Starting phenix.real_space_refine on Fri Apr 5 13:50:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/04_2024/8xv5_38692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/04_2024/8xv5_38692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/04_2024/8xv5_38692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/04_2024/8xv5_38692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/04_2024/8xv5_38692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/04_2024/8xv5_38692_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.016 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 16 5.16 5 C 2108 2.51 5 N 468 2.21 5 O 530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 456": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3122 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3110 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'PXM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.73 Number of scatterers: 3122 At special positions: 0 Unit cell: (70.72, 61.36, 79.04, 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 16 16.00 O 530 8.00 N 468 7.00 C 2108 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: 1.12 Conformation dependent library (CDL) restraints added in 566.0 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 33 through 39 removed outlier: 4.586A pdb=" N ILE A 36 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Proline residue: A 37 - end of helix No H-bonds generated for 'chain 'A' and resid 33 through 39' Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 56 through 74 removed outlier: 5.097A pdb=" N VAL A 65 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU A 66 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 68 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 80 through 98 Processing helix chain 'A' and resid 103 through 124 removed outlier: 3.796A pdb=" N GLN A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 130 No H-bonds generated for 'chain 'A' and resid 127 through 130' Processing helix chain 'A' and resid 136 through 162 removed outlier: 3.578A pdb=" N SER A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 188 Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 277 through 306 removed outlier: 5.490A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 336 removed outlier: 3.753A pdb=" N TYR A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 348 through 365 Processing helix chain 'A' and resid 369 through 394 Processing helix chain 'A' and resid 400 through 425 removed outlier: 3.536A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 458 removed outlier: 3.830A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 884 1.34 - 1.46: 790 1.46 - 1.58: 1516 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3218 Sorted by residual: bond pdb=" C3 PXM A 501 " pdb=" O3 PXM A 501 " ideal model delta sigma weight residual 1.340 1.397 -0.057 2.00e-02 2.50e+03 8.09e+00 bond pdb=" C PHE A 56 " pdb=" N PRO A 57 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.19e-02 7.06e+03 2.36e+00 bond pdb=" C2 PXM A 501 " pdb=" C2A PXM A 501 " ideal model delta sigma weight residual 1.498 1.528 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" CB PRO A 57 " pdb=" CG PRO A 57 " ideal model delta sigma weight residual 1.492 1.425 0.067 5.00e-02 4.00e+02 1.78e+00 bond pdb=" CA PHE A 56 " pdb=" C PHE A 56 " ideal model delta sigma weight residual 1.522 1.535 -0.014 1.26e-02 6.30e+03 1.15e+00 ... (remaining 3213 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.81: 86 106.81 - 113.63: 1729 113.63 - 120.45: 1385 120.45 - 127.27: 1163 127.27 - 134.09: 33 Bond angle restraints: 4396 Sorted by residual: angle pdb=" CA ILE A 36 " pdb=" C ILE A 36 " pdb=" N PRO A 37 " ideal model delta sigma weight residual 118.88 123.91 -5.03 1.54e+00 4.22e-01 1.07e+01 angle pdb=" CG1 ILE A 36 " pdb=" CB ILE A 36 " pdb=" CG2 ILE A 36 " ideal model delta sigma weight residual 110.70 101.83 8.87 3.00e+00 1.11e-01 8.75e+00 angle pdb=" N PHE A 56 " pdb=" CA PHE A 56 " pdb=" C PHE A 56 " ideal model delta sigma weight residual 113.16 117.22 -4.06 1.42e+00 4.96e-01 8.16e+00 angle pdb=" CA LEU A 415 " pdb=" CB LEU A 415 " pdb=" CG LEU A 415 " ideal model delta sigma weight residual 116.30 106.60 9.70 3.50e+00 8.16e-02 7.67e+00 angle pdb=" CA PRO A 37 " pdb=" N PRO A 37 " pdb=" CD PRO A 37 " ideal model delta sigma weight residual 112.00 108.19 3.81 1.40e+00 5.10e-01 7.42e+00 ... (remaining 4391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 1742 16.59 - 33.17: 61 33.17 - 49.76: 15 49.76 - 66.35: 0 66.35 - 82.93: 1 Dihedral angle restraints: 1819 sinusoidal: 667 harmonic: 1152 Sorted by residual: dihedral pdb=" CA VAL A 425 " pdb=" C VAL A 425 " pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta harmonic sigma weight residual -180.00 -157.58 -22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TYR A 142 " pdb=" C TYR A 142 " pdb=" N CYS A 143 " pdb=" CA CYS A 143 " ideal model delta harmonic sigma weight residual 180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 1816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 297 0.041 - 0.081: 150 0.081 - 0.122: 40 0.122 - 0.162: 11 0.162 - 0.203: 4 Chirality restraints: 502 Sorted by residual: chirality pdb=" CA TRP A 94 " pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CB TRP A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PHE A 56 " pdb=" N PHE A 56 " pdb=" C PHE A 56 " pdb=" CB PHE A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CA LYS A 80 " pdb=" N LYS A 80 " pdb=" C LYS A 80 " pdb=" CB LYS A 80 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 499 not shown) Planarity restraints: 527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 63 " 0.014 2.00e-02 2.50e+03 1.94e-02 7.56e+00 pdb=" CG TYR A 63 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 63 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 63 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 63 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 63 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 63 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 63 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 61 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C TYR A 61 " 0.043 2.00e-02 2.50e+03 pdb=" O TYR A 61 " -0.016 2.00e-02 2.50e+03 pdb=" N SER A 62 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 373 " 0.016 2.00e-02 2.50e+03 1.54e-02 4.74e+00 pdb=" CG TYR A 373 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 373 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 373 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 373 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 373 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 373 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 373 " -0.001 2.00e-02 2.50e+03 ... (remaining 524 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 903 2.80 - 3.33: 2968 3.33 - 3.85: 5288 3.85 - 4.38: 5975 4.38 - 4.90: 10248 Nonbonded interactions: 25382 Sorted by model distance: nonbonded pdb=" O ARG A 144 " pdb=" OG1 THR A 147 " model vdw 2.280 2.440 nonbonded pdb=" O LYS A 270 " pdb=" OG SER A 274 " model vdw 2.302 2.440 nonbonded pdb=" OE1 GLN A 294 " pdb=" OH TYR A 442 " model vdw 2.304 2.440 nonbonded pdb=" OH TYR A 151 " pdb=" OE2 GLU A 320 " model vdw 2.321 2.440 nonbonded pdb=" OH TYR A 61 " pdb=" OD2 ASP A 427 " model vdw 2.330 2.440 ... (remaining 25377 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 group one per residue 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: 0.790 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: 3.400 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 : 0.005 0.067 3218 Z= 0.335 Angle : 0.901 9.695 4396 Z= 0.482 Chirality : 0.053 0.203 502 Planarity : 0.008 0.054 527 Dihedral : 9.695 82.934 1083 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.33), residues: 384 helix: -2.04 (0.22), residues: 295 sheet: None (None), residues: 0 loop : -3.11 (0.60), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 94 HIS 0.003 0.001 HIS A 200 PHE 0.030 0.002 PHE A 439 TYR 0.046 0.003 TYR A 63 ARG 0.005 0.001 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 48 SER cc_start: 0.7409 (m) cc_final: 0.7182 (t) REVERT: A 52 THR cc_start: 0.7688 (m) cc_final: 0.7060 (p) REVERT: A 61 TYR cc_start: 0.6986 (m-10) cc_final: 0.6722 (m-10) REVERT: A 77 VAL cc_start: 0.7409 (m) cc_final: 0.7055 (p) REVERT: A 103 VAL cc_start: 0.8060 (m) cc_final: 0.7683 (t) REVERT: A 113 TYR cc_start: 0.7317 (t80) cc_final: 0.6984 (t80) REVERT: A 127 ILE cc_start: 0.8370 (mt) cc_final: 0.8159 (mt) REVERT: A 148 LEU cc_start: 0.8171 (mt) cc_final: 0.7943 (mm) REVERT: A 197 MET cc_start: 0.7178 (ttp) cc_final: 0.6370 (ttp) REVERT: A 198 PHE cc_start: 0.6933 (m-80) cc_final: 0.6537 (m-80) REVERT: A 319 VAL cc_start: 0.7907 (t) cc_final: 0.7576 (t) REVERT: A 325 PHE cc_start: 0.7773 (t80) cc_final: 0.7543 (t80) REVERT: A 362 LEU cc_start: 0.7408 (tp) cc_final: 0.7182 (tp) REVERT: A 373 TYR cc_start: 0.7509 (m-80) cc_final: 0.7296 (m-10) REVERT: A 399 ASN cc_start: 0.6986 (m-40) cc_final: 0.6662 (m-40) REVERT: A 455 MET cc_start: 0.5552 (mmm) cc_final: 0.5269 (mmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1040 time to fit residues: 16.8697 Evaluate side-chains 101 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 159 GLN A 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3218 Z= 0.250 Angle : 0.605 6.228 4396 Z= 0.317 Chirality : 0.041 0.146 502 Planarity : 0.005 0.040 527 Dihedral : 5.835 67.346 426 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.60 % Allowed : 7.51 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.40), residues: 384 helix: -0.27 (0.27), residues: 305 sheet: None (None), residues: 0 loop : -2.29 (0.70), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 94 HIS 0.005 0.002 HIS A 364 PHE 0.014 0.001 PHE A 99 TYR 0.022 0.002 TYR A 63 ARG 0.002 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.7639 (tmm) cc_final: 0.7326 (tmm) REVERT: A 61 TYR cc_start: 0.7220 (m-10) cc_final: 0.6886 (m-10) REVERT: A 92 ILE cc_start: 0.8020 (mt) cc_final: 0.7816 (mm) REVERT: A 113 TYR cc_start: 0.7321 (t80) cc_final: 0.7029 (t80) REVERT: A 161 LEU cc_start: 0.8159 (tp) cc_final: 0.7715 (tt) REVERT: A 167 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6891 (tmm) REVERT: A 197 MET cc_start: 0.7008 (ttp) cc_final: 0.6604 (ttp) REVERT: A 198 PHE cc_start: 0.6895 (m-80) cc_final: 0.6635 (m-80) REVERT: A 362 LEU cc_start: 0.7442 (tp) cc_final: 0.7199 (tp) REVERT: A 363 MET cc_start: 0.7313 (mtt) cc_final: 0.7091 (mtp) REVERT: A 389 ILE cc_start: 0.8456 (mt) cc_final: 0.8098 (mm) REVERT: A 399 ASN cc_start: 0.6996 (m-40) cc_final: 0.6694 (m-40) REVERT: A 416 VAL cc_start: 0.8117 (t) cc_final: 0.7891 (p) REVERT: A 420 ILE cc_start: 0.8232 (mt) cc_final: 0.7921 (mm) REVERT: A 428 GLN cc_start: 0.7145 (tt0) cc_final: 0.6891 (tt0) REVERT: A 455 MET cc_start: 0.5875 (mmm) cc_final: 0.5542 (mmm) outliers start: 12 outliers final: 7 residues processed: 116 average time/residue: 0.1040 time to fit residues: 15.6751 Evaluate side-chains 106 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 30 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 GLN A 310 GLN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3218 Z= 0.199 Angle : 0.568 6.709 4396 Z= 0.293 Chirality : 0.039 0.136 502 Planarity : 0.004 0.031 527 Dihedral : 5.560 67.346 426 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.90 % Allowed : 12.01 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.42), residues: 384 helix: 0.63 (0.29), residues: 302 sheet: None (None), residues: 0 loop : -2.19 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.006 0.002 HIS A 364 PHE 0.015 0.001 PHE A 99 TYR 0.018 0.001 TYR A 445 ARG 0.003 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.7702 (tmm) cc_final: 0.7346 (tmm) REVERT: A 113 TYR cc_start: 0.7280 (t80) cc_final: 0.6986 (t80) REVERT: A 124 TYR cc_start: 0.7098 (m-80) cc_final: 0.6433 (m-80) REVERT: A 151 TYR cc_start: 0.7153 (t80) cc_final: 0.6875 (t80) REVERT: A 161 LEU cc_start: 0.8031 (tp) cc_final: 0.7515 (tt) REVERT: A 167 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6784 (tmm) REVERT: A 197 MET cc_start: 0.7021 (ttp) cc_final: 0.6632 (ttp) REVERT: A 362 LEU cc_start: 0.7376 (tp) cc_final: 0.7138 (tp) REVERT: A 363 MET cc_start: 0.7295 (mtt) cc_final: 0.7073 (mtp) REVERT: A 389 ILE cc_start: 0.8411 (mt) cc_final: 0.8002 (mm) REVERT: A 397 ASN cc_start: 0.8238 (t0) cc_final: 0.8030 (t0) REVERT: A 399 ASN cc_start: 0.6979 (m-40) cc_final: 0.6632 (m-40) REVERT: A 428 GLN cc_start: 0.7138 (tt0) cc_final: 0.6862 (tt0) REVERT: A 455 MET cc_start: 0.5977 (mmm) cc_final: 0.5660 (mmm) outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 0.0958 time to fit residues: 13.0970 Evaluate side-chains 104 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 20 optimal weight: 0.0570 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3218 Z= 0.171 Angle : 0.536 5.771 4396 Z= 0.277 Chirality : 0.039 0.174 502 Planarity : 0.003 0.027 527 Dihedral : 5.469 68.351 426 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.20 % Allowed : 13.21 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.43), residues: 384 helix: 1.07 (0.29), residues: 302 sheet: None (None), residues: 0 loop : -2.01 (0.70), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 PHE 0.012 0.001 PHE A 198 TYR 0.016 0.001 TYR A 445 ARG 0.003 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.7677 (tmm) cc_final: 0.7331 (tmm) REVERT: A 113 TYR cc_start: 0.7253 (t80) cc_final: 0.6915 (t80) REVERT: A 124 TYR cc_start: 0.7065 (m-80) cc_final: 0.6380 (m-80) REVERT: A 151 TYR cc_start: 0.7178 (t80) cc_final: 0.6934 (t80) REVERT: A 161 LEU cc_start: 0.7862 (tp) cc_final: 0.7433 (tt) REVERT: A 167 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6654 (tmm) REVERT: A 280 TYR cc_start: 0.7083 (m-80) cc_final: 0.6737 (m-80) REVERT: A 362 LEU cc_start: 0.7369 (tp) cc_final: 0.7124 (tp) REVERT: A 363 MET cc_start: 0.7273 (mtt) cc_final: 0.7031 (mtp) REVERT: A 389 ILE cc_start: 0.8394 (mt) cc_final: 0.7939 (mm) REVERT: A 397 ASN cc_start: 0.8241 (t0) cc_final: 0.8029 (t0) REVERT: A 399 ASN cc_start: 0.6907 (m-40) cc_final: 0.6566 (m-40) REVERT: A 455 MET cc_start: 0.5968 (mmm) cc_final: 0.5718 (mmm) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 0.0955 time to fit residues: 13.4665 Evaluate side-chains 105 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3218 Z= 0.217 Angle : 0.558 5.627 4396 Z= 0.289 Chirality : 0.041 0.179 502 Planarity : 0.003 0.025 527 Dihedral : 5.474 68.310 426 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.20 % Allowed : 15.02 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.43), residues: 384 helix: 1.15 (0.29), residues: 303 sheet: None (None), residues: 0 loop : -1.86 (0.72), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.021 0.001 PHE A 198 TYR 0.016 0.001 TYR A 445 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.302 Fit side-chains REVERT: A 28 MET cc_start: 0.7625 (tmm) cc_final: 0.7183 (tmm) REVERT: A 40 SER cc_start: 0.7241 (p) cc_final: 0.6825 (t) REVERT: A 113 TYR cc_start: 0.7271 (t80) cc_final: 0.6968 (t80) REVERT: A 124 TYR cc_start: 0.7116 (m-80) cc_final: 0.6414 (m-80) REVERT: A 145 SER cc_start: 0.8421 (m) cc_final: 0.7965 (t) REVERT: A 151 TYR cc_start: 0.7189 (t80) cc_final: 0.6987 (t80) REVERT: A 167 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6739 (tmm) REVERT: A 280 TYR cc_start: 0.7101 (m-80) cc_final: 0.6789 (m-80) REVERT: A 362 LEU cc_start: 0.7399 (tp) cc_final: 0.7152 (tp) REVERT: A 363 MET cc_start: 0.7321 (mtt) cc_final: 0.7039 (mtp) REVERT: A 389 ILE cc_start: 0.8431 (mt) cc_final: 0.7989 (mm) REVERT: A 397 ASN cc_start: 0.8262 (t0) cc_final: 0.8059 (t0) REVERT: A 399 ASN cc_start: 0.6924 (m-40) cc_final: 0.6590 (m-40) REVERT: A 455 MET cc_start: 0.6066 (mmm) cc_final: 0.5847 (mmm) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.0948 time to fit residues: 13.0654 Evaluate side-chains 107 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.0010 chunk 36 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.0370 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 overall best weight: 0.0578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3218 Z= 0.129 Angle : 0.515 8.838 4396 Z= 0.262 Chirality : 0.038 0.177 502 Planarity : 0.003 0.025 527 Dihedral : 5.351 70.442 426 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.60 % Allowed : 16.52 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.43), residues: 384 helix: 1.54 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -1.58 (0.70), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.017 0.001 PHE A 198 TYR 0.016 0.001 TYR A 383 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.7666 (tmm) cc_final: 0.7369 (tmm) REVERT: A 107 GLN cc_start: 0.7392 (mt0) cc_final: 0.7071 (mt0) REVERT: A 124 TYR cc_start: 0.6931 (m-80) cc_final: 0.6247 (m-80) REVERT: A 359 SER cc_start: 0.7052 (m) cc_final: 0.6734 (p) REVERT: A 363 MET cc_start: 0.7219 (mtt) cc_final: 0.6943 (mtp) REVERT: A 397 ASN cc_start: 0.8251 (t0) cc_final: 0.8048 (t0) REVERT: A 399 ASN cc_start: 0.6850 (m-40) cc_final: 0.6443 (m-40) REVERT: A 455 MET cc_start: 0.6038 (mmm) cc_final: 0.5820 (mmm) outliers start: 12 outliers final: 9 residues processed: 99 average time/residue: 0.1102 time to fit residues: 14.0885 Evaluate side-chains 103 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 3218 Z= 0.302 Angle : 0.648 9.314 4396 Z= 0.330 Chirality : 0.044 0.205 502 Planarity : 0.004 0.038 527 Dihedral : 5.501 68.382 426 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.80 % Allowed : 16.52 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.43), residues: 384 helix: 1.22 (0.29), residues: 303 sheet: None (None), residues: 0 loop : -1.83 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.006 0.002 HIS A 364 PHE 0.019 0.002 PHE A 198 TYR 0.018 0.002 TYR A 445 ARG 0.007 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.346 Fit side-chains REVERT: A 18 ILE cc_start: 0.7345 (mm) cc_final: 0.7054 (tp) REVERT: A 28 MET cc_start: 0.7574 (tmm) cc_final: 0.7331 (tmm) REVERT: A 40 SER cc_start: 0.7370 (p) cc_final: 0.6964 (t) REVERT: A 113 TYR cc_start: 0.7337 (t80) cc_final: 0.7035 (t80) REVERT: A 124 TYR cc_start: 0.7156 (m-80) cc_final: 0.6505 (m-80) REVERT: A 145 SER cc_start: 0.8422 (m) cc_final: 0.7987 (t) REVERT: A 280 TYR cc_start: 0.7170 (m-80) cc_final: 0.6859 (m-80) REVERT: A 363 MET cc_start: 0.7283 (mtt) cc_final: 0.7068 (mtp) REVERT: A 393 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7501 (mt0) REVERT: A 399 ASN cc_start: 0.6924 (m-40) cc_final: 0.6603 (m-40) outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.0960 time to fit residues: 13.2634 Evaluate side-chains 104 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0870 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3218 Z= 0.203 Angle : 0.601 9.447 4396 Z= 0.299 Chirality : 0.041 0.199 502 Planarity : 0.004 0.037 527 Dihedral : 5.415 68.669 426 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.90 % Allowed : 18.32 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.43), residues: 384 helix: 1.38 (0.29), residues: 303 sheet: None (None), residues: 0 loop : -1.80 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.005 0.002 HIS A 364 PHE 0.020 0.001 PHE A 279 TYR 0.016 0.001 TYR A 445 ARG 0.007 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.347 Fit side-chains REVERT: A 28 MET cc_start: 0.7591 (tmm) cc_final: 0.7378 (tmm) REVERT: A 89 SER cc_start: 0.8009 (m) cc_final: 0.7788 (p) REVERT: A 113 TYR cc_start: 0.7261 (t80) cc_final: 0.6987 (t80) REVERT: A 124 TYR cc_start: 0.7109 (m-80) cc_final: 0.6425 (m-80) REVERT: A 145 SER cc_start: 0.8391 (m) cc_final: 0.7974 (t) REVERT: A 280 TYR cc_start: 0.7092 (m-80) cc_final: 0.6795 (m-80) REVERT: A 363 MET cc_start: 0.7281 (mtt) cc_final: 0.7039 (mtp) REVERT: A 393 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7537 (mt0) REVERT: A 399 ASN cc_start: 0.6949 (m-40) cc_final: 0.6665 (m-40) outliers start: 13 outliers final: 12 residues processed: 102 average time/residue: 0.0994 time to fit residues: 13.3768 Evaluate side-chains 103 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 0.0020 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 18 optimal weight: 0.0040 overall best weight: 0.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN A 393 GLN A 397 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3218 Z= 0.149 Angle : 0.596 10.751 4396 Z= 0.289 Chirality : 0.039 0.193 502 Planarity : 0.004 0.036 527 Dihedral : 5.378 70.204 426 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.60 % Allowed : 19.52 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.43), residues: 384 helix: 1.55 (0.30), residues: 300 sheet: None (None), residues: 0 loop : -1.62 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.005 0.001 HIS A 364 PHE 0.019 0.001 PHE A 279 TYR 0.016 0.001 TYR A 445 ARG 0.008 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.347 Fit side-chains REVERT: A 28 MET cc_start: 0.7627 (tmm) cc_final: 0.7198 (tmm) REVERT: A 86 GLN cc_start: 0.7859 (tt0) cc_final: 0.7652 (tt0) REVERT: A 89 SER cc_start: 0.7899 (m) cc_final: 0.7690 (p) REVERT: A 113 TYR cc_start: 0.7190 (t80) cc_final: 0.6933 (t80) REVERT: A 124 TYR cc_start: 0.7030 (m-80) cc_final: 0.6328 (m-80) REVERT: A 145 SER cc_start: 0.8363 (m) cc_final: 0.7931 (t) REVERT: A 359 SER cc_start: 0.7087 (m) cc_final: 0.6749 (p) REVERT: A 363 MET cc_start: 0.7205 (mtt) cc_final: 0.6946 (mtp) REVERT: A 393 GLN cc_start: 0.8089 (mm110) cc_final: 0.7542 (mt0) REVERT: A 399 ASN cc_start: 0.6885 (m-40) cc_final: 0.6567 (m-40) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.1019 time to fit residues: 13.2766 Evaluate side-chains 98 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 4 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3218 Z= 0.220 Angle : 0.649 11.501 4396 Z= 0.315 Chirality : 0.043 0.225 502 Planarity : 0.004 0.037 527 Dihedral : 5.414 69.687 426 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.00 % Allowed : 20.72 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.43), residues: 384 helix: 1.49 (0.29), residues: 302 sheet: None (None), residues: 0 loop : -1.78 (0.70), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 94 HIS 0.005 0.002 HIS A 364 PHE 0.024 0.002 PHE A 439 TYR 0.022 0.001 TYR A 79 ARG 0.008 0.001 ARG A 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.337 Fit side-chains REVERT: A 18 ILE cc_start: 0.7317 (mm) cc_final: 0.7026 (tp) REVERT: A 28 MET cc_start: 0.7576 (tmm) cc_final: 0.7374 (tmm) REVERT: A 61 TYR cc_start: 0.7079 (m-10) cc_final: 0.6781 (m-10) REVERT: A 89 SER cc_start: 0.7970 (m) cc_final: 0.7704 (p) REVERT: A 113 TYR cc_start: 0.7263 (t80) cc_final: 0.6985 (t80) REVERT: A 124 TYR cc_start: 0.7095 (m-80) cc_final: 0.6425 (m-80) REVERT: A 145 SER cc_start: 0.8383 (m) cc_final: 0.7950 (t) REVERT: A 280 TYR cc_start: 0.7063 (m-80) cc_final: 0.6776 (m-80) REVERT: A 359 SER cc_start: 0.7152 (m) cc_final: 0.6819 (p) REVERT: A 363 MET cc_start: 0.7213 (mtt) cc_final: 0.6974 (mtp) REVERT: A 399 ASN cc_start: 0.6930 (m-40) cc_final: 0.6607 (m-40) outliers start: 10 outliers final: 10 residues processed: 97 average time/residue: 0.1057 time to fit residues: 13.5587 Evaluate side-chains 100 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107156 restraints weight = 5301.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110112 restraints weight = 2503.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112103 restraints weight = 1422.398| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.413 3218 Z= 0.684 Angle : 1.379 65.900 4396 Z= 0.829 Chirality : 0.049 0.542 502 Planarity : 0.010 0.219 527 Dihedral : 5.412 69.688 426 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.00 % Allowed : 21.02 % Favored : 75.98 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.43), residues: 384 helix: 1.49 (0.29), residues: 302 sheet: None (None), residues: 0 loop : -1.78 (0.70), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 PHE 0.026 0.002 PHE A 439 TYR 0.021 0.002 TYR A 79 ARG 0.006 0.000 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1201.17 seconds wall clock time: 22 minutes 26.75 seconds (1346.75 seconds total)