Starting phenix.real_space_refine on Fri Aug 2 16:22:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/08_2024/8y65_38966.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/08_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_38966/08_2024/8y65_38966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/08_2024/8y65_38966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/08_2024/8y65_38966.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/08_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-5409/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: 2.81, per 1000 atoms: 0.79 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: 1.66 Conformation dependent library (CDL) restraints added in 696.2 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: 0.39 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: 0.96 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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 3.120 nonbonded pdb=" NE2 GLN A 328 " pdb=" OD1 ASN A 458 " model vdw 2.281 3.120 nonbonded pdb=" OE1 GLN A 328 " pdb=" ND2 ASN A 333 " model vdw 2.335 3.120 nonbonded pdb=" NZ LYS A 195 " pdb=" OE2 GLU A 288 " model vdw 2.343 3.120 nonbonded pdb=" O GLY A 136 " pdb=" OG1 THR A 140 " model vdw 2.353 3.040 ... (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: 0.280 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.460 Find NCS groups from input model: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- 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 : 0.374 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: 0.1515 time to fit residues: 5.8579 Evaluate side-chains 23 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 0.0370 chunk 41 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3655 Z= 0.184 Angle : 0.590 7.530 4989 Z= 0.292 Chirality : 0.041 0.135 592 Planarity : 0.005 0.045 618 Dihedral : 4.139 20.969 500 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: 1.80 (0.41), residues: 465 helix: 1.64 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.29 (0.69), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.002 0.000 HIS A 377 PHE 0.017 0.001 PHE A 276 TYR 0.005 0.001 TYR A 233 ARG 0.006 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 : 0.288 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.0885 time to fit residues: 3.5146 Evaluate side-chains 24 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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: 6.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.5481 moved from start: 0.1267 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= 0.203 Angle : 0.594 6.231 4989 Z= 0.295 Chirality : 0.042 0.130 592 Planarity : 0.004 0.035 618 Dihedral : 4.093 16.436 498 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.80 % Allowed : 8.78 % Favored : 90.43 % 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 (0.41), residues: 465 helix: 1.52 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -0.66 (0.68), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 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 28 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.353 Fit side-chains REVERT: A 324 MET cc_start: 0.7203 (mmm) cc_final: 0.6913 (mmm) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.1049 time to fit residues: 4.2124 Evaluate side-chains 25 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 0.6980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.5488 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3655 Z= 0.190 Angle : 0.578 5.461 4989 Z= 0.287 Chirality : 0.041 0.158 592 Planarity : 0.004 0.032 618 Dihedral : 4.046 15.762 498 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.86 % Allowed : 12.23 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.40), residues: 465 helix: 1.55 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -0.88 (0.66), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.010 0.001 PHE A 276 TYR 0.006 0.001 TYR A 258 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 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 19 time to evaluate : 0.372 Fit side-chains REVERT: A 262 GLU cc_start: -0.0361 (OUTLIER) cc_final: -0.1140 (tp30) outliers start: 7 outliers final: 4 residues processed: 24 average time/residue: 0.1051 time to fit residues: 3.8663 Evaluate side-chains 24 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 263 LYS 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: 1.9990 chunk 18 optimal weight: 0.0870 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.0370 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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: 0.5463 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3655 Z= 0.165 Angle : 0.545 5.547 4989 Z= 0.271 Chirality : 0.041 0.166 592 Planarity : 0.004 0.033 618 Dihedral : 3.969 15.366 498 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.86 % Allowed : 13.83 % 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: 1.73 (0.40), residues: 465 helix: 1.69 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.75 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.000 HIS A 377 PHE 0.010 0.001 PHE A 69 TYR 0.006 0.001 TYR A 258 ARG 0.003 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 30 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.351 Fit side-chains REVERT: A 155 MET cc_start: 0.6147 (mtt) cc_final: 0.5942 (mtm) REVERT: A 223 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7132 (tp30) outliers start: 7 outliers final: 3 residues processed: 28 average time/residue: 0.1050 time to fit residues: 4.3617 Evaluate side-chains 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 0.0070 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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: 0.5496 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3655 Z= 0.185 Angle : 0.577 8.339 4989 Z= 0.285 Chirality : 0.042 0.160 592 Planarity : 0.004 0.032 618 Dihedral : 4.008 15.348 498 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.86 % Allowed : 14.36 % 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: 1.61 (0.41), residues: 465 helix: 1.62 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.98 (0.65), residues: 98 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 0.009 0.001 PHE A 69 TYR 0.006 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 30 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.397 Fit side-chains REVERT: A 262 GLU cc_start: -0.0368 (OUTLIER) cc_final: -0.1169 (tp30) REVERT: A 324 MET cc_start: 0.7287 (mmm) cc_final: 0.7084 (mmm) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.1157 time to fit residues: 4.8622 Evaluate side-chains 28 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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: 0.0770 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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: 0.5474 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3655 Z= 0.165 Angle : 0.553 6.812 4989 Z= 0.273 Chirality : 0.041 0.163 592 Planarity : 0.004 0.033 618 Dihedral : 3.962 14.926 498 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.27 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: 1.71 (0.41), residues: 465 helix: 1.68 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.81 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.000 HIS A 377 PHE 0.012 0.001 PHE A 276 TYR 0.006 0.001 TYR A 258 ARG 0.002 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 29 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.365 Fit side-chains REVERT: A 262 GLU cc_start: -0.0363 (OUTLIER) cc_final: -0.1159 (tp30) REVERT: A 324 MET cc_start: 0.7290 (mmm) cc_final: 0.7081 (mmm) outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.1239 time to fit residues: 4.8266 Evaluate side-chains 27 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.5534 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3655 Z= 0.201 Angle : 0.583 6.669 4989 Z= 0.291 Chirality : 0.042 0.165 592 Planarity : 0.004 0.031 618 Dihedral : 4.073 14.943 498 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.13 % Allowed : 14.89 % Favored : 82.98 % 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: 1.50 (0.40), residues: 465 helix: 1.53 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -0.98 (0.66), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.003 0.001 HIS A 377 PHE 0.008 0.001 PHE A 69 TYR 0.006 0.001 TYR A 258 ARG 0.002 0.000 ARG A 171 *********************** 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 35 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.384 Fit side-chains REVERT: A 262 GLU cc_start: -0.0320 (OUTLIER) cc_final: -0.1157 (tp30) REVERT: A 324 MET cc_start: 0.7229 (mmm) cc_final: 0.7021 (mmm) outliers start: 8 outliers final: 6 residues processed: 31 average time/residue: 0.1290 time to fit residues: 5.5564 Evaluate side-chains 31 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL 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 Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.0070 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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: 0.5507 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3655 Z= 0.177 Angle : 0.565 7.420 4989 Z= 0.280 Chirality : 0.041 0.178 592 Planarity : 0.004 0.033 618 Dihedral : 4.052 14.672 498 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.60 % Allowed : 15.96 % 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: 1.68 (0.40), residues: 465 helix: 1.64 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.70 (0.64), residues: 102 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 0.009 0.001 PHE A 69 TYR 0.006 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 : 0.390 Fit side-chains REVERT: A 262 GLU cc_start: -0.0360 (OUTLIER) cc_final: -0.1173 (tp30) outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.1060 time to fit residues: 4.1223 Evaluate side-chains 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.0270 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 0.0170 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3655 Z= 0.159 Angle : 0.548 8.051 4989 Z= 0.273 Chirality : 0.040 0.192 592 Planarity : 0.004 0.034 618 Dihedral : 3.949 14.685 498 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.86 % Allowed : 16.22 % Favored : 81.91 % 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: 1.80 (0.41), residues: 465 helix: 1.72 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.67 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.009 0.001 PHE A 69 TYR 0.006 0.001 TYR A 327 ARG 0.003 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 27 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.391 Fit side-chains REVERT: A 262 GLU cc_start: -0.0533 (OUTLIER) cc_final: -0.1095 (tp30) REVERT: A 427 CYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7269 (t) outliers start: 7 outliers final: 4 residues processed: 25 average time/residue: 0.1005 time to fit residues: 3.9519 Evaluate side-chains 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.0060 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.4778 r_free = 0.4778 target = 0.270944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.247768 restraints weight = 4013.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.251947 restraints weight = 2472.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.254875 restraints weight = 1706.744| |-----------------------------------------------------------------------------| r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3655 Z= 0.201 Angle : 0.602 11.064 4989 Z= 0.296 Chirality : 0.042 0.177 592 Planarity : 0.004 0.031 618 Dihedral : 4.118 14.976 498 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: 1.58 (0.40), residues: 465 helix: 1.57 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.76 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 315 HIS 0.002 0.001 HIS A 377 PHE 0.008 0.001 PHE A 69 TYR 0.006 0.001 TYR A 312 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: 1016.21 seconds wall clock time: 18 minutes 33.69 seconds (1113.69 seconds total)