Starting phenix.real_space_refine on Thu Nov 14 01:18:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/11_2024/8g92_29860.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/11_2024/8g92_29860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/11_2024/8g92_29860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/11_2024/8g92_29860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/11_2024/8g92_29860.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g92_29860/11_2024/8g92_29860.cif" } resolution = 3.6 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= 0.002 sd= 0.050 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 17 5.16 5 C 2117 2.51 5 N 529 2.21 5 O 548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3211 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3186 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 12, 'TRANS': 402} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'YUX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.20, per 1000 atoms: 1.00 Number of scatterers: 3211 At special positions: 0 Unit cell: (69.72, 64.74, 81.34, 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 17 16.00 O 548 8.00 N 529 7.00 C 2117 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 - 3.00 Amino acid : True - 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: 0.93 Conformation dependent library (CDL) restraints added in 404.2 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 93.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 100 through 125 removed outlier: 3.854A pdb=" N ALA A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 165 removed outlier: 3.883A pdb=" N ALA A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.712A pdb=" N ASP A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 186 removed outlier: 4.049A pdb=" N ILE A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 222 removed outlier: 3.600A pdb=" N TYR A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.955A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 257 Proline residue: A 239 - end of helix removed outlier: 4.239A pdb=" N TYR A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 265 removed outlier: 4.045A pdb=" N LEU A 263 " --> pdb=" O TRP A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.947A pdb=" N ILE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 313 through 347 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 361 through 389 removed outlier: 4.673A pdb=" N PHE A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 419 removed outlier: 3.533A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 442 removed outlier: 3.723A pdb=" N SER A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 451 removed outlier: 3.629A pdb=" N ILE A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 470 Processing helix chain 'A' and resid 474 through 489 removed outlier: 3.644A pdb=" N SER A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 539 removed outlier: 4.255A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 822 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: 0.83 Time building geometry restraints manager: 1.01 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: 967 1.34 - 1.46: 545 1.46 - 1.57: 1748 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3286 Sorted by residual: bond pdb=" C07 YUX A 601 " pdb=" C08 YUX A 601 " ideal model delta sigma weight residual 1.460 1.532 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C04 YUX A 601 " pdb=" C05 YUX A 601 " ideal model delta sigma weight residual 1.481 1.530 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C05 YUX A 601 " pdb=" N06 YUX A 601 " ideal model delta sigma weight residual 1.291 1.335 -0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" C11 YUX A 601 " pdb=" C12 YUX A 601 " ideal model delta sigma weight residual 1.500 1.537 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" N24 YUX A 601 " pdb=" O25 YUX A 601 " ideal model delta sigma weight residual 1.367 1.339 0.028 2.00e-02 2.50e+03 1.99e+00 ... (remaining 3281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4315 1.56 - 3.11: 114 3.11 - 4.67: 18 4.67 - 6.23: 9 6.23 - 7.79: 2 Bond angle restraints: 4458 Sorted by residual: angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 121.39 -7.79 1.90e+00 2.77e-01 1.68e+01 angle pdb=" C THR A 121 " pdb=" N VAL A 122 " pdb=" CA VAL A 122 " ideal model delta sigma weight residual 121.19 116.43 4.76 1.59e+00 3.96e-01 8.96e+00 angle pdb=" C PHE A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 120.31 116.15 4.16 1.52e+00 4.33e-01 7.48e+00 angle pdb=" C04 YUX A 601 " pdb=" C05 YUX A 601 " pdb=" O25 YUX A 601 " ideal model delta sigma weight residual 119.00 126.78 -7.78 3.00e+00 1.11e-01 6.73e+00 angle pdb=" C ALA A 395 " pdb=" N ASP A 396 " pdb=" CA ASP A 396 " ideal model delta sigma weight residual 120.97 124.39 -3.42 1.48e+00 4.57e-01 5.34e+00 ... (remaining 4453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 1635 14.28 - 28.55: 193 28.55 - 42.83: 53 42.83 - 57.10: 9 57.10 - 71.38: 3 Dihedral angle restraints: 1893 sinusoidal: 710 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ARG A 264 " pdb=" C ARG A 264 " pdb=" N VAL A 265 " pdb=" CA VAL A 265 " ideal model delta harmonic sigma weight residual -180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG A 227 " pdb=" CD ARG A 227 " pdb=" NE ARG A 227 " pdb=" CZ ARG A 227 " ideal model delta sinusoidal sigma weight residual -90.00 -134.97 44.97 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CA TYR A 235 " pdb=" C TYR A 235 " pdb=" N PHE A 236 " pdb=" CA PHE A 236 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 1890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 340 0.036 - 0.071: 145 0.071 - 0.107: 29 0.107 - 0.143: 7 0.143 - 0.178: 1 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA TRP A 178 " pdb=" N TRP A 178 " pdb=" C TRP A 178 " pdb=" CB TRP A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE A 452 " pdb=" N ILE A 452 " pdb=" C ILE A 452 " pdb=" CB ILE A 452 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 519 not shown) Planarity restraints: 542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.018 2.00e-02 2.50e+03 1.23e-02 3.80e+00 pdb=" CG TRP A 178 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 266 " 0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 267 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 178 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C TRP A 178 " -0.023 2.00e-02 2.50e+03 pdb=" O TRP A 178 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 179 " 0.008 2.00e-02 2.50e+03 ... (remaining 539 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 604 2.75 - 3.29: 3321 3.29 - 3.83: 5533 3.83 - 4.36: 6354 4.36 - 4.90: 10830 Nonbonded interactions: 26642 Sorted by model distance: nonbonded pdb=" O GLY A 219 " pdb=" NH1 ARG A 227 " model vdw 2.219 3.120 nonbonded pdb=" OH TYR A 246 " pdb=" O GLY A 333 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARG A 487 " pdb=" OD2 ASP A 492 " model vdw 2.302 3.120 nonbonded pdb=" OG SER A 250 " pdb=" OG SER A 363 " model vdw 2.315 3.040 nonbonded pdb=" NH1 ARG A 530 " pdb=" OE2 GLU A 534 " model vdw 2.332 3.120 ... (remaining 26637 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.170 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 3286 Z= 0.340 Angle : 0.675 7.787 4458 Z= 0.381 Chirality : 0.040 0.178 522 Planarity : 0.004 0.038 542 Dihedral : 13.627 71.381 1135 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % 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: -1.13 (0.38), residues: 409 helix: -0.45 (0.25), residues: 356 sheet: None (None), residues: 0 loop : -1.68 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.019 0.002 PHE A 234 TYR 0.009 0.001 TYR A 246 ARG 0.004 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.7741 (mptt) cc_final: 0.7058 (mtmm) REVERT: A 192 TYR cc_start: 0.7513 (m-80) cc_final: 0.7310 (m-80) REVERT: A 394 ARG cc_start: 0.5818 (mtt180) cc_final: 0.5562 (mtt180) REVERT: A 481 PHE cc_start: 0.8928 (t80) cc_final: 0.8634 (t80) REVERT: A 530 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6856 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1569 time to fit residues: 16.5985 Evaluate side-chains 64 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 190 GLN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3286 Z= 0.226 Angle : 0.612 7.310 4458 Z= 0.324 Chirality : 0.040 0.164 522 Planarity : 0.004 0.039 542 Dihedral : 5.584 43.643 459 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.38 % Allowed : 16.67 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.42), residues: 409 helix: 0.88 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.93 (0.91), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 178 HIS 0.002 0.001 HIS A 341 PHE 0.016 0.002 PHE A 234 TYR 0.018 0.002 TYR A 426 ARG 0.005 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.7673 (mptt) cc_final: 0.7190 (mttp) REVERT: A 192 TYR cc_start: 0.7470 (m-80) cc_final: 0.7258 (m-80) REVERT: A 394 ARG cc_start: 0.5848 (mtt180) cc_final: 0.5614 (mtt180) REVERT: A 422 ILE cc_start: 0.8096 (tt) cc_final: 0.7701 (mm) REVERT: A 481 PHE cc_start: 0.8906 (t80) cc_final: 0.8599 (t80) REVERT: A 530 ARG cc_start: 0.7162 (ttt-90) cc_final: 0.6747 (tmt-80) outliers start: 8 outliers final: 5 residues processed: 74 average time/residue: 0.1156 time to fit residues: 11.0458 Evaluate side-chains 68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 362 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3286 Z= 0.212 Angle : 0.592 7.209 4458 Z= 0.307 Chirality : 0.039 0.162 522 Planarity : 0.004 0.038 542 Dihedral : 5.520 47.976 459 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.27 % Allowed : 18.15 % Favored : 78.57 % 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: 1.70 (0.42), residues: 409 helix: 1.39 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.55 (0.94), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 178 HIS 0.007 0.002 HIS A 341 PHE 0.015 0.001 PHE A 234 TYR 0.011 0.001 TYR A 426 ARG 0.004 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.7592 (mptt) cc_final: 0.6809 (mtmm) REVERT: A 161 LEU cc_start: 0.8275 (mp) cc_final: 0.7981 (mp) REVERT: A 192 TYR cc_start: 0.7473 (m-80) cc_final: 0.7252 (m-80) REVERT: A 394 ARG cc_start: 0.5923 (mtt180) cc_final: 0.5677 (mtt180) REVERT: A 407 SER cc_start: 0.8762 (t) cc_final: 0.8468 (p) REVERT: A 422 ILE cc_start: 0.7953 (tt) cc_final: 0.7545 (mm) REVERT: A 481 PHE cc_start: 0.8882 (t80) cc_final: 0.8572 (t80) REVERT: A 530 ARG cc_start: 0.7155 (ttt-90) cc_final: 0.6759 (tmt-80) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.1196 time to fit residues: 11.4033 Evaluate side-chains 70 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 484 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3286 Z= 0.254 Angle : 0.639 10.172 4458 Z= 0.325 Chirality : 0.042 0.343 522 Planarity : 0.004 0.037 542 Dihedral : 5.705 52.743 459 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.98 % Allowed : 19.64 % Favored : 77.38 % 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: 1.87 (0.43), residues: 409 helix: 1.45 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.07 (1.05), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 178 HIS 0.006 0.002 HIS A 341 PHE 0.016 0.002 PHE A 234 TYR 0.017 0.002 TYR A 426 ARG 0.005 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.7616 (mptt) cc_final: 0.6939 (mtmm) REVERT: A 161 LEU cc_start: 0.8206 (mp) cc_final: 0.7898 (mp) REVERT: A 192 TYR cc_start: 0.7469 (m-80) cc_final: 0.7251 (m-80) REVERT: A 407 SER cc_start: 0.8799 (t) cc_final: 0.8503 (p) REVERT: A 422 ILE cc_start: 0.7885 (tt) cc_final: 0.7427 (mm) REVERT: A 481 PHE cc_start: 0.8897 (t80) cc_final: 0.8588 (t80) REVERT: A 530 ARG cc_start: 0.7121 (ttt-90) cc_final: 0.6724 (tmt-80) outliers start: 10 outliers final: 9 residues processed: 77 average time/residue: 0.1140 time to fit residues: 11.3591 Evaluate side-chains 69 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 484 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3286 Z= 0.225 Angle : 0.614 8.153 4458 Z= 0.313 Chirality : 0.040 0.165 522 Planarity : 0.004 0.036 542 Dihedral : 5.691 54.153 459 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.57 % Allowed : 21.73 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.43), residues: 409 helix: 1.57 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.01 (1.06), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.015 0.001 PHE A 234 TYR 0.014 0.001 TYR A 426 ARG 0.004 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.342 Fit side-chains REVERT: A 102 LYS cc_start: 0.7571 (mptt) cc_final: 0.6900 (mtmm) REVERT: A 161 LEU cc_start: 0.8132 (mp) cc_final: 0.7809 (mp) REVERT: A 192 TYR cc_start: 0.7474 (m-80) cc_final: 0.7266 (m-80) REVERT: A 407 SER cc_start: 0.8811 (t) cc_final: 0.8497 (p) REVERT: A 413 LEU cc_start: 0.8918 (mm) cc_final: 0.8578 (tt) REVERT: A 422 ILE cc_start: 0.7797 (tt) cc_final: 0.7290 (mm) REVERT: A 481 PHE cc_start: 0.8879 (t80) cc_final: 0.8596 (t80) REVERT: A 530 ARG cc_start: 0.7089 (ttt-90) cc_final: 0.6694 (tmt-80) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.1128 time to fit residues: 11.5378 Evaluate side-chains 74 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 484 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 18 optimal weight: 0.0060 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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: 0.7775 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3286 Z= 0.179 Angle : 0.601 8.592 4458 Z= 0.307 Chirality : 0.038 0.150 522 Planarity : 0.004 0.037 542 Dihedral : 5.443 53.020 459 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.08 % Allowed : 24.11 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.43), residues: 409 helix: 1.78 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.18 (0.99), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 178 HIS 0.001 0.001 HIS A 341 PHE 0.014 0.001 PHE A 234 TYR 0.012 0.001 TYR A 426 ARG 0.003 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.351 Fit side-chains REVERT: A 102 LYS cc_start: 0.7534 (mptt) cc_final: 0.6902 (mtmm) REVERT: A 161 LEU cc_start: 0.8011 (mp) cc_final: 0.7640 (mp) REVERT: A 192 TYR cc_start: 0.7503 (m-80) cc_final: 0.7273 (m-80) REVERT: A 334 MET cc_start: 0.8664 (tpt) cc_final: 0.8340 (tpt) REVERT: A 407 SER cc_start: 0.8800 (t) cc_final: 0.8490 (p) REVERT: A 413 LEU cc_start: 0.8901 (mm) cc_final: 0.8602 (tt) REVERT: A 481 PHE cc_start: 0.8835 (t80) cc_final: 0.8571 (t80) REVERT: A 530 ARG cc_start: 0.7013 (ttt-90) cc_final: 0.6575 (tmt-80) outliers start: 7 outliers final: 7 residues processed: 71 average time/residue: 0.1356 time to fit residues: 12.2294 Evaluate side-chains 68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 484 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7847 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3286 Z= 0.240 Angle : 0.624 8.110 4458 Z= 0.319 Chirality : 0.040 0.171 522 Planarity : 0.004 0.038 542 Dihedral : 5.646 54.941 459 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.68 % Allowed : 23.51 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.43), residues: 409 helix: 1.69 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.12 (0.97), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 178 HIS 0.002 0.001 HIS A 341 PHE 0.014 0.002 PHE A 234 TYR 0.010 0.001 TYR A 426 ARG 0.005 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.353 Fit side-chains REVERT: A 102 LYS cc_start: 0.7505 (mptt) cc_final: 0.6820 (mtmm) REVERT: A 161 LEU cc_start: 0.8089 (mp) cc_final: 0.7717 (mp) REVERT: A 192 TYR cc_start: 0.7498 (m-80) cc_final: 0.7276 (m-80) REVERT: A 407 SER cc_start: 0.8798 (t) cc_final: 0.8507 (p) REVERT: A 413 LEU cc_start: 0.8929 (mm) cc_final: 0.8603 (tt) REVERT: A 481 PHE cc_start: 0.8862 (t80) cc_final: 0.8636 (t80) REVERT: A 530 ARG cc_start: 0.6979 (ttt-90) cc_final: 0.6582 (tmt-80) outliers start: 9 outliers final: 9 residues processed: 73 average time/residue: 0.1161 time to fit residues: 11.2099 Evaluate side-chains 71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 484 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 0.0670 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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: 0.7827 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3286 Z= 0.217 Angle : 0.615 8.284 4458 Z= 0.312 Chirality : 0.039 0.162 522 Planarity : 0.004 0.038 542 Dihedral : 5.635 54.924 459 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.27 % Allowed : 24.11 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.42), residues: 409 helix: 1.80 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -0.25 (0.88), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.014 0.001 PHE A 234 TYR 0.015 0.001 TYR A 426 ARG 0.004 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.7510 (mptt) cc_final: 0.6814 (mtmm) REVERT: A 161 LEU cc_start: 0.8083 (mp) cc_final: 0.7709 (mp) REVERT: A 407 SER cc_start: 0.8780 (t) cc_final: 0.8498 (p) REVERT: A 413 LEU cc_start: 0.8921 (mm) cc_final: 0.8598 (tt) REVERT: A 481 PHE cc_start: 0.8864 (t80) cc_final: 0.8641 (t80) REVERT: A 530 ARG cc_start: 0.6951 (ttt-90) cc_final: 0.6571 (tmt-80) outliers start: 11 outliers final: 10 residues processed: 73 average time/residue: 0.1496 time to fit residues: 13.4548 Evaluate side-chains 71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 484 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7848 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3286 Z= 0.239 Angle : 0.631 8.828 4458 Z= 0.321 Chirality : 0.040 0.168 522 Planarity : 0.004 0.039 542 Dihedral : 5.686 55.765 459 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.27 % Allowed : 23.81 % Favored : 72.92 % 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: 2.21 (0.42), residues: 409 helix: 1.73 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -0.25 (0.88), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.013 0.002 PHE A 234 TYR 0.013 0.001 TYR A 426 ARG 0.004 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.7531 (mptt) cc_final: 0.6840 (mtmm) REVERT: A 161 LEU cc_start: 0.8099 (mp) cc_final: 0.7728 (mp) REVERT: A 407 SER cc_start: 0.8790 (t) cc_final: 0.8515 (p) REVERT: A 413 LEU cc_start: 0.8915 (mm) cc_final: 0.8590 (tt) REVERT: A 481 PHE cc_start: 0.8856 (t80) cc_final: 0.8643 (t80) REVERT: A 530 ARG cc_start: 0.6945 (ttt-90) cc_final: 0.6565 (tmt-80) outliers start: 11 outliers final: 11 residues processed: 68 average time/residue: 0.1496 time to fit residues: 12.7967 Evaluate side-chains 74 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 484 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3286 Z= 0.185 Angle : 0.600 8.659 4458 Z= 0.304 Chirality : 0.039 0.150 522 Planarity : 0.004 0.038 542 Dihedral : 5.459 54.175 459 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.68 % Allowed : 25.00 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.42), residues: 409 helix: 1.82 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -0.16 (0.87), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 178 HIS 0.002 0.001 HIS A 341 PHE 0.015 0.001 PHE A 234 TYR 0.012 0.001 TYR A 120 ARG 0.003 0.000 ARG A 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.7457 (mptt) cc_final: 0.6822 (mtmm) REVERT: A 126 LEU cc_start: 0.8272 (tp) cc_final: 0.7717 (mt) REVERT: A 161 LEU cc_start: 0.8048 (mp) cc_final: 0.7664 (mp) REVERT: A 407 SER cc_start: 0.8786 (t) cc_final: 0.8501 (p) REVERT: A 413 LEU cc_start: 0.8899 (mm) cc_final: 0.8604 (tt) REVERT: A 481 PHE cc_start: 0.8815 (t80) cc_final: 0.8573 (t80) REVERT: A 530 ARG cc_start: 0.6931 (ttt-90) cc_final: 0.6534 (tmt-80) outliers start: 9 outliers final: 9 residues processed: 68 average time/residue: 0.1477 time to fit residues: 12.4040 Evaluate side-chains 71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 484 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.170194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131872 restraints weight = 4482.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135826 restraints weight = 2824.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138454 restraints weight = 2123.127| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3286 Z= 0.232 Angle : 0.638 9.104 4458 Z= 0.323 Chirality : 0.040 0.163 522 Planarity : 0.004 0.039 542 Dihedral : 5.554 54.033 459 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.27 % Allowed : 24.40 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.42), residues: 409 helix: 1.77 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -0.15 (0.88), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.013 0.001 PHE A 234 TYR 0.013 0.001 TYR A 339 ARG 0.004 0.000 ARG A 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1020.69 seconds wall clock time: 19 minutes 30.33 seconds (1170.33 seconds total)