Starting phenix.real_space_refine on Sat May 10 02:58:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jwh_36683/05_2025/8jwh_36683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jwh_36683/05_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_36683/05_2025/8jwh_36683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jwh_36683/05_2025/8jwh_36683.map" model { file = "/net/cci-nas-00/data/ceres_data/8jwh_36683/05_2025/8jwh_36683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jwh_36683/05_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-5687/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: 3.29, per 1000 atoms: 0.68 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: 1.23 Conformation dependent library (CDL) restraints added in 575.8 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: 0.57 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: 1.44 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: 0.010 Normalize map: mean=0, sd=1: 0.810 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: 0.040 Set scattering table: 0.040 Process input model: 15.920 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.170 ------------------------------------------------------------------------------- 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 : 0.602 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: 0.1454 time to fit residues: 16.4526 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 : 0.503 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142439 restraints weight = 7450.270| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.65 r_work: 0.3742 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6653 (mm-30) REVERT: A 539 MET cc_start: 0.7450 (tmm) cc_final: 0.7051 (tmm) outliers start: 25 outliers final: 13 residues processed: 97 average time/residue: 0.1450 time to fit residues: 18.8606 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 : 0.567 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.170423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145254 restraints weight = 7510.886| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.67 r_work: 0.3777 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1519 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= 0.158 Angle : 0.672 8.190 6809 Z= 0.344 Chirality : 0.043 0.149 710 Planarity : 0.006 0.069 881 Dihedral : 5.624 32.081 642 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.98 % Allowed : 27.89 % Favored : 68.12 % 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: -0.18 (0.34), residues: 595 helix: 0.41 (0.25), residues: 400 sheet: -4.22 (1.21), residues: 10 loop : -0.84 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 548 HIS 0.005 0.001 HIS A 355 PHE 0.012 0.002 PHE A 351 TYR 0.015 0.002 TYR A 497 ARG 0.005 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05938 ( 297) hydrogen bonds : angle 5.22643 ( 864) SS BOND : bond 0.00211 ( 3) SS BOND : angle 0.44869 ( 6) covalent geometry : bond 0.00322 ( 5007) covalent geometry : angle 0.67207 ( 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 100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6763 (mm-30) REVERT: A 220 GLU cc_start: 0.7070 (tt0) cc_final: 0.6748 (tt0) REVERT: A 539 MET cc_start: 0.7472 (tmm) cc_final: 0.7156 (tmm) outliers start: 21 outliers final: 13 residues processed: 94 average time/residue: 0.1479 time to fit residues: 18.6582 Evaluate side-chains 83 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 56 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.167507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.141736 restraints weight = 7647.981| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.72 r_work: 0.3734 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5010 Z= 0.181 Angle : 0.689 8.019 6809 Z= 0.353 Chirality : 0.044 0.148 710 Planarity : 0.006 0.061 881 Dihedral : 5.532 30.696 642 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.12 % Allowed : 26.94 % Favored : 67.93 % 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: 0.49 (0.25), residues: 394 sheet: -3.96 (1.21), residues: 10 loop : -0.85 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 548 HIS 0.004 0.001 HIS A 247 PHE 0.017 0.002 PHE A 351 TYR 0.018 0.002 TYR A 497 ARG 0.003 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.06162 ( 297) hydrogen bonds : angle 5.23852 ( 864) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.53037 ( 6) covalent geometry : bond 0.00388 ( 5007) covalent geometry : angle 0.68863 ( 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 102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6884 (mmmt) REVERT: A 127 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7037 (mm-30) REVERT: A 539 MET cc_start: 0.7509 (tmm) cc_final: 0.7194 (tmm) outliers start: 27 outliers final: 20 residues processed: 95 average time/residue: 0.1390 time to fit residues: 17.9715 Evaluate side-chains 90 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 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 57 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.167632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141923 restraints weight = 7616.350| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.70 r_work: 0.3724 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2029 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= 0.178 Angle : 0.687 8.308 6809 Z= 0.349 Chirality : 0.044 0.147 710 Planarity : 0.005 0.060 881 Dihedral : 5.472 29.835 642 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.12 % Allowed : 28.08 % 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: -0.03 (0.34), residues: 595 helix: 0.55 (0.25), residues: 393 sheet: -3.89 (1.26), residues: 10 loop : -0.80 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 548 HIS 0.004 0.001 HIS A 247 PHE 0.016 0.001 PHE A 351 TYR 0.017 0.002 TYR A 497 ARG 0.002 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.06051 ( 297) hydrogen bonds : angle 5.19464 ( 864) SS BOND : bond 0.00278 ( 3) SS BOND : angle 0.54112 ( 6) covalent geometry : bond 0.00384 ( 5007) covalent geometry : angle 0.68715 ( 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 100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6840 (mmmt) REVERT: A 127 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 145 TRP cc_start: 0.6741 (t60) cc_final: 0.6499 (t60) REVERT: A 287 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.5664 (tt0) REVERT: A 539 MET cc_start: 0.7484 (tmm) cc_final: 0.7200 (tmm) outliers start: 27 outliers final: 19 residues processed: 94 average time/residue: 0.1361 time to fit residues: 17.4878 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 : 0.544 ------------------------------------------------------------------------------- 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 287 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.170158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144550 restraints weight = 7631.522| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.72 r_work: 0.3758 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5010 Z= 0.152 Angle : 0.666 8.372 6809 Z= 0.337 Chirality : 0.043 0.149 710 Planarity : 0.005 0.056 881 Dihedral : 5.311 29.082 642 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.74 % Allowed : 28.84 % 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: 0.16 (0.34), residues: 595 helix: 0.70 (0.25), residues: 393 sheet: -3.99 (1.26), residues: 10 loop : -0.74 (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 355 PHE 0.012 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 0.05696 ( 297) hydrogen bonds : angle 5.06078 ( 864) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.48966 ( 6) covalent geometry : bond 0.00319 ( 5007) covalent geometry : angle 0.66625 ( 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 98 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6987 (mmmt) REVERT: A 390 MET cc_start: 0.7727 (mmm) cc_final: 0.7410 (mmm) REVERT: A 592 TRP cc_start: 0.3703 (OUTLIER) cc_final: 0.2307 (m100) outliers start: 25 outliers final: 14 residues processed: 93 average time/residue: 0.1336 time to fit residues: 16.8342 Evaluate side-chains 82 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 592 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.167755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.142185 restraints weight = 7513.409| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.67 r_work: 0.3733 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5010 Z= 0.174 Angle : 0.685 9.168 6809 Z= 0.349 Chirality : 0.044 0.151 710 Planarity : 0.005 0.057 881 Dihedral : 5.386 29.697 642 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.17 % Allowed : 29.41 % 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: 0.12 (0.34), residues: 595 helix: 0.66 (0.25), residues: 392 sheet: -4.31 (1.15), residues: 10 loop : -0.71 (0.49), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 150 HIS 0.005 0.001 HIS A 247 PHE 0.017 0.002 PHE A 351 TYR 0.017 0.002 TYR A 497 ARG 0.011 0.001 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05965 ( 297) hydrogen bonds : angle 5.10868 ( 864) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.46051 ( 6) covalent geometry : bond 0.00378 ( 5007) covalent geometry : angle 0.68490 ( 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 88 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6890 (mmmt) REVERT: A 390 MET cc_start: 0.7707 (mmm) cc_final: 0.7417 (mmm) REVERT: A 592 TRP cc_start: 0.3692 (OUTLIER) cc_final: 0.2371 (m100) outliers start: 22 outliers final: 16 residues processed: 83 average time/residue: 0.1266 time to fit residues: 14.6819 Evaluate side-chains 82 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 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 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 277 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 445 VAL 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: 0.9980 chunk 8 optimal weight: 0.0370 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 27 optimal weight: 0.0670 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.172985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.147757 restraints weight = 7505.424| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.68 r_work: 0.3804 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5010 Z= 0.138 Angle : 0.646 8.811 6809 Z= 0.325 Chirality : 0.042 0.150 710 Planarity : 0.005 0.057 881 Dihedral : 5.130 28.851 642 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.66 % Allowed : 30.36 % 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: 0.38 (0.35), residues: 595 helix: 0.86 (0.25), residues: 392 sheet: -3.15 (1.39), residues: 10 loop : -0.67 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 150 HIS 0.005 0.001 HIS A 355 PHE 0.010 0.001 PHE A 351 TYR 0.015 0.001 TYR A 497 ARG 0.009 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05270 ( 297) hydrogen bonds : angle 4.92564 ( 864) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.43993 ( 6) covalent geometry : bond 0.00283 ( 5007) covalent geometry : angle 0.64568 ( 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 85 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7003 (mmmt) REVERT: A 256 PHE cc_start: 0.7181 (m-10) cc_final: 0.6300 (m-80) REVERT: A 390 MET cc_start: 0.7817 (mmm) cc_final: 0.7460 (mmm) REVERT: A 553 GLU cc_start: 0.7905 (pp20) cc_final: 0.7483 (mm-30) REVERT: A 592 TRP cc_start: 0.3677 (OUTLIER) cc_final: 0.2546 (m100) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.1190 time to fit residues: 13.6921 Evaluate side-chains 77 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 277 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE 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: 3.9990 chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.168887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143269 restraints weight = 7455.949| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.65 r_work: 0.3744 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5010 Z= 0.175 Angle : 0.692 9.155 6809 Z= 0.352 Chirality : 0.045 0.224 710 Planarity : 0.005 0.059 881 Dihedral : 5.312 32.378 642 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.61 % Allowed : 31.12 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.24 (0.34), residues: 595 helix: 0.73 (0.25), residues: 392 sheet: -3.42 (1.28), residues: 10 loop : -0.66 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 150 HIS 0.005 0.001 HIS A 247 PHE 0.017 0.001 PHE A 351 TYR 0.018 0.002 TYR A 497 ARG 0.010 0.001 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05842 ( 297) hydrogen bonds : angle 5.06498 ( 864) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.45009 ( 6) covalent geometry : bond 0.00384 ( 5007) covalent geometry : angle 0.69223 ( 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 87 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7121 (mmmt) REVERT: A 390 MET cc_start: 0.7774 (mmm) cc_final: 0.7397 (mmm) REVERT: A 592 TRP cc_start: 0.3822 (OUTLIER) cc_final: 0.2587 (m100) outliers start: 19 outliers final: 14 residues processed: 83 average time/residue: 0.1227 time to fit residues: 14.2926 Evaluate side-chains 82 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 445 VAL 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: 0.5980 chunk 58 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.173029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147724 restraints weight = 7496.536| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.69 r_work: 0.3801 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2596 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= 0.140 Angle : 0.659 8.580 6809 Z= 0.332 Chirality : 0.043 0.206 710 Planarity : 0.005 0.058 881 Dihedral : 5.155 33.137 642 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.47 % Allowed : 31.50 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.37 (0.34), residues: 595 helix: 0.85 (0.25), residues: 392 sheet: -2.84 (1.35), residues: 10 loop : -0.68 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 150 HIS 0.005 0.001 HIS A 355 PHE 0.010 0.001 PHE A 351 TYR 0.017 0.001 TYR A 497 ARG 0.009 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.05306 ( 297) hydrogen bonds : angle 4.93527 ( 864) SS BOND : bond 0.00097 ( 3) SS BOND : angle 0.40680 ( 6) covalent geometry : bond 0.00292 ( 5007) covalent geometry : angle 0.65892 ( 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 84 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7097 (mmmt) REVERT: A 256 PHE cc_start: 0.7147 (m-10) cc_final: 0.6283 (m-80) REVERT: A 553 GLU cc_start: 0.7955 (pp20) cc_final: 0.7598 (mm-30) REVERT: A 592 TRP cc_start: 0.3912 (OUTLIER) cc_final: 0.2717 (m100) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.1221 time to fit residues: 14.1668 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 : 0.554 ------------------------------------------------------------------------------- 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 277 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE 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: 0.0970 chunk 27 optimal weight: 0.0870 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 57 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 0.0170 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.177797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.153064 restraints weight = 7516.187| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.67 r_work: 0.3893 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5010 Z= 0.132 Angle : 0.643 10.397 6809 Z= 0.322 Chirality : 0.042 0.192 710 Planarity : 0.005 0.058 881 Dihedral : 4.946 34.866 642 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.85 % Allowed : 30.74 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.58 (0.34), residues: 595 helix: 0.99 (0.25), residues: 393 sheet: -0.30 (1.18), residues: 20 loop : -0.72 (0.52), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 150 HIS 0.005 0.001 HIS A 355 PHE 0.008 0.001 PHE A 420 TYR 0.016 0.001 TYR A 23 ARG 0.009 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 297) hydrogen bonds : angle 4.82683 ( 864) SS BOND : bond 0.00069 ( 3) SS BOND : angle 0.35844 ( 6) covalent geometry : bond 0.00266 ( 5007) covalent geometry : angle 0.64283 ( 6803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.39 seconds wall clock time: 40 minutes 41.84 seconds (2441.84 seconds total)