) REVERT: A 356 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: A 391 VAL cc_start: 0.7967 (p) cc_final: 0.7633 (t) REVERT: A 398 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6148 (mp0) REVERT: B 206 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6977 (pp) outliers start: 21 outliers final: 7 residues processed: 96 average time/residue: 0.5448 time to fit residues: 56.0764 Evaluate side-chains 92 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 50.0000 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 4118 Z= 0.316 Angle : 0.800 13.588 5624 Z= 0.396 Chirality : 0.047 0.214 661 Planarity : 0.006 0.068 721 Dihedral : 7.427 56.756 642 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.44 % Allowed : 31.60 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.91 (0.34), residues: 585 helix: -0.20 (0.28), residues: 349 sheet: 0.52 (0.53), residues: 107 loop : -2.38 (0.47), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 174 HIS 0.003 0.001 HIS A 292 PHE 0.012 0.001 PHE B 227 TYR 0.018 0.002 TYR A 445 ARG 0.005 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.428 Fit side-chains REVERT: A 80 VAL cc_start: 0.8191 (p) cc_final: 0.7834 (m) REVERT: A 94 CYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6511 (m) REVERT: A 105 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6436 (m-10) REVERT: A 126 PHE cc_start: 0.6649 (m-10) cc_final: 0.6386 (m-10) REVERT: A 138 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.6899 (m-80) REVERT: A 139 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: A 141 LYS cc_start: 0.5636 (pmtt) cc_final: 0.4979 (ptpt) REVERT: A 356 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: A 391 VAL cc_start: 0.7957 (p) cc_final: 0.7634 (t) REVERT: A 393 LEU cc_start: 0.8377 (mt) cc_final: 0.8012 (mp) REVERT: A 398 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: B 206 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6859 (pp) outliers start: 21 outliers final: 11 residues processed: 90 average time/residue: 0.6028 time to fit residues: 58.2138 Evaluate side-chains 95 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.0570 chunk 6 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4118 Z= 0.205 Angle : 0.737 14.502 5624 Z= 0.353 Chirality : 0.043 0.249 661 Planarity : 0.005 0.070 721 Dihedral : 6.803 56.842 642 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.21 % Allowed : 31.90 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.35), residues: 585 helix: 0.19 (0.29), residues: 352 sheet: 0.86 (0.52), residues: 106 loop : -2.48 (0.47), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 174 HIS 0.005 0.001 HIS A 292 PHE 0.022 0.001 PHE A 27 TYR 0.010 0.001 TYR A 70 ARG 0.003 0.000 ARG B 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.410 Fit side-chains REVERT: A 94 CYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6544 (m) REVERT: A 105 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6529 (m-10) REVERT: A 138 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: A 139 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: A 141 LYS cc_start: 0.5294 (pmtt) cc_final: 0.4837 (pttm) REVERT: A 356 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6489 (m-10) REVERT: A 391 VAL cc_start: 0.7886 (p) cc_final: 0.7547 (t) outliers start: 17 outliers final: 6 residues processed: 88 average time/residue: 0.5610 time to fit residues: 52.7942 Evaluate side-chains 83 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 50.0000 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.234966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.206981 restraints weight = 4774.476| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.11 r_work: 0.4302 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4195 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4118 Z= 0.214 Angle : 0.730 13.795 5624 Z= 0.355 Chirality : 0.044 0.234 661 Planarity : 0.006 0.069 721 Dihedral : 5.755 48.330 637 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.29 % Allowed : 34.66 % Favored : 61.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.35), residues: 585 helix: 0.24 (0.29), residues: 348 sheet: 0.92 (0.53), residues: 106 loop : -2.27 (0.47), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.004 0.001 HIS A 292 PHE 0.035 0.002 PHE A 307 TYR 0.013 0.001 TYR A 70 ARG 0.005 0.001 ARG A 411 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1799.17 seconds wall clock time: 33 minutes 22.86 seconds (2002.86 seconds total)