Starting phenix.real_space_refine on Sun Mar 10 18:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/03_2024/7uuy_26806_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/03_2024/7uuy_26806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/03_2024/7uuy_26806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/03_2024/7uuy_26806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/03_2024/7uuy_26806_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuy_26806/03_2024/7uuy_26806_updated.pdb" } resolution = 3.3 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= 0.003 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 2512 2.51 5 N 601 2.21 5 O 668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3809 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3809 Unusual residues: {'3PH': 1} Classifications: {'peptide': 503, 'undetermined': 1} Link IDs: {'PTRANS': 24, 'TRANS': 478, None: 1} Not linked: pdbres="ASP A 561 " pdbres="3PH A 701 " Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 2.69, per 1000 atoms: 0.71 Number of scatterers: 3809 At special positions: 0 Unit cell: (66.216, 85.44, 85.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 1 15.00 O 668 8.00 N 601 7.00 C 2512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 483 " distance=2.03 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: 1.77 Conformation dependent library (CDL) restraints added in 711.2 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 0 sheets defined 73.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 54 through 65 Proline residue: A 58 - end of helix removed outlier: 3.656A pdb=" N ALA A 64 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 85 through 100 removed outlier: 3.723A pdb=" N LEU A 95 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER A 98 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 99 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 100 " --> pdb=" O ASN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 127 through 160 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 165 through 179 Processing helix chain 'A' and resid 190 through 212 removed outlier: 4.173A pdb=" N VAL A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.559A pdb=" N LEU A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 269 removed outlier: 4.036A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR A 269 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 306 Processing helix chain 'A' and resid 312 through 315 No H-bonds generated for 'chain 'A' and resid 312 through 315' Processing helix chain 'A' and resid 321 through 334 removed outlier: 4.560A pdb=" N MET A 325 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.820A pdb=" N PHE A 333 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 334 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 369 removed outlier: 3.643A pdb=" N THR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 374 No H-bonds generated for 'chain 'A' and resid 371 through 374' Processing helix chain 'A' and resid 379 through 408 removed outlier: 3.626A pdb=" N PHE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 removed outlier: 3.624A pdb=" N GLY A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.670A pdb=" N LEU A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 465 removed outlier: 3.568A pdb=" N THR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 473 No H-bonds generated for 'chain 'A' and resid 470 through 473' Processing helix chain 'A' and resid 523 through 542 removed outlier: 4.055A pdb=" N GLY A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 530 " --> pdb=" O GLY A 527 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR A 531 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 532 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET A 535 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS A 537 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 541 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' 239 hydrogen bonds defined for protein. 618 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: 1.03 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 615 1.33 - 1.45: 1036 1.45 - 1.57: 2202 1.57 - 1.69: 2 1.69 - 1.82: 42 Bond restraints: 3897 Sorted by residual: bond pdb=" O14 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.527 1.654 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" O11 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.703 1.645 0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.526 1.491 0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" O13 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.522 1.491 0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C1 3PH A 701 " pdb=" O11 3PH A 701 " ideal model delta sigma weight residual 1.385 1.409 -0.024 2.00e-02 2.50e+03 1.47e+00 ... (remaining 3892 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.81: 126 106.81 - 113.61: 2186 113.61 - 120.40: 1567 120.40 - 127.20: 1386 127.20 - 134.00: 48 Bond angle restraints: 5313 Sorted by residual: angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" C VAL A 270 " ideal model delta sigma weight residual 112.29 108.82 3.47 9.40e-01 1.13e+00 1.36e+01 angle pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " pdb=" O14 3PH A 701 " ideal model delta sigma weight residual 113.84 104.61 9.23 3.00e+00 1.11e-01 9.48e+00 angle pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " pdb=" O13 3PH A 701 " ideal model delta sigma weight residual 115.12 123.51 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" CB MET A 23 " pdb=" CG MET A 23 " pdb=" SD MET A 23 " ideal model delta sigma weight residual 112.70 118.57 -5.87 3.00e+00 1.11e-01 3.82e+00 angle pdb=" N GLY A 93 " pdb=" CA GLY A 93 " pdb=" C GLY A 93 " ideal model delta sigma weight residual 112.49 110.13 2.36 1.21e+00 6.83e-01 3.81e+00 ... (remaining 5308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2041 15.79 - 31.58: 162 31.58 - 47.37: 39 47.37 - 63.16: 10 63.16 - 78.96: 6 Dihedral angle restraints: 2258 sinusoidal: 838 harmonic: 1420 Sorted by residual: dihedral pdb=" CA LEU A 558 " pdb=" CB LEU A 558 " pdb=" CG LEU A 558 " pdb=" CD1 LEU A 558 " ideal model delta sinusoidal sigma weight residual 180.00 123.13 56.87 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN A 136 " pdb=" CA GLN A 136 " pdb=" CB GLN A 136 " pdb=" CG GLN A 136 " ideal model delta sinusoidal sigma weight residual -180.00 -123.34 -56.66 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" N ASN A 97 " pdb=" CA ASN A 97 " pdb=" CB ASN A 97 " pdb=" CG ASN A 97 " ideal model delta sinusoidal sigma weight residual 60.00 116.64 -56.64 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 489 0.039 - 0.078: 122 0.078 - 0.117: 24 0.117 - 0.156: 0 0.156 - 0.195: 1 Chirality restraints: 636 Sorted by residual: chirality pdb=" C2 3PH A 701 " pdb=" C1 3PH A 701 " pdb=" C3 3PH A 701 " pdb=" O21 3PH A 701 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" CA PRO A 312 " pdb=" N PRO A 312 " pdb=" C PRO A 312 " pdb=" CB PRO A 312 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA PRO A 337 " pdb=" N PRO A 337 " pdb=" C PRO A 337 " pdb=" CB PRO A 337 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.20e-01 ... (remaining 633 not shown) Planarity restraints: 644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 195 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C VAL A 195 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 195 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 311 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 312 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 247 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C PHE A 247 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE A 247 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 248 " 0.009 2.00e-02 2.50e+03 ... (remaining 641 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 46 2.63 - 3.20: 3769 3.20 - 3.77: 5987 3.77 - 4.33: 8184 4.33 - 4.90: 13811 Nonbonded interactions: 31797 Sorted by model distance: nonbonded pdb=" ND2 ASN A 262 " pdb=" OE1 GLN A 265 " model vdw 2.067 2.520 nonbonded pdb=" O HIS A 273 " pdb=" OG1 THR A 274 " model vdw 2.097 2.440 nonbonded pdb=" ND2 ASN A 441 " pdb=" O GLY A 546 " model vdw 2.211 2.520 nonbonded pdb=" OD1 ASP A 311 " pdb=" OH TYR A 324 " model vdw 2.228 2.440 nonbonded pdb=" O HIS A 226 " pdb=" OG SER A 227 " model vdw 2.332 2.440 ... (remaining 31792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 5.120 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.240 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 0.127 3897 Z= 0.233 Angle : 0.580 9.235 5313 Z= 0.291 Chirality : 0.035 0.195 636 Planarity : 0.004 0.045 644 Dihedral : 13.503 78.955 1357 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.25 % Allowed : 10.83 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.41), residues: 495 helix: 1.24 (0.30), residues: 359 sheet: None (None), residues: 0 loop : -1.54 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 15 HIS 0.001 0.000 HIS A 273 PHE 0.010 0.001 PHE A 304 TYR 0.023 0.001 TYR A 17 ARG 0.006 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.6749 (mtm) cc_final: 0.6330 (mtp) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.1414 time to fit residues: 10.6485 Evaluate side-chains 57 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3897 Z= 0.237 Angle : 0.558 7.710 5313 Z= 0.275 Chirality : 0.039 0.164 636 Planarity : 0.004 0.046 644 Dihedral : 8.016 87.150 579 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.76 % Allowed : 10.83 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.41), residues: 495 helix: 1.23 (0.29), residues: 365 sheet: None (None), residues: 0 loop : -1.45 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 559 HIS 0.001 0.000 HIS A 273 PHE 0.012 0.002 PHE A 12 TYR 0.017 0.001 TYR A 17 ARG 0.004 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 516 ASP cc_start: 0.8001 (t0) cc_final: 0.7740 (t0) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.1342 time to fit residues: 11.1335 Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.0060 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 44 optimal weight: 0.3980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3897 Z= 0.182 Angle : 0.517 6.516 5313 Z= 0.254 Chirality : 0.037 0.163 636 Planarity : 0.004 0.044 644 Dihedral : 7.796 88.355 579 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.02 % Allowed : 13.60 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.41), residues: 495 helix: 1.38 (0.29), residues: 365 sheet: None (None), residues: 0 loop : -1.38 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.001 0.001 HIS A 226 PHE 0.029 0.002 PHE A 12 TYR 0.014 0.001 TYR A 17 ARG 0.005 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7859 (tp) cc_final: 0.7580 (tp) REVERT: A 68 MET cc_start: 0.7776 (tpp) cc_final: 0.7308 (tpp) REVERT: A 324 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: A 516 ASP cc_start: 0.7945 (t0) cc_final: 0.7614 (t0) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.1314 time to fit residues: 11.0829 Evaluate side-chains 63 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 chunk 43 optimal weight: 0.0170 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3897 Z= 0.165 Angle : 0.499 6.979 5313 Z= 0.245 Chirality : 0.037 0.189 636 Planarity : 0.004 0.042 644 Dihedral : 7.674 89.409 579 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.77 % Allowed : 13.85 % Favored : 83.38 % 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: 1.25 (0.41), residues: 495 helix: 1.56 (0.29), residues: 365 sheet: None (None), residues: 0 loop : -1.27 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.001 0.000 HIS A 273 PHE 0.038 0.002 PHE A 12 TYR 0.013 0.001 TYR A 17 ARG 0.006 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.444 Fit side-chains REVERT: A 11 THR cc_start: 0.8238 (m) cc_final: 0.7923 (p) REVERT: A 61 LEU cc_start: 0.7851 (tp) cc_final: 0.7558 (tp) REVERT: A 97 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.7968 (t0) REVERT: A 324 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: A 516 ASP cc_start: 0.7886 (t0) cc_final: 0.7497 (t0) outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 0.1455 time to fit residues: 12.3303 Evaluate side-chains 63 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 12 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3897 Z= 0.193 Angle : 0.507 7.222 5313 Z= 0.249 Chirality : 0.037 0.177 636 Planarity : 0.004 0.042 644 Dihedral : 7.611 88.316 579 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.77 % Allowed : 14.86 % Favored : 82.37 % 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: 1.25 (0.40), residues: 495 helix: 1.57 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.26 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.001 0.000 HIS A 226 PHE 0.023 0.002 PHE A 12 TYR 0.010 0.001 TYR A 348 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.385 Fit side-chains REVERT: A 17 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: A 61 LEU cc_start: 0.7811 (tp) cc_final: 0.7574 (tp) REVERT: A 97 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8016 (t0) REVERT: A 324 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: A 516 ASP cc_start: 0.7916 (t0) cc_final: 0.7508 (t0) outliers start: 11 outliers final: 7 residues processed: 61 average time/residue: 0.1302 time to fit residues: 10.4033 Evaluate side-chains 64 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.0040 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3897 Z= 0.177 Angle : 0.502 8.157 5313 Z= 0.245 Chirality : 0.037 0.191 636 Planarity : 0.004 0.041 644 Dihedral : 7.541 86.890 579 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.77 % Allowed : 15.87 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.41), residues: 495 helix: 1.54 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.16 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.000 0.000 HIS A 226 PHE 0.017 0.001 PHE A 12 TYR 0.011 0.001 TYR A 17 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.418 Fit side-chains REVERT: A 17 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: A 61 LEU cc_start: 0.7755 (tp) cc_final: 0.7518 (tp) REVERT: A 97 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8123 (t0) REVERT: A 324 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: A 516 ASP cc_start: 0.7920 (t0) cc_final: 0.7496 (t0) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.1302 time to fit residues: 10.5434 Evaluate side-chains 62 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3897 Z= 0.203 Angle : 0.514 8.370 5313 Z= 0.251 Chirality : 0.038 0.194 636 Planarity : 0.004 0.042 644 Dihedral : 7.444 85.593 579 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.27 % Allowed : 15.62 % Favored : 81.11 % 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: 1.30 (0.41), residues: 495 helix: 1.54 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.19 (0.62), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 15 HIS 0.000 0.000 HIS A 226 PHE 0.016 0.002 PHE A 12 TYR 0.011 0.001 TYR A 17 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.436 Fit side-chains REVERT: A 12 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: A 17 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: A 61 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7522 (tp) REVERT: A 97 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8243 (t0) REVERT: A 324 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: A 516 ASP cc_start: 0.7928 (t0) cc_final: 0.7555 (t0) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 0.1358 time to fit residues: 10.3507 Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 0.0670 chunk 43 optimal weight: 0.0030 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 0.2928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3897 Z= 0.167 Angle : 0.547 14.294 5313 Z= 0.257 Chirality : 0.037 0.185 636 Planarity : 0.004 0.042 644 Dihedral : 7.314 84.533 579 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.52 % Allowed : 17.13 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.41), residues: 495 helix: 1.61 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.26 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.000 0.000 HIS A 226 PHE 0.015 0.001 PHE A 12 TYR 0.011 0.001 TYR A 348 ARG 0.004 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.415 Fit side-chains REVERT: A 12 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: A 17 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: A 23 MET cc_start: 0.7400 (tpp) cc_final: 0.7040 (ttm) REVERT: A 61 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7505 (tp) REVERT: A 516 ASP cc_start: 0.7897 (t0) cc_final: 0.7460 (t0) outliers start: 10 outliers final: 5 residues processed: 60 average time/residue: 0.1412 time to fit residues: 11.2155 Evaluate side-chains 63 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3897 Z= 0.216 Angle : 0.563 14.378 5313 Z= 0.266 Chirality : 0.038 0.181 636 Planarity : 0.004 0.042 644 Dihedral : 7.031 83.520 577 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.02 % Allowed : 18.64 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.41), residues: 495 helix: 1.47 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -1.32 (0.64), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 245 HIS 0.000 0.000 HIS A 273 PHE 0.016 0.002 PHE A 343 TYR 0.011 0.001 TYR A 17 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.448 Fit side-chains REVERT: A 12 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: A 17 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.6777 (m-80) REVERT: A 23 MET cc_start: 0.7420 (tpp) cc_final: 0.7008 (ttm) REVERT: A 61 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7532 (tp) REVERT: A 516 ASP cc_start: 0.7940 (t0) cc_final: 0.7558 (t0) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.1395 time to fit residues: 10.0526 Evaluate side-chains 58 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3897 Z= 0.193 Angle : 0.563 14.411 5313 Z= 0.266 Chirality : 0.038 0.184 636 Planarity : 0.004 0.043 644 Dihedral : 6.950 82.126 577 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.02 % Allowed : 18.64 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.41), residues: 495 helix: 1.51 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -1.33 (0.64), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 245 HIS 0.000 0.000 HIS A 226 PHE 0.015 0.002 PHE A 12 TYR 0.011 0.001 TYR A 17 ARG 0.003 0.000 ARG A 374 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.439 Fit side-chains REVERT: A 12 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: A 17 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: A 23 MET cc_start: 0.7278 (tpp) cc_final: 0.6870 (ttm) REVERT: A 61 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7741 (tp) REVERT: A 516 ASP cc_start: 0.7924 (t0) cc_final: 0.7534 (t0) outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 0.1424 time to fit residues: 10.1507 Evaluate side-chains 59 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.134008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110692 restraints weight = 5263.522| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.69 r_work: 0.3172 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3897 Z= 0.237 Angle : 0.572 14.243 5313 Z= 0.271 Chirality : 0.039 0.185 636 Planarity : 0.004 0.045 644 Dihedral : 6.927 80.773 577 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.27 % Allowed : 18.64 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.41), residues: 495 helix: 1.47 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.97 (0.64), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 458 HIS 0.000 0.000 HIS A 226 PHE 0.017 0.002 PHE A 343 TYR 0.011 0.001 TYR A 118 ARG 0.006 0.000 ARG A 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.62 seconds wall clock time: 23 minutes 34.70 seconds (1414.70 seconds total)