Starting phenix.real_space_refine on Fri Dec 27 12:33:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jwh_36683/12_2024/8jwh_36683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jwh_36683/12_2024/8jwh_36683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jwh_36683/12_2024/8jwh_36683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jwh_36683/12_2024/8jwh_36683.map" model { file = "/net/cci-nas-00/data/ceres_data/8jwh_36683/12_2024/8jwh_36683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jwh_36683/12_2024/8jwh_36683.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 29 5.16 5 C 3115 2.51 5 N 806 2.21 5 O 920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 3.47, per 1000 atoms: 0.71 Number of scatterers: 4870 At special positions: 0 Unit cell: (77.0408, 84.5774, 69.5042, 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 29 16.00 O 920 8.00 N 806 7.00 C 3115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 524 " distance=2.03 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: 1.25 Conformation dependent library (CDL) restraints added in 603.7 milliseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 3 sheets defined 70.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 35 Processing helix chain 'A' and resid 37 through 64 removed outlier: 3.584A pdb=" N VAL A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 70 removed outlier: 4.100A pdb=" N GLU A 69 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.635A pdb=" N LEU A 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 112 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 139 through 176 removed outlier: 4.530A pdb=" N LYS A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 201 through 234 Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 285 through 300 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 347 through 367 removed outlier: 3.645A pdb=" N TYR A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 379 through 395 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 413 through 448 Proline residue: A 433 - end of helix Processing helix chain 'A' and resid 453 through 466 removed outlier: 4.404A pdb=" N LYS A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 484 Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.987A pdb=" N TYR A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.519A pdb=" N LYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 removed outlier: 4.036A pdb=" N GLY A 543 " --> pdb=" O MET A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 563 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 245 removed outlier: 6.211A pdb=" N LEU A 244 " --> pdb=" O VAL A 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 332 297 hydrogen bonds defined for protein. 864 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: 1.34 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1569 1.34 - 1.46: 1197 1.46 - 1.58: 2190 1.58 - 1.70: 1 1.70 - 1.81: 50 Bond restraints: 5007 Sorted by residual: bond pdb=" C GLU A 127 " pdb=" N PRO A 128 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.53e+00 bond pdb=" CB PRO A 66 " pdb=" CG PRO A 66 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.16e+00 bond pdb=" C ASN A 116 " pdb=" N PRO A 117 " ideal model delta sigma weight residual 1.332 1.350 -0.017 8.90e-03 1.26e+04 3.73e+00 bond pdb=" C GLU A 571 " pdb=" N PRO A 572 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.55e+00 bond pdb=" C LYS A 216 " pdb=" N PRO A 217 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.38e-02 5.25e+03 3.05e+00 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 6437 1.66 - 3.32: 301 3.32 - 4.98: 45 4.98 - 6.63: 13 6.63 - 8.29: 7 Bond angle restraints: 6803 Sorted by residual: angle pdb=" CA PRO A 66 " pdb=" N PRO A 66 " pdb=" CD PRO A 66 " ideal model delta sigma weight residual 112.00 103.71 8.29 1.40e+00 5.10e-01 3.51e+01 angle pdb=" N VAL A 275 " pdb=" CA VAL A 275 " pdb=" C VAL A 275 " ideal model delta sigma weight residual 106.21 112.43 -6.22 1.07e+00 8.73e-01 3.38e+01 angle pdb=" N ASN A 119 " pdb=" CA ASN A 119 " pdb=" C ASN A 119 " ideal model delta sigma weight residual 108.69 101.49 7.20 1.80e+00 3.09e-01 1.60e+01 angle pdb=" N VAL A 300 " pdb=" CA VAL A 300 " pdb=" C VAL A 300 " ideal model delta sigma weight residual 112.98 108.45 4.53 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C ASN A 119 " pdb=" CA ASN A 119 " pdb=" CB ASN A 119 " ideal model delta sigma weight residual 110.17 113.61 -3.44 9.90e-01 1.02e+00 1.21e+01 ... (remaining 6798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2455 17.96 - 35.92: 362 35.92 - 53.88: 111 53.88 - 71.84: 19 71.84 - 89.80: 12 Dihedral angle restraints: 2959 sinusoidal: 1205 harmonic: 1754 Sorted by residual: dihedral pdb=" CA ASN A 119 " pdb=" C ASN A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta harmonic sigma weight residual -180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA GLU A 127 " pdb=" C GLU A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual 180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLN A 121 " pdb=" C GLN A 121 " pdb=" N GLU A 122 " pdb=" CA GLU A 122 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 2956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 442 0.035 - 0.071: 185 0.071 - 0.106: 62 0.106 - 0.141: 17 0.141 - 0.176: 4 Chirality restraints: 710 Sorted by residual: chirality pdb=" CA PRO A 120 " pdb=" N PRO A 120 " pdb=" C PRO A 120 " pdb=" CB PRO A 120 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA PRO A 240 " pdb=" N PRO A 240 " pdb=" C PRO A 240 " pdb=" CB PRO A 240 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CB THR A 107 " pdb=" CA THR A 107 " pdb=" OG1 THR A 107 " pdb=" CG2 THR A 107 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 707 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 65 " -0.090 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO A 66 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 116 " -0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO A 117 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 481 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.15e+00 pdb=" N PRO A 482 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 482 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 482 " 0.037 5.00e-02 4.00e+02 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 117 2.69 - 3.24: 5058 3.24 - 3.79: 8284 3.79 - 4.35: 10541 4.35 - 4.90: 17198 Nonbonded interactions: 41198 Sorted by model distance: nonbonded pdb=" OH TYR A 219 " pdb=" O VAL A 467 " model vdw 2.135 3.040 nonbonded pdb=" OE1 GLU A 209 " pdb=" OH TYR A 436 " model vdw 2.187 3.040 nonbonded pdb=" O THR A 107 " pdb=" OG1 THR A 111 " model vdw 2.193 3.040 nonbonded pdb=" O ALA A 483 " pdb=" OG SER A 489 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 152 " pdb=" OE1 GLU A 153 " model vdw 2.235 3.040 ... (remaining 41193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.520 Find NCS groups from input model: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 0.114 5007 Z= 0.250 Angle : 0.840 8.292 6803 Z= 0.504 Chirality : 0.045 0.176 710 Planarity : 0.008 0.131 881 Dihedral : 19.175 89.805 1820 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.76 % Allowed : 28.65 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.43 (0.34), residues: 595 helix: 0.30 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.27 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 455 HIS 0.006 0.001 HIS A 355 PHE 0.012 0.002 PHE A 420 TYR 0.014 0.002 TYR A 367 ARG 0.002 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6511 (mm-30) REVERT: A 220 GLU cc_start: 0.6823 (tt0) cc_final: 0.6455 (tt0) outliers start: 4 outliers final: 0 residues processed: 83 average time/residue: 0.1519 time to fit residues: 16.9350 Evaluate side-chains 72 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5007 Z= 0.240 Angle : 0.704 7.948 6803 Z= 0.364 Chirality : 0.045 0.160 710 Planarity : 0.006 0.081 881 Dihedral : 5.768 33.108 642 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.55 % Allowed : 26.38 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.31 (0.33), residues: 595 helix: 0.34 (0.25), residues: 398 sheet: -4.42 (1.20), residues: 10 loop : -0.94 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 455 HIS 0.005 0.001 HIS A 355 PHE 0.016 0.002 PHE A 351 TYR 0.019 0.002 TYR A 367 ARG 0.003 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6583 (mm-30) REVERT: A 220 GLU cc_start: 0.6893 (tt0) cc_final: 0.6506 (tt0) REVERT: A 439 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8038 (mm-30) REVERT: A 539 MET cc_start: 0.7571 (tmm) cc_final: 0.7151 (tmm) outliers start: 24 outliers final: 10 residues processed: 100 average time/residue: 0.1598 time to fit residues: 21.2747 Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 581 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5007 Z= 0.208 Angle : 0.677 8.131 6803 Z= 0.344 Chirality : 0.043 0.149 710 Planarity : 0.006 0.069 881 Dihedral : 5.559 31.938 642 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.80 % Allowed : 28.27 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.18 % 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: -0.15 (0.33), residues: 595 helix: 0.47 (0.25), residues: 398 sheet: -4.22 (1.26), residues: 10 loop : -0.92 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 PHE 0.013 0.002 PHE A 351 TYR 0.015 0.002 TYR A 497 ARG 0.006 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6868 (mm-30) REVERT: A 220 GLU cc_start: 0.6860 (tt0) cc_final: 0.6507 (tt0) REVERT: A 539 MET cc_start: 0.7589 (tmm) cc_final: 0.7291 (tmm) outliers start: 20 outliers final: 15 residues processed: 93 average time/residue: 0.1414 time to fit residues: 18.1840 Evaluate side-chains 83 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 493 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5007 Z= 0.177 Angle : 0.645 8.197 6803 Z= 0.326 Chirality : 0.042 0.151 710 Planarity : 0.005 0.061 881 Dihedral : 5.171 31.083 642 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.98 % Allowed : 28.84 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.11 (0.34), residues: 595 helix: 0.66 (0.25), residues: 399 sheet: -4.11 (1.30), residues: 10 loop : -0.79 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 548 HIS 0.005 0.001 HIS A 355 PHE 0.010 0.001 PHE A 297 TYR 0.014 0.001 TYR A 497 ARG 0.004 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7117 (mm-30) REVERT: A 220 GLU cc_start: 0.6804 (tt0) cc_final: 0.6462 (tt0) REVERT: A 256 PHE cc_start: 0.6977 (m-10) cc_final: 0.5971 (m-80) REVERT: A 333 LEU cc_start: 0.7539 (mt) cc_final: 0.7162 (mt) REVERT: A 539 MET cc_start: 0.7508 (tmm) cc_final: 0.7272 (tmm) outliers start: 21 outliers final: 13 residues processed: 98 average time/residue: 0.1439 time to fit residues: 19.2982 Evaluate side-chains 82 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 493 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5007 Z= 0.211 Angle : 0.659 8.560 6803 Z= 0.335 Chirality : 0.043 0.185 710 Planarity : 0.005 0.057 881 Dihedral : 5.177 29.631 642 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.42 % Allowed : 29.03 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.34), residues: 595 helix: 0.69 (0.25), residues: 399 sheet: -4.02 (1.32), residues: 10 loop : -0.68 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 PHE 0.015 0.001 PHE A 351 TYR 0.016 0.002 TYR A 497 ARG 0.003 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7031 (mmmt) REVERT: A 220 GLU cc_start: 0.6887 (tt0) cc_final: 0.6586 (tt0) REVERT: A 390 MET cc_start: 0.7787 (mmm) cc_final: 0.7397 (mmm) REVERT: A 539 MET cc_start: 0.7443 (tmm) cc_final: 0.7185 (tmm) REVERT: A 592 TRP cc_start: 0.3639 (OUTLIER) cc_final: 0.2221 (m100) outliers start: 18 outliers final: 11 residues processed: 90 average time/residue: 0.1671 time to fit residues: 19.7883 Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 26 optimal weight: 0.0570 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5007 Z= 0.203 Angle : 0.657 8.446 6803 Z= 0.334 Chirality : 0.043 0.152 710 Planarity : 0.005 0.057 881 Dihedral : 5.160 28.959 642 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.80 % Allowed : 29.79 % Favored : 66.41 % 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: 0.29 (0.34), residues: 595 helix: 0.82 (0.25), residues: 393 sheet: -4.16 (1.25), residues: 10 loop : -0.72 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 150 HIS 0.004 0.001 HIS A 355 PHE 0.013 0.001 PHE A 351 TYR 0.016 0.002 TYR A 497 ARG 0.002 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7063 (mmmt) REVERT: A 220 GLU cc_start: 0.6920 (tt0) cc_final: 0.6626 (tt0) REVERT: A 390 MET cc_start: 0.7803 (mmm) cc_final: 0.7447 (mmm) REVERT: A 539 MET cc_start: 0.7401 (tmm) cc_final: 0.7189 (tmm) REVERT: A 592 TRP cc_start: 0.3621 (OUTLIER) cc_final: 0.2366 (m100) outliers start: 20 outliers final: 14 residues processed: 85 average time/residue: 0.1539 time to fit residues: 17.8707 Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.0370 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5007 Z= 0.179 Angle : 0.636 8.701 6803 Z= 0.322 Chirality : 0.042 0.151 710 Planarity : 0.005 0.055 881 Dihedral : 5.045 29.179 642 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.17 % Allowed : 29.03 % Favored : 66.79 % 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: 0.40 (0.34), residues: 595 helix: 0.88 (0.25), residues: 393 sheet: -3.39 (1.35), residues: 10 loop : -0.64 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 150 HIS 0.003 0.001 HIS A 355 PHE 0.011 0.001 PHE A 351 TYR 0.013 0.001 TYR A 497 ARG 0.006 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6974 (mmmt) REVERT: A 220 GLU cc_start: 0.6872 (tt0) cc_final: 0.6586 (tt0) REVERT: A 390 MET cc_start: 0.7849 (mmm) cc_final: 0.7445 (mmm) REVERT: A 592 TRP cc_start: 0.3555 (OUTLIER) cc_final: 0.2419 (m100) outliers start: 22 outliers final: 15 residues processed: 84 average time/residue: 0.1373 time to fit residues: 15.9184 Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5007 Z= 0.211 Angle : 0.658 8.417 6803 Z= 0.335 Chirality : 0.043 0.152 710 Planarity : 0.005 0.055 881 Dihedral : 5.129 29.559 642 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.98 % Allowed : 29.79 % Favored : 66.22 % 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: 0.33 (0.34), residues: 595 helix: 0.81 (0.25), residues: 392 sheet: -3.45 (1.28), residues: 10 loop : -0.63 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 PHE 0.015 0.001 PHE A 351 TYR 0.018 0.002 TYR A 497 ARG 0.006 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7016 (mmmt) REVERT: A 127 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7015 (pp20) REVERT: A 253 TRP cc_start: 0.8053 (OUTLIER) cc_final: 0.7168 (m-90) REVERT: A 390 MET cc_start: 0.7859 (mmm) cc_final: 0.7478 (mmm) REVERT: A 592 TRP cc_start: 0.3679 (OUTLIER) cc_final: 0.2539 (m100) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 0.1341 time to fit residues: 15.5312 Evaluate side-chains 86 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.0060 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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: 0.7509 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5007 Z= 0.180 Angle : 0.633 8.954 6803 Z= 0.321 Chirality : 0.041 0.149 710 Planarity : 0.005 0.054 881 Dihedral : 4.990 29.100 642 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.61 % Allowed : 30.17 % Favored : 66.22 % 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: 0.43 (0.35), residues: 595 helix: 0.90 (0.25), residues: 393 sheet: -3.11 (1.29), residues: 10 loop : -0.66 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 PHE 0.011 0.001 PHE A 351 TYR 0.015 0.001 TYR A 497 ARG 0.006 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6991 (mmmt) REVERT: A 127 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7070 (pp20) REVERT: A 253 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.7301 (m-90) REVERT: A 349 ASP cc_start: 0.6811 (m-30) cc_final: 0.6504 (m-30) REVERT: A 494 PHE cc_start: 0.6313 (OUTLIER) cc_final: 0.5775 (m-80) REVERT: A 553 GLU cc_start: 0.7810 (pp20) cc_final: 0.7377 (mm-30) REVERT: A 592 TRP cc_start: 0.3488 (OUTLIER) cc_final: 0.2429 (m100) outliers start: 19 outliers final: 12 residues processed: 83 average time/residue: 0.1448 time to fit residues: 16.5145 Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5007 Z= 0.224 Angle : 0.676 8.577 6803 Z= 0.346 Chirality : 0.043 0.149 710 Planarity : 0.005 0.054 881 Dihedral : 5.129 29.510 642 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.23 % Allowed : 30.36 % Favored : 66.41 % 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: 0.29 (0.34), residues: 595 helix: 0.76 (0.25), residues: 393 sheet: -2.98 (1.27), residues: 10 loop : -0.65 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 588 HIS 0.004 0.001 HIS A 355 PHE 0.015 0.001 PHE A 351 TYR 0.016 0.002 TYR A 497 ARG 0.003 0.000 ARG A 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7008 (mmmt) REVERT: A 127 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7051 (pp20) REVERT: A 253 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.7264 (m-90) REVERT: A 349 ASP cc_start: 0.6831 (m-30) cc_final: 0.6543 (m-30) REVERT: A 592 TRP cc_start: 0.3723 (OUTLIER) cc_final: 0.2516 (m100) outliers start: 17 outliers final: 13 residues processed: 81 average time/residue: 0.1269 time to fit residues: 14.5287 Evaluate side-chains 84 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.172290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147002 restraints weight = 7449.612| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.67 r_work: 0.3800 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5007 Z= 0.204 Angle : 0.665 8.427 6803 Z= 0.339 Chirality : 0.042 0.150 710 Planarity : 0.005 0.055 881 Dihedral : 5.098 28.168 642 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.61 % Allowed : 29.79 % Favored : 66.60 % 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: 0.34 (0.34), residues: 595 helix: 0.80 (0.25), residues: 393 sheet: -2.36 (1.36), residues: 10 loop : -0.67 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 588 HIS 0.004 0.001 HIS A 355 PHE 0.013 0.001 PHE A 351 TYR 0.015 0.001 TYR A 497 ARG 0.003 0.000 ARG A 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1320.86 seconds wall clock time: 24 minutes 52.60 seconds (1492.60 seconds total)