Starting phenix.real_space_refine on Sun Mar 10 17:06:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd5_38266/03_2024/8xd5_38266_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd5_38266/03_2024/8xd5_38266.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd5_38266/03_2024/8xd5_38266_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd5_38266/03_2024/8xd5_38266_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd5_38266/03_2024/8xd5_38266_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd5_38266/03_2024/8xd5_38266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd5_38266/03_2024/8xd5_38266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd5_38266/03_2024/8xd5_38266_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd5_38266/03_2024/8xd5_38266_neut_updated.pdb" } resolution = 2.75 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 15 5.16 5 C 2126 2.51 5 N 568 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ASP 397": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3378 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3289 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 89 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 31} Link IDs: {None: 32} Time building chain proxies: 2.45, per 1000 atoms: 0.73 Number of scatterers: 3378 At special positions: 0 Unit cell: (67.68, 75.952, 69.184, 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 15 16.00 P 3 15.00 O 666 8.00 N 568 7.00 C 2126 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: 1.48 Conformation dependent library (CDL) restraints added in 754.6 milliseconds 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: 766 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 4 sheets defined 47.7% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 4.618A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 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: 5.689A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.207A 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 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 324 through 332 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 345 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 removed outlier: 3.762A pdb=" N SER A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.623A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 74 removed outlier: 6.799A 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: 6.180A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.214A 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: 6.808A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 162 hydrogen bonds defined for protein. 471 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: 0.91 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1064 1.34 - 1.45: 425 1.45 - 1.57: 1900 1.57 - 1.69: 5 1.69 - 1.80: 29 Bond restraints: 3423 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C3N NAP A 500 " pdb=" C4N NAP A 500 " ideal model delta sigma weight residual 1.390 1.511 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C4A NAP A 500 " pdb=" C5A NAP A 500 " ideal model delta sigma weight residual 1.385 1.469 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5A NAP A 500 " pdb=" C6A NAP A 500 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C4N NAP A 500 " pdb=" C5N NAP A 500 " ideal model delta sigma weight residual 1.384 1.457 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 3418 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.46: 153 107.46 - 114.65: 2016 114.65 - 121.83: 1738 121.83 - 129.02: 709 129.02 - 136.20: 32 Bond angle restraints: 4648 Sorted by residual: angle pdb=" N GLN A 60 " pdb=" CA GLN A 60 " pdb=" C GLN A 60 " ideal model delta sigma weight residual 109.07 101.46 7.61 1.61e+00 3.86e-01 2.23e+01 angle pdb=" N GLU A 325 " pdb=" CA GLU A 325 " pdb=" C GLU A 325 " ideal model delta sigma weight residual 111.07 106.73 4.34 1.07e+00 8.73e-01 1.64e+01 angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 118.97 122.38 -3.41 1.04e+00 9.25e-01 1.08e+01 angle pdb=" N VAL A 300 " pdb=" CA VAL A 300 " pdb=" C VAL A 300 " ideal model delta sigma weight residual 113.42 109.80 3.62 1.17e+00 7.31e-01 9.60e+00 angle pdb=" C2A NAP A 500 " pdb=" N3A NAP A 500 " pdb=" C4A NAP A 500 " ideal model delta sigma weight residual 111.82 120.86 -9.04 3.00e+00 1.11e-01 9.09e+00 ... (remaining 4643 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.93: 1838 17.93 - 35.85: 178 35.85 - 53.77: 44 53.77 - 71.70: 21 71.70 - 89.62: 7 Dihedral angle restraints: 2088 sinusoidal: 888 harmonic: 1200 Sorted by residual: 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 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CB GLU A 371 " pdb=" CG GLU A 371 " pdb=" CD GLU A 371 " pdb=" OE1 GLU A 371 " ideal model delta sinusoidal sigma weight residual 0.00 -84.13 84.13 1 3.00e+01 1.11e-03 9.58e+00 dihedral pdb=" CA ARG A 16 " pdb=" CB ARG A 16 " pdb=" CG ARG A 16 " pdb=" CD ARG A 16 " ideal model delta sinusoidal sigma weight residual -60.00 -119.28 59.28 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 387 0.047 - 0.093: 77 0.093 - 0.139: 36 0.139 - 0.186: 3 0.186 - 0.232: 3 Chirality restraints: 506 Sorted by residual: chirality pdb=" CA GLN A 60 " pdb=" N GLN A 60 " pdb=" C GLN A 60 " pdb=" CB GLN A 60 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C2B NAP A 500 " pdb=" C1B NAP A 500 " pdb=" C3B NAP A 500 " pdb=" O2B NAP A 500 " both_signs ideal model delta sigma weight residual False -2.75 -2.53 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1B NAP A 500 " pdb=" C2B NAP A 500 " pdb=" N9A NAP A 500 " pdb=" O4B NAP A 500 " both_signs ideal model delta sigma weight residual False 2.31 2.50 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 503 not shown) Planarity restraints: 590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 297 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C ILE A 297 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 297 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 298 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 150 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 18 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C ALA A 18 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA A 18 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN A 19 " 0.010 2.00e-02 2.50e+03 ... (remaining 587 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1449 2.94 - 3.43: 3428 3.43 - 3.92: 6117 3.92 - 4.41: 7241 4.41 - 4.90: 11354 Nonbonded interactions: 29589 Sorted by model distance: nonbonded pdb=" O VAL A 317 " pdb=" ND2 ASN A 344 " model vdw 2.447 2.520 nonbonded pdb=" O GLU A 286 " pdb=" NZ LYS A 310 " model vdw 2.464 2.520 nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 601 " model vdw 2.468 2.520 nonbonded pdb=" O LEU A 99 " pdb=" O HOH A 601 " model vdw 2.473 2.440 nonbonded pdb=" NE ARG A 58 " pdb=" OD2 ASP A 140 " model vdw 2.500 2.520 ... (remaining 29584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 3.570 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 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 0.128 3423 Z= 0.399 Angle : 0.735 9.045 4648 Z= 0.421 Chirality : 0.047 0.232 506 Planarity : 0.004 0.042 590 Dihedral : 16.879 89.618 1322 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.80 % Allowed : 3.22 % Favored : 92.98 % 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: 0.89 (0.43), residues: 417 helix: 1.30 (0.37), residues: 210 sheet: 0.53 (0.74), residues: 60 loop : -0.30 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.003 0.001 HIS A 61 PHE 0.009 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 36 *********************** 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 88 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.387 Fit side-chains REVERT: A 167 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8560 (mmpt) REVERT: A 204 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8449 (tttp) outliers start: 13 outliers final: 4 residues processed: 82 average time/residue: 1.5937 time to fit residues: 133.5172 Evaluate side-chains 62 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 351 SER 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: 2.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.0030 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3423 Z= 0.152 Angle : 0.471 4.837 4648 Z= 0.247 Chirality : 0.042 0.134 506 Planarity : 0.005 0.043 590 Dihedral : 12.588 89.287 540 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.05 % Allowed : 11.40 % Favored : 86.55 % 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: 1.48 (0.43), residues: 417 helix: 2.04 (0.37), residues: 209 sheet: 0.56 (0.72), residues: 61 loop : -0.33 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.004 0.001 HIS A 61 PHE 0.008 0.001 PHE A 341 TYR 0.010 0.001 TYR A 225 ARG 0.007 0.000 ARG A 246 *********************** 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 64 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.529 Fit side-chains REVERT: A 167 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8653 (mmpt) REVERT: A 246 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8289 (mtm110) REVERT: A 388 HIS cc_start: 0.9176 (OUTLIER) cc_final: 0.8515 (t70) outliers start: 7 outliers final: 2 residues processed: 59 average time/residue: 1.6960 time to fit residues: 102.1918 Evaluate side-chains 51 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3423 Z= 0.192 Angle : 0.464 4.182 4648 Z= 0.241 Chirality : 0.043 0.135 506 Planarity : 0.004 0.044 590 Dihedral : 11.298 79.777 531 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.34 % Allowed : 12.57 % Favored : 85.09 % 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: 1.55 (0.43), residues: 417 helix: 2.05 (0.37), residues: 211 sheet: 0.44 (0.71), residues: 61 loop : -0.16 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.003 0.001 HIS A 61 PHE 0.012 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.007 0.001 ARG A 370 *********************** 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 59 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.437 Fit side-chains REVERT: A 12 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8235 (mtmm) REVERT: A 16 ARG cc_start: 0.8288 (tmm-80) cc_final: 0.7908 (ttm170) REVERT: A 167 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8704 (mmpt) REVERT: A 388 HIS cc_start: 0.9233 (OUTLIER) cc_final: 0.8560 (t70) outliers start: 8 outliers final: 2 residues processed: 54 average time/residue: 1.7654 time to fit residues: 97.4995 Evaluate side-chains 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.0470 chunk 19 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3423 Z= 0.135 Angle : 0.446 6.063 4648 Z= 0.231 Chirality : 0.042 0.131 506 Planarity : 0.004 0.044 590 Dihedral : 10.238 71.349 528 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.46 % Allowed : 13.45 % Favored : 85.09 % 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: 1.66 (0.43), residues: 417 helix: 2.15 (0.36), residues: 211 sheet: 0.47 (0.70), residues: 61 loop : -0.12 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.001 0.000 HIS A 61 PHE 0.006 0.001 PHE A 341 TYR 0.006 0.001 TYR A 225 ARG 0.003 0.000 ARG A 16 *********************** 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 55 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.407 Fit side-chains REVERT: A 12 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8203 (mtmm) REVERT: A 16 ARG cc_start: 0.8274 (tmm-80) cc_final: 0.7934 (ttm170) REVERT: A 167 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8682 (mmpt) REVERT: A 388 HIS cc_start: 0.9094 (OUTLIER) cc_final: 0.8671 (t70) outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 1.8574 time to fit residues: 98.6754 Evaluate side-chains 51 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN 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: 6.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3423 Z= 0.297 Angle : 0.501 7.306 4648 Z= 0.260 Chirality : 0.044 0.137 506 Planarity : 0.005 0.049 590 Dihedral : 10.868 81.574 528 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.46 % Allowed : 15.50 % Favored : 83.04 % 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: 1.51 (0.43), residues: 417 helix: 1.98 (0.36), residues: 211 sheet: 0.47 (0.70), residues: 61 loop : -0.15 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 61 PHE 0.016 0.002 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** 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 56 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.416 Fit side-chains REVERT: A 12 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8219 (mtmm) REVERT: A 16 ARG cc_start: 0.8331 (tmm-80) cc_final: 0.7980 (ttm170) REVERT: A 167 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8691 (mmpt) REVERT: A 388 HIS cc_start: 0.9249 (OUTLIER) cc_final: 0.8618 (t70) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 1.7755 time to fit residues: 96.1664 Evaluate side-chains 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN 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: 3.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3423 Z= 0.162 Angle : 0.462 5.271 4648 Z= 0.242 Chirality : 0.042 0.131 506 Planarity : 0.004 0.047 590 Dihedral : 10.241 75.865 528 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.46 % Allowed : 15.20 % Favored : 83.33 % 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: 1.62 (0.43), residues: 417 helix: 2.08 (0.36), residues: 211 sheet: 0.50 (0.71), residues: 61 loop : -0.11 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.001 0.001 HIS A 61 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** 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 54 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.367 Fit side-chains REVERT: A 12 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8205 (mtmm) REVERT: A 16 ARG cc_start: 0.8305 (tmm-80) cc_final: 0.7985 (ttm170) REVERT: A 167 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8657 (mmpt) REVERT: A 388 HIS cc_start: 0.9130 (OUTLIER) cc_final: 0.8708 (t70) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 1.8880 time to fit residues: 98.2657 Evaluate side-chains 52 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 266 GLU 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: 4.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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: 0.8874 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3423 Z= 0.347 Angle : 0.505 4.220 4648 Z= 0.267 Chirality : 0.045 0.137 506 Planarity : 0.005 0.050 590 Dihedral : 11.140 87.542 528 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.17 % Allowed : 15.20 % Favored : 83.63 % 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: 1.41 (0.43), residues: 417 helix: 1.93 (0.36), residues: 210 sheet: 0.47 (0.70), residues: 61 loop : -0.27 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.017 0.002 PHE A 341 TYR 0.012 0.002 TYR A 363 ARG 0.002 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 51 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.425 Fit side-chains REVERT: A 12 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8214 (mttm) REVERT: A 16 ARG cc_start: 0.8322 (tmm-80) cc_final: 0.7984 (ttm170) REVERT: A 167 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8776 (mmtt) REVERT: A 271 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8536 (ttpt) REVERT: A 388 HIS cc_start: 0.9253 (OUTLIER) cc_final: 0.8675 (t70) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 1.8376 time to fit residues: 92.0420 Evaluate side-chains 51 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 266 GLU 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: 2.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8836 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3423 Z= 0.194 Angle : 0.453 4.087 4648 Z= 0.237 Chirality : 0.042 0.129 506 Planarity : 0.004 0.049 590 Dihedral : 10.380 80.559 528 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.46 % Allowed : 15.20 % Favored : 83.33 % 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: 1.58 (0.43), residues: 417 helix: 2.07 (0.36), residues: 210 sheet: 0.45 (0.70), residues: 61 loop : -0.14 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 355 HIS 0.002 0.001 HIS A 61 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.002 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 54 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.402 Fit side-chains REVERT: A 12 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8209 (mtmm) REVERT: A 16 ARG cc_start: 0.8291 (tmm-80) cc_final: 0.7975 (ttm170) REVERT: A 167 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8760 (mmtt) REVERT: A 388 HIS cc_start: 0.9121 (OUTLIER) cc_final: 0.8691 (t70) REVERT: A 389 LYS cc_start: 0.8989 (tptt) cc_final: 0.8783 (tptm) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 1.8981 time to fit residues: 98.8957 Evaluate side-chains 51 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 266 GLU 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: 8.9990 chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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: 0.8856 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3423 Z= 0.263 Angle : 0.480 4.201 4648 Z= 0.252 Chirality : 0.044 0.133 506 Planarity : 0.004 0.048 590 Dihedral : 10.561 81.709 528 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.88 % Allowed : 14.91 % Favored : 84.21 % 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: 1.51 (0.43), residues: 417 helix: 2.00 (0.36), residues: 210 sheet: 0.42 (0.70), residues: 61 loop : -0.15 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.002 0.001 HIS A 61 PHE 0.013 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.002 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 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.403 Fit side-chains REVERT: A 12 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8213 (mtmm) REVERT: A 16 ARG cc_start: 0.8312 (tmm-80) cc_final: 0.7991 (ttm170) REVERT: A 167 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8766 (mmtt) REVERT: A 389 LYS cc_start: 0.8992 (tptt) cc_final: 0.8786 (tptm) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 1.8545 time to fit residues: 92.8496 Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 266 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 9.9990 chunk 3 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8796 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3423 Z= 0.133 Angle : 0.431 4.028 4648 Z= 0.224 Chirality : 0.042 0.132 506 Planarity : 0.004 0.046 590 Dihedral : 9.319 68.593 526 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.58 % Allowed : 15.50 % Favored : 83.92 % 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: 1.76 (0.43), residues: 417 helix: 2.21 (0.36), residues: 210 sheet: 0.46 (0.70), residues: 61 loop : 0.00 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.006 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.003 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 51 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.429 Fit side-chains REVERT: A 12 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8204 (mtmm) REVERT: A 16 ARG cc_start: 0.8272 (tmm-80) cc_final: 0.7978 (ttm170) REVERT: A 167 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8702 (mmtt) outliers start: 2 outliers final: 3 residues processed: 50 average time/residue: 1.9244 time to fit residues: 98.1950 Evaluate side-chains 52 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.0070 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- 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 = 0.3030 r_free = 0.3030 target = 0.099971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.075475 restraints weight = 4347.173| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 1.64 r_work: 0.2523 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2409 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3423 Z= 0.195 Angle : 0.454 3.982 4648 Z= 0.237 Chirality : 0.042 0.132 506 Planarity : 0.004 0.046 590 Dihedral : 9.396 68.986 526 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 15.20 % Favored : 83.92 % 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: 1.68 (0.43), residues: 417 helix: 2.15 (0.36), residues: 210 sheet: 0.42 (0.70), residues: 61 loop : -0.05 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.23 seconds wall clock time: 36 minutes 33.79 seconds (2193.79 seconds total)