Starting phenix.real_space_refine on Mon Jun 24 16:08:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/06_2024/8znb_60266_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/06_2024/8znb_60266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/06_2024/8znb_60266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/06_2024/8znb_60266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/06_2024/8znb_60266_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/06_2024/8znb_60266_updated.pdb" } resolution = 2.53 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2113 2.51 5 N 564 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3342 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Conformer: "B" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} bond proxies already assigned to first conformer: 3321 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 69 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 21} Link IDs: {None: 21} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 89 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 89 " occ=0.50 Time building chain proxies: 4.11, per 1000 atoms: 1.23 Number of scatterers: 3342 At special positions: 0 Unit cell: (66.176, 61.664, 73.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 648 8.00 N 564 7.00 C 2113 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: 1.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 4 sheets defined 48.6% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.745A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.722A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 6.136A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.701A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.548A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.664A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 74 removed outlier: 6.926A pdb=" N GLY A 106 " --> pdb=" O ARG A 73 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.691A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.932A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 152 hydrogen bonds defined for protein. 451 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: 0.86 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 938 1.33 - 1.45: 548 1.45 - 1.57: 1881 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3399 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.612 0.221 3.80e-02 6.93e+02 3.38e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.603 0.154 3.50e-02 8.16e+02 1.93e+01 bond pdb=" C PRO A 252 " pdb=" N ASP A 253 " ideal model delta sigma weight residual 1.335 1.384 -0.050 1.36e-02 5.41e+03 1.33e+01 bond pdb=" C2B NDP A 500 " pdb=" O2B NDP A 500 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.90e-02 1.19e+03 1.02e+01 bond pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 1.368 1.448 -0.080 3.20e-02 9.77e+02 6.22e+00 ... (remaining 3394 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.52: 162 107.52 - 114.30: 1937 114.30 - 121.09: 1550 121.09 - 127.87: 931 127.87 - 134.66: 37 Bond angle restraints: 4617 Sorted by residual: angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 132.14 -24.40 1.95e+00 2.62e-01 1.56e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 118.94 -15.10 1.91e+00 2.73e-01 6.22e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 119.33 -14.40 2.66e+00 1.41e-01 2.93e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.57 -9.05 1.91e+00 2.74e-01 2.24e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.31 5.15 1.17e+00 7.36e-01 1.95e+01 ... (remaining 4612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1819 17.98 - 35.97: 143 35.97 - 53.95: 36 53.95 - 71.94: 10 71.94 - 89.92: 7 Dihedral angle restraints: 2015 sinusoidal: 822 harmonic: 1193 Sorted by residual: dihedral pdb=" CA THR A 148 " pdb=" C THR A 148 " pdb=" N ASN A 149 " pdb=" CA ASN A 149 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.45 16.55 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 303 " pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " pdb=" OE1 GLU A 303 " ideal model delta sinusoidal sigma weight residual 0.00 88.04 -88.04 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 2012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 400 0.052 - 0.104: 84 0.104 - 0.156: 16 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 502 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.45 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.41 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.56 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 499 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 150 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 393 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ILE A 393 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE A 393 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS A 394 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 394 " -0.013 2.00e-02 2.50e+03 1.09e-02 1.79e+00 pdb=" CG HIS A 394 " 0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS A 394 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 394 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 394 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 394 " -0.011 2.00e-02 2.50e+03 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1295 2.92 - 3.41: 3461 3.41 - 3.91: 6025 3.91 - 4.40: 6824 4.40 - 4.90: 10961 Nonbonded interactions: 28566 Sorted by model distance: nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 601 " model vdw 2.421 2.520 nonbonded pdb=" OH TYR A 408 " pdb=" O LYS A 419 " model vdw 2.443 2.440 nonbonded pdb=" OE1 GLU A 354 " pdb=" O HOH A 602 " model vdw 2.449 2.440 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.449 2.520 nonbonded pdb=" NZ LYS A 177 " pdb=" OE2 GLU A 354 " model vdw 2.464 2.520 ... (remaining 28561 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=0.50 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: 0.700 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: 3.450 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.840 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 : 0.007 0.221 3399 Z= 0.497 Angle : 0.945 24.400 4617 Z= 0.541 Chirality : 0.047 0.260 502 Planarity : 0.005 0.045 589 Dihedral : 15.547 89.920 1255 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.06 % Allowed : 0.59 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.41), residues: 417 helix: 1.83 (0.37), residues: 202 sheet: -0.52 (0.69), residues: 64 loop : -1.15 (0.45), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 92 HIS 0.008 0.002 HIS A 394 PHE 0.010 0.002 PHE A 341 TYR 0.013 0.002 TYR A 226 ARG 0.003 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.390 Fit side-chains REVERT: A 187 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7563 (ttm110) REVERT: A 333 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8192 (mtpt) REVERT: A 386 ASN cc_start: 0.8503 (m-40) cc_final: 0.8166 (m110) REVERT: A 388 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.7957 (t70) outliers start: 7 outliers final: 0 residues processed: 86 average time/residue: 1.2684 time to fit residues: 111.9840 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 267 HIS ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3399 Z= 0.213 Angle : 0.517 8.581 4617 Z= 0.271 Chirality : 0.045 0.138 502 Planarity : 0.004 0.048 589 Dihedral : 6.334 51.677 470 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.24 % Allowed : 11.47 % Favored : 85.29 % 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: 0.81 (0.41), residues: 417 helix: 2.05 (0.37), residues: 201 sheet: -0.38 (0.68), residues: 64 loop : -1.13 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 PHE 0.010 0.002 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.400 Fit side-chains REVERT: A 214 LYS cc_start: 0.8349 (mttm) cc_final: 0.8100 (mppt) REVERT: A 333 LYS cc_start: 0.8470 (mtpp) cc_final: 0.8244 (mtmt) REVERT: A 388 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.7821 (t70) outliers start: 11 outliers final: 3 residues processed: 74 average time/residue: 1.3000 time to fit residues: 98.7418 Evaluate side-chains 66 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3399 Z= 0.195 Angle : 0.519 6.490 4617 Z= 0.267 Chirality : 0.045 0.152 502 Planarity : 0.004 0.051 589 Dihedral : 5.378 51.408 466 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.06 % Allowed : 15.59 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.41), residues: 417 helix: 2.09 (0.37), residues: 201 sheet: -0.18 (0.70), residues: 64 loop : -1.15 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.001 0.000 HIS A 267 PHE 0.010 0.002 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.342 Fit side-chains REVERT: A 214 LYS cc_start: 0.8368 (mttm) cc_final: 0.8105 (mppt) REVERT: A 252 PRO cc_start: 0.8036 (Cg_endo) cc_final: 0.7777 (Cg_exo) REVERT: A 297 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8450 (pp) REVERT: A 333 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8202 (mtpt) REVERT: A 388 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.7540 (t70) REVERT: A 389 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8355 (mmmm) outliers start: 7 outliers final: 1 residues processed: 62 average time/residue: 1.2711 time to fit residues: 81.0478 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3399 Z= 0.164 Angle : 0.485 6.168 4617 Z= 0.252 Chirality : 0.044 0.147 502 Planarity : 0.004 0.050 589 Dihedral : 5.329 54.260 466 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.65 % Allowed : 14.71 % Favored : 82.65 % 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: 0.95 (0.41), residues: 417 helix: 2.15 (0.37), residues: 201 sheet: -0.09 (0.71), residues: 64 loop : -1.15 (0.44), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.002 0.000 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.392 Fit side-chains REVERT: A 214 LYS cc_start: 0.8386 (mttm) cc_final: 0.8135 (mppt) REVERT: A 218 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7901 (tp40) REVERT: A 297 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8413 (pp) REVERT: A 333 LYS cc_start: 0.8456 (mtpp) cc_final: 0.8212 (mtpt) REVERT: A 388 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.7468 (t70) outliers start: 9 outliers final: 2 residues processed: 62 average time/residue: 1.2018 time to fit residues: 76.7929 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.0870 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3399 Z= 0.141 Angle : 0.484 9.600 4617 Z= 0.241 Chirality : 0.043 0.152 502 Planarity : 0.004 0.048 589 Dihedral : 5.229 57.087 466 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.35 % Allowed : 15.59 % Favored : 82.06 % 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: 1.15 (0.42), residues: 417 helix: 2.22 (0.37), residues: 202 sheet: 0.18 (0.74), residues: 62 loop : -1.00 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 92 HIS 0.002 0.000 HIS A 267 PHE 0.007 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.390 Fit side-chains REVERT: A 214 LYS cc_start: 0.8364 (mttm) cc_final: 0.8130 (mppt) REVERT: A 297 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8359 (pp) REVERT: A 333 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8212 (mtpt) REVERT: A 388 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.7380 (t70) outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 1.2526 time to fit residues: 78.6789 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3399 Z= 0.155 Angle : 0.491 9.076 4617 Z= 0.246 Chirality : 0.043 0.153 502 Planarity : 0.004 0.047 589 Dihedral : 5.290 59.167 466 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.18 % Allowed : 17.35 % Favored : 81.47 % 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: 1.15 (0.42), residues: 417 helix: 2.20 (0.37), residues: 202 sheet: 0.23 (0.75), residues: 62 loop : -1.01 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 382 HIS 0.002 0.000 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.374 Fit side-chains REVERT: A 297 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8369 (pp) REVERT: A 333 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8221 (mtmt) REVERT: A 388 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.7340 (t70) outliers start: 4 outliers final: 1 residues processed: 56 average time/residue: 1.2697 time to fit residues: 73.2080 Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 0.0370 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 193 GLN A 234 GLN A 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3399 Z= 0.227 Angle : 0.541 11.830 4617 Z= 0.271 Chirality : 0.045 0.160 502 Planarity : 0.004 0.047 589 Dihedral : 5.574 59.267 466 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.18 % Allowed : 18.53 % Favored : 80.29 % 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: 1.05 (0.42), residues: 417 helix: 2.12 (0.37), residues: 205 sheet: 0.18 (0.74), residues: 62 loop : -1.12 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.001 0.001 HIS A 267 PHE 0.011 0.002 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.006 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.375 Fit side-chains REVERT: A 214 LYS cc_start: 0.8517 (mttm) cc_final: 0.8044 (mppt) REVERT: A 297 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8387 (pp) REVERT: A 333 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8217 (mtpt) REVERT: A 388 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.7436 (t70) outliers start: 4 outliers final: 1 residues processed: 57 average time/residue: 1.2954 time to fit residues: 76.0950 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 0.0970 chunk 28 optimal weight: 9.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3399 Z= 0.144 Angle : 0.492 9.532 4617 Z= 0.245 Chirality : 0.043 0.149 502 Planarity : 0.004 0.048 589 Dihedral : 5.258 59.616 466 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.18 % Allowed : 19.12 % Favored : 79.71 % 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: 1.18 (0.42), residues: 417 helix: 2.30 (0.37), residues: 199 sheet: 0.22 (0.74), residues: 62 loop : -1.04 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.002 0.000 HIS A 267 PHE 0.007 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.006 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.380 Fit side-chains REVERT: A 214 LYS cc_start: 0.8505 (mttm) cc_final: 0.8025 (mppt) REVERT: A 297 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8344 (pp) REVERT: A 333 LYS cc_start: 0.8433 (mtpp) cc_final: 0.8119 (mtpt) REVERT: A 388 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.7263 (t70) outliers start: 4 outliers final: 1 residues processed: 53 average time/residue: 1.3250 time to fit residues: 72.3716 Evaluate side-chains 54 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.0040 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3399 Z= 0.197 Angle : 0.524 10.130 4617 Z= 0.261 Chirality : 0.044 0.164 502 Planarity : 0.004 0.048 589 Dihedral : 5.418 59.649 466 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.18 % Allowed : 19.12 % Favored : 79.71 % 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: 1.10 (0.42), residues: 417 helix: 2.15 (0.37), residues: 205 sheet: 0.17 (0.74), residues: 62 loop : -1.06 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 PHE 0.009 0.002 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.006 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.379 Fit side-chains REVERT: A 214 LYS cc_start: 0.8490 (mttm) cc_final: 0.7988 (mppt) REVERT: A 233 GLU cc_start: 0.7725 (tp30) cc_final: 0.7518 (mm-30) REVERT: A 297 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8388 (pp) REVERT: A 333 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8141 (mtpt) REVERT: A 388 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.7359 (t70) outliers start: 4 outliers final: 1 residues processed: 52 average time/residue: 1.2686 time to fit residues: 67.9829 Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0030 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3399 Z= 0.151 Angle : 0.491 8.913 4617 Z= 0.244 Chirality : 0.043 0.160 502 Planarity : 0.004 0.048 589 Dihedral : 5.218 59.159 466 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.18 % Allowed : 19.12 % Favored : 79.71 % 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: 1.18 (0.42), residues: 417 helix: 2.33 (0.37), residues: 199 sheet: 0.16 (0.73), residues: 62 loop : -1.04 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.001 0.000 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.006 0.000 ARG A 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.376 Fit side-chains REVERT: A 214 LYS cc_start: 0.8439 (mttm) cc_final: 0.7917 (mppt) REVERT: A 297 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8323 (pp) REVERT: A 388 HIS cc_start: 0.8888 (OUTLIER) cc_final: 0.7234 (t70) outliers start: 4 outliers final: 1 residues processed: 54 average time/residue: 1.2829 time to fit residues: 71.3454 Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 0.0000 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.089248 restraints weight = 11719.771| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.92 r_work: 0.2762 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3399 Z= 0.162 Angle : 0.505 10.558 4617 Z= 0.250 Chirality : 0.043 0.159 502 Planarity : 0.005 0.060 589 Dihedral : 5.256 58.647 466 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.88 % Allowed : 19.41 % Favored : 79.71 % 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: 1.17 (0.42), residues: 417 helix: 2.26 (0.37), residues: 201 sheet: 0.12 (0.73), residues: 62 loop : -0.98 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 30 HIS 0.002 0.000 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.006 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1934.88 seconds wall clock time: 34 minutes 41.93 seconds (2081.93 seconds total)