Starting phenix.real_space_refine on Thu Jul 18 20:50:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/07_2024/8y65_38966.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/07_2024/8y65_38966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/07_2024/8y65_38966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/07_2024/8y65_38966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/07_2024/8y65_38966.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/07_2024/8y65_38966.cif" } resolution = 3.51 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= 0.007 sd= 0.171 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 2355 2.51 5 N 574 2.21 5 O 623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3565 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3553 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 442} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.00, per 1000 atoms: 0.84 Number of scatterers: 3565 At special positions: 0 Unit cell: (84.5383, 62.5803, 69.1677, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 623 8.00 N 574 7.00 C 2355 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: 1.52 Conformation dependent library (CDL) restraints added in 671.8 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 86.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 54 through 76 removed outlier: 4.372A pdb=" N PHE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 102 through 132 removed outlier: 4.794A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 157 through 162 removed outlier: 4.116A pdb=" N ALA A 161 " --> pdb=" O CYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 193 removed outlier: 3.742A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Proline residue: A 186 - end of helix removed outlier: 3.848A pdb=" N GLU A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.625A pdb=" N LEU A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 removed outlier: 4.096A pdb=" N VAL A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 removed outlier: 3.589A pdb=" N ALA A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.799A pdb=" N LEU A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.501A pdb=" N ILE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 313 through 331 removed outlier: 4.333A pdb=" N GLY A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 352 through 379 removed outlier: 4.064A pdb=" N LEU A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 404 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.043A pdb=" N VAL A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 4.708A pdb=" N GLY A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 476 Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 481 through 499 Processing helix chain 'A' and resid 506 through 518 271 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 1.66 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: 1101 1.34 - 1.46: 872 1.46 - 1.58: 1664 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3655 Sorted by residual: bond pdb=" C4 URC A 601 " pdb=" C5 URC A 601 " ideal model delta sigma weight residual 1.358 1.470 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C6 URC A 601 " pdb=" N1 URC A 601 " ideal model delta sigma weight residual 1.398 1.317 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C8 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 1.396 1.316 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.10e+01 bond pdb=" C2 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.376 1.311 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 3650 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.91: 111 106.91 - 114.25: 2130 114.25 - 121.59: 2076 121.59 - 128.92: 643 128.92 - 136.26: 29 Bond angle restraints: 4989 Sorted by residual: angle pdb=" N7 URC A 601 " pdb=" C8 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 104.73 118.77 -14.04 3.00e+00 1.11e-01 2.19e+01 angle pdb=" N ILE A 436 " pdb=" CA ILE A 436 " pdb=" C ILE A 436 " ideal model delta sigma weight residual 112.96 108.33 4.63 1.00e+00 1.00e+00 2.15e+01 angle pdb=" CA ILE A 335 " pdb=" C ILE A 335 " pdb=" N TRP A 336 " ideal model delta sigma weight residual 118.13 123.44 -5.31 1.37e+00 5.33e-01 1.50e+01 angle pdb=" N1 URC A 601 " pdb=" C2 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 114.62 124.69 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N ILE A 335 " pdb=" CA ILE A 335 " pdb=" C ILE A 335 " ideal model delta sigma weight residual 113.00 108.67 4.33 1.30e+00 5.92e-01 1.11e+01 ... (remaining 4984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 1911 17.37 - 34.73: 166 34.73 - 52.10: 26 52.10 - 69.46: 4 69.46 - 86.83: 4 Dihedral angle restraints: 2111 sinusoidal: 781 harmonic: 1330 Sorted by residual: dihedral pdb=" CA GLY A 331 " pdb=" C GLY A 331 " pdb=" N LEU A 332 " pdb=" CA LEU A 332 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CB GLU A 223 " pdb=" CG GLU A 223 " pdb=" CD GLU A 223 " pdb=" OE1 GLU A 223 " ideal model delta sinusoidal sigma weight residual 0.00 -86.83 86.83 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 287 " pdb=" CG GLU A 287 " pdb=" CD GLU A 287 " pdb=" OE1 GLU A 287 " ideal model delta sinusoidal sigma weight residual 0.00 86.24 -86.24 1 3.00e+01 1.11e-03 9.97e+00 ... (remaining 2108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 425 0.039 - 0.079: 125 0.079 - 0.118: 37 0.118 - 0.158: 3 0.158 - 0.197: 2 Chirality restraints: 592 Sorted by residual: chirality pdb=" CB ILE A 335 " pdb=" CA ILE A 335 " pdb=" CG1 ILE A 335 " pdb=" CG2 ILE A 335 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ILE A 348 " pdb=" N ILE A 348 " pdb=" C ILE A 348 " pdb=" CB ILE A 348 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 589 not shown) Planarity restraints: 618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 381 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 382 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 255 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 256 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 335 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C ILE A 335 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 335 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP A 336 " 0.014 2.00e-02 2.50e+03 ... (remaining 615 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 673 2.76 - 3.30: 3548 3.30 - 3.83: 6129 3.83 - 4.37: 6408 4.37 - 4.90: 11451 Nonbonded interactions: 28209 Sorted by model distance: nonbonded pdb=" NH2 ARG A 96 " pdb=" O GLY A 162 " model vdw 2.231 2.520 nonbonded pdb=" NE2 GLN A 328 " pdb=" OD1 ASN A 458 " model vdw 2.281 2.520 nonbonded pdb=" OE1 GLN A 328 " pdb=" ND2 ASN A 333 " model vdw 2.335 2.520 nonbonded pdb=" NZ LYS A 195 " pdb=" OE2 GLU A 288 " model vdw 2.343 2.520 nonbonded pdb=" O GLY A 136 " pdb=" OG1 THR A 140 " model vdw 2.353 2.440 ... (remaining 28204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.280 Find NCS groups from input model: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5316 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 : 0.004 0.112 3655 Z= 0.275 Angle : 0.734 14.038 4989 Z= 0.355 Chirality : 0.041 0.197 592 Planarity : 0.005 0.063 618 Dihedral : 13.646 86.828 1263 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.27 % Allowed : 0.27 % Favored : 99.47 % 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: 1.81 (0.42), residues: 465 helix: 1.61 (0.29), residues: 363 sheet: None (None), residues: 0 loop : -0.14 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.002 0.000 HIS A 377 PHE 0.012 0.001 PHE A 208 TYR 0.007 0.001 TYR A 327 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.330 Fit side-chains REVERT: A 400 ILE cc_start: 0.7317 (tp) cc_final: 0.6686 (tt) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.1405 time to fit residues: 5.4412 Evaluate side-chains 23 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.0030 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3655 Z= 0.168 Angle : 0.574 7.361 4989 Z= 0.283 Chirality : 0.040 0.135 592 Planarity : 0.005 0.044 618 Dihedral : 4.070 20.336 500 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.27 % Allowed : 4.26 % Favored : 95.48 % 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: 1.87 (0.41), residues: 465 helix: 1.70 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.33 (0.70), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.001 0.000 HIS A 377 PHE 0.017 0.001 PHE A 276 TYR 0.005 0.001 TYR A 507 ARG 0.005 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.358 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.1011 time to fit residues: 3.9947 Evaluate side-chains 24 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5459 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3655 Z= 0.196 Angle : 0.578 6.787 4989 Z= 0.285 Chirality : 0.041 0.136 592 Planarity : 0.004 0.036 618 Dihedral : 4.014 17.121 498 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.80 % Allowed : 7.45 % Favored : 91.76 % 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 (0.41), residues: 465 helix: 1.66 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.49 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.011 0.001 PHE A 276 TYR 0.007 0.001 TYR A 233 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.401 Fit side-chains REVERT: A 324 MET cc_start: 0.7310 (mmm) cc_final: 0.7059 (mmm) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.0809 time to fit residues: 3.4546 Evaluate side-chains 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3655 Z= 0.205 Angle : 0.581 5.483 4989 Z= 0.290 Chirality : 0.041 0.157 592 Planarity : 0.004 0.031 618 Dihedral : 4.102 16.195 498 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.33 % Allowed : 12.50 % Favored : 86.17 % 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: 1.52 (0.40), residues: 465 helix: 1.53 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -0.93 (0.66), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.003 0.001 HIS A 377 PHE 0.013 0.001 PHE A 276 TYR 0.007 0.001 TYR A 233 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.333 Fit side-chains REVERT: A 262 GLU cc_start: -0.0387 (OUTLIER) cc_final: -0.1224 (tp30) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 0.0843 time to fit residues: 3.5305 Evaluate side-chains 24 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.0020 chunk 39 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3655 Z= 0.153 Angle : 0.529 6.043 4989 Z= 0.263 Chirality : 0.040 0.167 592 Planarity : 0.004 0.033 618 Dihedral : 3.923 15.981 498 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.33 % Allowed : 13.56 % Favored : 85.11 % 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: 1.84 (0.41), residues: 465 helix: 1.77 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.73 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.001 0.000 HIS A 377 PHE 0.010 0.001 PHE A 69 TYR 0.006 0.001 TYR A 258 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.305 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 24 average time/residue: 0.0812 time to fit residues: 3.1177 Evaluate side-chains 24 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.0270 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3655 Z= 0.153 Angle : 0.536 8.174 4989 Z= 0.263 Chirality : 0.040 0.162 592 Planarity : 0.004 0.033 618 Dihedral : 3.848 15.659 498 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.33 % Allowed : 14.36 % Favored : 84.31 % 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: 1.98 (0.41), residues: 465 helix: 1.87 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.69 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.001 0.000 HIS A 377 PHE 0.009 0.001 PHE A 69 TYR 0.005 0.001 TYR A 258 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.375 Fit side-chains REVERT: A 262 GLU cc_start: -0.0504 (OUTLIER) cc_final: -0.1261 (tp30) REVERT: A 324 MET cc_start: 0.7225 (mmm) cc_final: 0.6992 (mmm) outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.1279 time to fit residues: 4.6920 Evaluate side-chains 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5480 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3655 Z= 0.180 Angle : 0.552 6.523 4989 Z= 0.272 Chirality : 0.040 0.159 592 Planarity : 0.004 0.032 618 Dihedral : 3.922 15.326 498 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.60 % Allowed : 14.63 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.40), residues: 465 helix: 1.81 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.67 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.002 0.000 HIS A 377 PHE 0.009 0.001 PHE A 69 TYR 0.005 0.001 TYR A 258 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.344 Fit side-chains REVERT: A 262 GLU cc_start: -0.0465 (OUTLIER) cc_final: -0.1266 (tp30) REVERT: A 324 MET cc_start: 0.7171 (mmm) cc_final: 0.6958 (mmm) outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.0860 time to fit residues: 3.4646 Evaluate side-chains 27 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 0.0030 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3655 Z= 0.176 Angle : 0.551 6.537 4989 Z= 0.274 Chirality : 0.040 0.163 592 Planarity : 0.004 0.032 618 Dihedral : 3.914 15.059 498 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.13 % Allowed : 15.43 % Favored : 82.45 % 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: 1.89 (0.41), residues: 465 helix: 1.80 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.72 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.002 0.001 HIS A 377 PHE 0.009 0.001 PHE A 69 TYR 0.005 0.001 TYR A 258 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.385 Fit side-chains REVERT: A 211 ILE cc_start: 0.7339 (tp) cc_final: 0.7092 (tt) REVERT: A 262 GLU cc_start: -0.0490 (OUTLIER) cc_final: -0.1303 (tp30) REVERT: A 427 CYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7274 (t) outliers start: 8 outliers final: 4 residues processed: 28 average time/residue: 0.0866 time to fit residues: 3.8467 Evaluate side-chains 28 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 427 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.0980 chunk 32 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5454 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3655 Z= 0.156 Angle : 0.530 7.456 4989 Z= 0.262 Chirality : 0.040 0.182 592 Planarity : 0.004 0.032 618 Dihedral : 3.860 15.018 498 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.60 % Allowed : 16.22 % Favored : 82.18 % 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: 1.94 (0.41), residues: 465 helix: 1.83 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.63 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.002 0.000 HIS A 377 PHE 0.015 0.001 PHE A 276 TYR 0.005 0.001 TYR A 258 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.373 Fit side-chains REVERT: A 211 ILE cc_start: 0.7315 (tp) cc_final: 0.7072 (tt) REVERT: A 262 GLU cc_start: -0.0637 (OUTLIER) cc_final: -0.1268 (tp30) REVERT: A 427 CYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7268 (t) outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 0.0892 time to fit residues: 4.0251 Evaluate side-chains 28 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 427 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.0030 chunk 36 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 chunk 11 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.1826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5397 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3655 Z= 0.151 Angle : 0.550 11.103 4989 Z= 0.266 Chirality : 0.039 0.189 592 Planarity : 0.004 0.034 618 Dihedral : 3.755 15.137 498 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.60 % Allowed : 16.22 % Favored : 82.18 % 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: 2.12 (0.41), residues: 465 helix: 1.92 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.45 (0.67), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.001 0.000 HIS A 377 PHE 0.009 0.001 PHE A 69 TYR 0.005 0.001 TYR A 258 ARG 0.002 0.000 ARG A 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.392 Fit side-chains REVERT: A 174 MET cc_start: 0.6234 (mmm) cc_final: 0.5603 (mmm) REVERT: A 324 MET cc_start: 0.7199 (mmm) cc_final: 0.6850 (mmm) REVERT: A 427 CYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7311 (t) outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 0.0844 time to fit residues: 3.6660 Evaluate side-chains 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 30.0000 chunk 31 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.273730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.250965 restraints weight = 4005.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.255039 restraints weight = 2466.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.257996 restraints weight = 1702.307| |-----------------------------------------------------------------------------| r_work (final): 0.4620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5490 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3655 Z= 0.184 Angle : 0.562 10.125 4989 Z= 0.274 Chirality : 0.040 0.165 592 Planarity : 0.004 0.032 618 Dihedral : 3.845 15.212 498 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.86 % Allowed : 15.96 % Favored : 82.18 % 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: 1.93 (0.41), residues: 465 helix: 1.81 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.59 (0.66), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.008 0.001 PHE A 69 TYR 0.006 0.001 TYR A 258 ARG 0.004 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1019.38 seconds wall clock time: 19 minutes 2.50 seconds (1142.50 seconds total)