Starting phenix.real_space_refine on Sun Apr 27 06:11:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jwh_36683/04_2025/8jwh_36683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jwh_36683/04_2025/8jwh_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_36683/04_2025/8jwh_36683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jwh_36683/04_2025/8jwh_36683.map" model { file = "/net/cci-nas-00/data/ceres_data/8jwh_36683/04_2025/8jwh_36683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jwh_36683/04_2025/8jwh_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 3.52, per 1000 atoms: 0.72 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: 1.29 Conformation dependent library (CDL) restraints added in 570.5 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: 0.48 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: 1.38 Time building geometry restraints manager: 1.51 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: 0.390 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.140 Find NCS groups from input model: 0.070 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- 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 5010 Z= 0.193 Angle : 0.839 8.292 6809 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 Details of bonding type rmsd hydrogen bonds : bond 0.14451 ( 297) hydrogen bonds : angle 6.89555 ( 864) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.57465 ( 6) covalent geometry : bond 0.00387 ( 5007) covalent geometry : angle 0.83967 ( 6803) *********************** 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 : 0.567 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: 0.1456 time to fit residues: 16.2800 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 : 0.566 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.167687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142399 restraints weight = 7450.270| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.66 r_work: 0.3740 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5010 Z= 0.202 Angle : 0.729 7.788 6809 Z= 0.378 Chirality : 0.047 0.161 710 Planarity : 0.006 0.081 881 Dihedral : 5.892 32.986 642 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.74 % Allowed : 26.57 % Favored : 68.69 % 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: -0.40 (0.33), residues: 595 helix: 0.22 (0.24), residues: 398 sheet: None (None), residues: 0 loop : -1.07 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 548 HIS 0.005 0.001 HIS A 355 PHE 0.020 0.002 PHE A 351 TYR 0.021 0.002 TYR A 367 ARG 0.004 0.001 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.06545 ( 297) hydrogen bonds : angle 5.49745 ( 864) SS BOND : bond 0.00363 ( 3) SS BOND : angle 0.59987 ( 6) covalent geometry : bond 0.00442 ( 5007) covalent geometry : angle 0.72955 ( 6803) *********************** 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 102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6658 (mm-30) REVERT: A 539 MET cc_start: 0.7448 (tmm) cc_final: 0.7048 (tmm) outliers start: 25 outliers final: 13 residues processed: 97 average time/residue: 0.1460 time to fit residues: 19.0647 Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 179 GLU 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 347 THR 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 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.171418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146254 restraints weight = 7576.989| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.72 r_work: 0.3789 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5010 Z= 0.151 Angle : 0.665 8.282 6809 Z= 0.340 Chirality : 0.043 0.149 710 Planarity : 0.006 0.069 881 Dihedral : 5.557 32.202 642 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.61 % Allowed : 28.46 % 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: -0.13 (0.34), residues: 595 helix: 0.46 (0.25), residues: 400 sheet: -4.23 (1.25), residues: 10 loop : -0.84 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 331 HIS 0.005 0.001 HIS A 355 PHE 0.011 0.002 PHE A 351 TYR 0.014 0.001 TYR A 497 ARG 0.005 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05796 ( 297) hydrogen bonds : angle 5.18423 ( 864) SS BOND : bond 0.00203 ( 3) SS BOND : angle 0.42075 ( 6) covalent geometry : bond 0.00304 ( 5007) covalent geometry : angle 0.66558 ( 6803) *********************** 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 101 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6923 (mm-30) REVERT: A 220 GLU cc_start: 0.7049 (tt0) cc_final: 0.6731 (tt0) REVERT: A 349 ASP cc_start: 0.6765 (m-30) cc_final: 0.6512 (m-30) REVERT: A 539 MET cc_start: 0.7496 (tmm) cc_final: 0.7157 (tmm) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 0.1521 time to fit residues: 19.5021 Evaluate side-chains 80 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 215 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.166923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140231 restraints weight = 7674.036| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.78 r_work: 0.3724 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5010 Z= 0.190 Angle : 0.697 8.122 6809 Z= 0.359 Chirality : 0.045 0.149 710 Planarity : 0.006 0.061 881 Dihedral : 5.556 30.600 642 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.74 % Allowed : 27.70 % Favored : 67.55 % 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: -0.13 (0.34), residues: 595 helix: 0.47 (0.25), residues: 394 sheet: -3.94 (1.24), residues: 10 loop : -0.86 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 548 HIS 0.005 0.001 HIS A 487 PHE 0.018 0.002 PHE A 351 TYR 0.019 0.002 TYR A 497 ARG 0.003 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.06268 ( 297) hydrogen bonds : angle 5.25796 ( 864) SS BOND : bond 0.00308 ( 3) SS BOND : angle 0.55641 ( 6) covalent geometry : bond 0.00411 ( 5007) covalent geometry : angle 0.69724 ( 6803) *********************** 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 99 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6889 (mmmt) REVERT: A 127 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7063 (mm-30) REVERT: A 539 MET cc_start: 0.7641 (tmm) cc_final: 0.7358 (tmm) outliers start: 25 outliers final: 18 residues processed: 92 average time/residue: 0.1311 time to fit residues: 16.6921 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 : 0.575 ------------------------------------------------------------------------------- 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 95 SER 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 179 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 HIS 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 314 MET 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 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 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 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 = 0.4192 r_free = 0.4192 target = 0.168506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142737 restraints weight = 7603.133| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.72 r_work: 0.3732 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5010 Z= 0.170 Angle : 0.683 10.283 6809 Z= 0.346 Chirality : 0.044 0.149 710 Planarity : 0.005 0.059 881 Dihedral : 5.455 29.952 642 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.31 % Allowed : 28.27 % 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: -0.01 (0.34), residues: 595 helix: 0.56 (0.25), residues: 393 sheet: -3.88 (1.26), residues: 10 loop : -0.82 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 548 HIS 0.004 0.001 HIS A 247 PHE 0.015 0.001 PHE A 351 TYR 0.016 0.002 TYR A 497 ARG 0.003 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05980 ( 297) hydrogen bonds : angle 5.18676 ( 864) SS BOND : bond 0.00249 ( 3) SS BOND : angle 0.52885 ( 6) covalent geometry : bond 0.00363 ( 5007) covalent geometry : angle 0.68358 ( 6803) *********************** 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 101 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6888 (mmmt) REVERT: A 127 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7374 (mm-30) REVERT: A 145 TRP cc_start: 0.6691 (t60) cc_final: 0.6450 (t60) REVERT: A 539 MET cc_start: 0.7419 (tmm) cc_final: 0.7091 (tmm) outliers start: 28 outliers final: 20 residues processed: 94 average time/residue: 0.1327 time to fit residues: 17.2559 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 : 0.575 ------------------------------------------------------------------------------- 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 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 HIS 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 306 THR 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 347 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 41 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.169863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144278 restraints weight = 7617.443| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.71 r_work: 0.3762 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5010 Z= 0.154 Angle : 0.672 9.373 6809 Z= 0.338 Chirality : 0.043 0.150 710 Planarity : 0.005 0.055 881 Dihedral : 5.320 29.175 642 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.55 % Allowed : 29.03 % 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: 0.14 (0.34), residues: 595 helix: 0.69 (0.25), residues: 393 sheet: -3.99 (1.28), residues: 10 loop : -0.77 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 548 HIS 0.004 0.001 HIS A 247 PHE 0.013 0.001 PHE A 351 TYR 0.016 0.002 TYR A 497 ARG 0.002 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05704 ( 297) hydrogen bonds : angle 5.06681 ( 864) SS BOND : bond 0.00188 ( 3) SS BOND : angle 0.48406 ( 6) covalent geometry : bond 0.00323 ( 5007) covalent geometry : angle 0.67247 ( 6803) *********************** 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 100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7005 (mmmt) REVERT: A 539 MET cc_start: 0.7455 (tmm) cc_final: 0.7158 (tmm) REVERT: A 592 TRP cc_start: 0.3750 (OUTLIER) cc_final: 0.2338 (m100) outliers start: 24 outliers final: 17 residues processed: 94 average time/residue: 0.1267 time to fit residues: 16.5740 Evaluate side-chains 85 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 179 GLU 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 314 MET 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 23 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4227 r_free = 0.4227 target = 0.171548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.146138 restraints weight = 7483.167| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.68 r_work: 0.3780 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5010 Z= 0.146 Angle : 0.664 9.107 6809 Z= 0.335 Chirality : 0.043 0.151 710 Planarity : 0.005 0.055 881 Dihedral : 5.212 29.815 642 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.98 % Allowed : 29.22 % 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: 0.29 (0.34), residues: 595 helix: 0.81 (0.25), residues: 392 sheet: -3.65 (1.28), residues: 10 loop : -0.72 (0.49), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 150 HIS 0.004 0.001 HIS A 355 PHE 0.012 0.001 PHE A 351 TYR 0.014 0.001 TYR A 497 ARG 0.013 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05530 ( 297) hydrogen bonds : angle 4.98656 ( 864) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.52730 ( 6) covalent geometry : bond 0.00306 ( 5007) covalent geometry : angle 0.66366 ( 6803) *********************** 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 91 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7007 (mmmt) REVERT: A 390 MET cc_start: 0.7730 (mmm) cc_final: 0.7407 (mmm) REVERT: A 539 MET cc_start: 0.7511 (tmm) cc_final: 0.7304 (tmm) REVERT: A 592 TRP cc_start: 0.3631 (OUTLIER) cc_final: 0.2395 (m100) outliers start: 21 outliers final: 14 residues processed: 87 average time/residue: 0.1301 time to fit residues: 15.6323 Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 277 ASP Chi-restraints excluded: chain A residue 326 CYS 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 57 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.172773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147522 restraints weight = 7517.231| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.66 r_work: 0.3801 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5010 Z= 0.142 Angle : 0.655 8.966 6809 Z= 0.329 Chirality : 0.043 0.208 710 Planarity : 0.005 0.055 881 Dihedral : 5.130 29.218 642 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.98 % Allowed : 29.22 % 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: 0.35 (0.35), residues: 595 helix: 0.85 (0.25), residues: 392 sheet: -3.52 (1.32), residues: 10 loop : -0.69 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 150 HIS 0.004 0.001 HIS A 355 PHE 0.012 0.001 PHE A 351 TYR 0.016 0.001 TYR A 497 ARG 0.010 0.001 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05394 ( 297) hydrogen bonds : angle 4.93655 ( 864) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.33664 ( 6) covalent geometry : bond 0.00293 ( 5007) covalent geometry : angle 0.65475 ( 6803) *********************** 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 94 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7106 (mmmt) REVERT: A 253 TRP cc_start: 0.7953 (OUTLIER) cc_final: 0.7042 (m-90) REVERT: A 592 TRP cc_start: 0.3853 (OUTLIER) cc_final: 0.2668 (m100) outliers start: 21 outliers final: 14 residues processed: 89 average time/residue: 0.1705 time to fit residues: 21.2599 Evaluate side-chains 86 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 149 SER 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 277 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 493 SER 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 54 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.174134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.149215 restraints weight = 7458.830| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.65 r_work: 0.3825 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5010 Z= 0.138 Angle : 0.648 8.900 6809 Z= 0.326 Chirality : 0.043 0.202 710 Planarity : 0.005 0.056 881 Dihedral : 5.031 29.370 642 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.23 % Allowed : 30.17 % 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: 0.45 (0.35), residues: 595 helix: 0.90 (0.25), residues: 392 sheet: -3.13 (1.34), residues: 10 loop : -0.59 (0.51), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 150 HIS 0.005 0.001 HIS A 355 PHE 0.011 0.001 PHE A 351 TYR 0.016 0.001 TYR A 497 ARG 0.009 0.001 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05297 ( 297) hydrogen bonds : angle 4.89064 ( 864) SS BOND : bond 0.00121 ( 3) SS BOND : angle 0.46358 ( 6) covalent geometry : bond 0.00285 ( 5007) covalent geometry : angle 0.64811 ( 6803) *********************** 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: 17 poor density : 71 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7113 (mmmt) REVERT: A 253 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.7124 (m-90) REVERT: A 349 ASP cc_start: 0.6789 (m-30) cc_final: 0.6586 (m-30) REVERT: A 553 GLU cc_start: 0.7929 (pp20) cc_final: 0.7475 (mm-30) REVERT: A 592 TRP cc_start: 0.3711 (OUTLIER) cc_final: 0.2562 (m100) outliers start: 17 outliers final: 14 residues processed: 84 average time/residue: 0.1811 time to fit residues: 22.3987 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 : 0.620 ------------------------------------------------------------------------------- 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 149 SER 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 277 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 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 44 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.173250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.147915 restraints weight = 7511.628| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.66 r_work: 0.3823 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5010 Z= 0.138 Angle : 0.655 8.868 6809 Z= 0.328 Chirality : 0.042 0.160 710 Planarity : 0.005 0.055 881 Dihedral : 5.023 29.807 642 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.42 % Allowed : 30.17 % 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: 0.50 (0.35), residues: 595 helix: 0.93 (0.25), residues: 392 sheet: -2.94 (1.32), residues: 10 loop : -0.57 (0.52), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 150 HIS 0.005 0.001 HIS A 355 PHE 0.011 0.001 PHE A 351 TYR 0.017 0.001 TYR A 23 ARG 0.010 0.001 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 297) hydrogen bonds : angle 4.85657 ( 864) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.44306 ( 6) covalent geometry : bond 0.00285 ( 5007) covalent geometry : angle 0.65535 ( 6803) ********************** 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 89 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7067 (mmmt) REVERT: A 253 TRP cc_start: 0.7866 (OUTLIER) cc_final: 0.7134 (m-90) REVERT: A 390 MET cc_start: 0.7668 (mmm) cc_final: 0.7338 (mmm) REVERT: A 553 GLU cc_start: 0.7916 (pp20) cc_final: 0.7495 (mm-30) REVERT: A 592 TRP cc_start: 0.3904 (OUTLIER) cc_final: 0.2699 (m100) outliers start: 18 outliers final: 14 residues processed: 85 average time/residue: 0.1328 time to fit residues: 16.1240 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 : 0.569 ------------------------------------------------------------------------------- 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 149 SER 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 277 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 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 25 optimal weight: 4.9990 chunk 27 optimal weight: 0.0060 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** 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 = 0.4266 r_free = 0.4266 target = 0.174597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.149650 restraints weight = 7579.275| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.68 r_work: 0.3849 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5010 Z= 0.135 Angle : 0.657 8.977 6809 Z= 0.329 Chirality : 0.041 0.142 710 Planarity : 0.005 0.056 881 Dihedral : 4.965 29.001 642 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.04 % Allowed : 29.98 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.35), residues: 595 helix: 0.97 (0.25), residues: 392 sheet: -2.92 (1.32), residues: 10 loop : -0.57 (0.52), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 150 HIS 0.005 0.001 HIS A 355 PHE 0.009 0.001 PHE A 351 TYR 0.015 0.001 TYR A 497 ARG 0.009 0.001 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 297) hydrogen bonds : angle 4.83637 ( 864) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.54737 ( 6) covalent geometry : bond 0.00279 ( 5007) covalent geometry : angle 0.65757 ( 6803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2524.32 seconds wall clock time: 44 minutes 59.66 seconds (2699.66 seconds total)