Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:10:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/11_2022/7cko_30389_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/11_2022/7cko_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_30389/11_2022/7cko_30389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/11_2022/7cko_30389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/11_2022/7cko_30389_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cko_30389/11_2022/7cko_30389_updated.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 2.91, per 1000 atoms: 0.72 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: 1.60 Conformation dependent library (CDL) restraints added in 937.4 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: 0.56 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: 1.26 Time building geometry restraints manager: 1.76 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: 2046 15.71 - 31.42: 187 31.42 - 47.13: 74 47.13 - 62.84: 28 62.84 - 78.55: 4 Dihedral angle restraints: 2339 sinusoidal: 677 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 2336 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 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. 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.780 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 16.580 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 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 : 16.636 78.549 1283 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.06 % Favored : 90.77 % Rotamer Outliers : 12.88 % 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 *********************** 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 : 0.414 Fit side-chains outliers start: 42 outliers final: 10 residues processed: 85 average time/residue: 0.7722 time to fit residues: 68.9863 Evaluate side-chains 57 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 0.1199 time to fit residues: 1.0662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 4118 Z= 0.243 Angle : 0.688 7.428 5624 Z= 0.354 Chirality : 0.043 0.206 661 Planarity : 0.006 0.065 721 Dihedral : 4.836 26.440 628 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 9.20 % 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: -1.37 (0.34), residues: 585 helix: -0.46 (0.28), residues: 355 sheet: 0.59 (0.49), residues: 111 loop : -3.44 (0.45), residues: 119 *********************** 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 105 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 75 time to evaluate : 0.426 Fit side-chains outliers start: 30 outliers final: 12 residues processed: 91 average time/residue: 0.5804 time to fit residues: 56.3944 Evaluate side-chains 84 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.5755 time to fit residues: 3.0696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 50.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.6547 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 4118 Z= 0.417 Angle : 0.808 9.277 5624 Z= 0.424 Chirality : 0.050 0.282 661 Planarity : 0.007 0.066 721 Dihedral : 5.574 30.532 628 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 9.51 % 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: -1.60 (0.33), residues: 585 helix: -0.65 (0.27), residues: 349 sheet: 0.56 (0.51), residues: 102 loop : -3.17 (0.42), residues: 134 *********************** 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 108 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 77 time to evaluate : 0.437 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 98 average time/residue: 0.4636 time to fit residues: 49.3074 Evaluate side-chains 89 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 3 average time/residue: 0.0762 time to fit residues: 0.9425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4118 Z= 0.213 Angle : 0.685 8.472 5624 Z= 0.343 Chirality : 0.044 0.222 661 Planarity : 0.006 0.067 721 Dihedral : 4.966 31.192 628 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 8.59 % 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: -0.73 (0.35), residues: 585 helix: 0.04 (0.29), residues: 352 sheet: 0.58 (0.49), residues: 111 loop : -2.79 (0.48), residues: 122 *********************** 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 109 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 0.453 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 100 average time/residue: 0.5369 time to fit residues: 57.5488 Evaluate side-chains 94 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.0527 time to fit residues: 0.8480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 50.0000 chunk 23 optimal weight: 0.2980 chunk 47 optimal weight: 20.0000 chunk 38 optimal weight: 40.0000 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.4905 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= 0.232 Angle : 0.702 8.506 5624 Z= 0.347 Chirality : 0.044 0.184 661 Planarity : 0.006 0.067 721 Dihedral : 4.910 34.125 628 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 9.82 % 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: -0.51 (0.35), residues: 585 helix: 0.15 (0.29), residues: 354 sheet: 0.75 (0.50), residues: 111 loop : -2.62 (0.49), residues: 120 *********************** 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 113 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 81 time to evaluate : 0.443 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 103 average time/residue: 0.5508 time to fit residues: 60.6087 Evaluate side-chains 91 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.431 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.0387 time to fit residues: 0.7369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 50.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.6443 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 4118 Z= 0.257 Angle : 0.749 12.753 5624 Z= 0.366 Chirality : 0.045 0.194 661 Planarity : 0.006 0.066 721 Dihedral : 4.954 34.542 628 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 7.36 % 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: -0.46 (0.35), residues: 585 helix: 0.20 (0.29), residues: 350 sheet: 0.85 (0.51), residues: 109 loop : -2.61 (0.47), residues: 126 *********************** 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 102 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 0.370 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 96 average time/residue: 0.5272 time to fit residues: 54.1315 Evaluate side-chains 90 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.0368 time to fit residues: 0.6961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 50.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4118 Z= 0.220 Angle : 0.730 12.960 5624 Z= 0.350 Chirality : 0.044 0.180 661 Planarity : 0.005 0.067 721 Dihedral : 4.719 34.613 628 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 6.75 % 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: -0.38 (0.35), residues: 585 helix: 0.28 (0.29), residues: 348 sheet: 0.95 (0.50), residues: 110 loop : -2.67 (0.47), residues: 127 *********************** 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 98 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.430 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 92 average time/residue: 0.5032 time to fit residues: 49.8658 Evaluate side-chains 87 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.0570 time to fit residues: 1.0432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- 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: 0.6505 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 4118 Z= 0.316 Angle : 0.809 13.615 5624 Z= 0.396 Chirality : 0.047 0.175 661 Planarity : 0.006 0.066 721 Dihedral : 5.183 32.250 628 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 6.13 % 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: -0.64 (0.35), residues: 585 helix: -0.03 (0.29), residues: 350 sheet: 0.87 (0.54), residues: 107 loop : -2.42 (0.47), residues: 128 *********************** 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 96 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.423 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 91 average time/residue: 0.5784 time to fit residues: 56.2466 Evaluate side-chains 89 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.0397 time to fit residues: 0.8279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 0.0070 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 50.0000 chunk 57 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- 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: 0.6487 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 4118 Z= 0.288 Angle : 0.796 13.697 5624 Z= 0.388 Chirality : 0.046 0.173 661 Planarity : 0.006 0.067 721 Dihedral : 5.021 33.388 628 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 5.21 % 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: -0.72 (0.35), residues: 585 helix: -0.06 (0.29), residues: 350 sheet: 0.73 (0.53), residues: 107 loop : -2.43 (0.48), residues: 128 *********************** 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 93 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.435 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 88 average time/residue: 0.4965 time to fit residues: 47.3187 Evaluate side-chains 84 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0394 time to fit residues: 0.6750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 42 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.6416 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4118 Z= 0.218 Angle : 0.761 13.300 5624 Z= 0.363 Chirality : 0.044 0.178 661 Planarity : 0.005 0.068 721 Dihedral : 4.804 33.534 628 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 4.91 % 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: -0.48 (0.36), residues: 585 helix: 0.14 (0.29), residues: 349 sheet: 0.91 (0.53), residues: 106 loop : -2.43 (0.47), residues: 130 ********************** 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 92 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.453 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 90 average time/residue: 0.5507 time to fit residues: 53.0627 Evaluate side-chains 84 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0431 time to fit residues: 0.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 40 optimal weight: 30.0000 chunk 2 optimal weight: 0.0050 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 50.0000 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 overall best weight: 0.5732 ------------------------------------------------------------------------------- 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** A 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.236467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.208094 restraints weight = 4767.043| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.12 r_work: 0.4354 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4345 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.4336 rms_B_bonded: 2.00 restraints_weight: 0.1250 r_work: 0.4326 rms_B_bonded: 2.08 restraints_weight: 0.0625 r_work: 0.4316 rms_B_bonded: 2.21 restraints_weight: 0.0312 r_work: 0.4304 rms_B_bonded: 2.37 restraints_weight: 0.0156 r_work: 0.4292 rms_B_bonded: 2.57 restraints_weight: 0.0078 r_work: 0.4278 rms_B_bonded: 2.80 restraints_weight: 0.0039 r_work: 0.4262 rms_B_bonded: 3.09 restraints_weight: 0.0020 r_work: 0.4245 rms_B_bonded: 3.42 restraints_weight: 0.0010 r_work: 0.4226 rms_B_bonded: 3.82 restraints_weight: 0.0005 r_work: 0.4204 rms_B_bonded: 4.28 restraints_weight: 0.0002 r_work: 0.4180 rms_B_bonded: 4.81 restraints_weight: 0.0001 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.5794 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= 0.211 Angle : 0.755 12.941 5624 Z= 0.360 Chirality : 0.044 0.174 661 Planarity : 0.005 0.070 721 Dihedral : 4.641 32.496 628 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 3.99 % 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: -0.27 (0.35), residues: 585 helix: 0.28 (0.29), residues: 348 sheet: 1.02 (0.53), residues: 106 loop : -2.26 (0.47), residues: 131 =============================================================================== Job complete usr+sys time: 1541.87 seconds wall clock time: 28 minutes 34.45 seconds (1714.45 seconds total)