Starting phenix.real_space_refine on Fri May 9 17:43:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhr_36285/05_2025/8jhr_36285.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhr_36285/05_2025/8jhr_36285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jhr_36285/05_2025/8jhr_36285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhr_36285/05_2025/8jhr_36285.map" model { file = "/net/cci-nas-00/data/ceres_data/8jhr_36285/05_2025/8jhr_36285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhr_36285/05_2025/8jhr_36285.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.048 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 19 5.16 5 C 2166 2.51 5 N 548 2.21 5 O 569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3302 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 14, 'TRANS': 415} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'YUX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.95, per 1000 atoms: 0.89 Number of scatterers: 3302 At special positions: 0 Unit cell: (85.85, 60.35, 66.3, 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 19 16.00 O 569 8.00 N 548 7.00 C 2166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 420.5 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 90.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 98 through 134 removed outlier: 4.753A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 165 removed outlier: 3.578A pdb=" N ALA A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 167 through 186 removed outlier: 3.819A pdb=" N SER A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 222 Proline residue: A 215 - end of helix removed outlier: 4.163A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 236 through 257 removed outlier: 3.759A pdb=" N LEU A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.521A pdb=" N TRP A 261 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 removed outlier: 4.388A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.867A pdb=" N ARG A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 350 Proline residue: A 337 - end of helix removed outlier: 4.422A pdb=" N ALA A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 removed outlier: 3.689A pdb=" N LYS A 361 " --> pdb=" O CYS A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 361' Processing helix chain 'A' and resid 362 through 389 removed outlier: 4.050A pdb=" N PHE A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 418 removed outlier: 3.527A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.753A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.669A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.545A pdb=" N THR A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 537 removed outlier: 4.435A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 834 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: 1.04 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1004 1.34 - 1.46: 626 1.46 - 1.58: 1717 1.58 - 1.69: 5 1.69 - 1.81: 28 Bond restraints: 3380 Sorted by residual: bond pdb=" C07 YUX A 601 " pdb=" C08 YUX A 601 " ideal model delta sigma weight residual 1.460 1.611 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C04 YUX A 601 " pdb=" C05 YUX A 601 " ideal model delta sigma weight residual 1.481 1.591 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C11 YUX A 601 " pdb=" C12 YUX A 601 " ideal model delta sigma weight residual 1.500 1.592 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C07 YUX A 601 " pdb=" N06 YUX A 601 " ideal model delta sigma weight residual 1.367 1.452 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C05 YUX A 601 " pdb=" N06 YUX A 601 " ideal model delta sigma weight residual 1.291 1.364 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 3375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 4461 1.89 - 3.78: 92 3.78 - 5.66: 30 5.66 - 7.55: 6 7.55 - 9.44: 2 Bond angle restraints: 4591 Sorted by residual: angle pdb=" N VAL A 265 " pdb=" CA VAL A 265 " pdb=" C VAL A 265 " ideal model delta sigma weight residual 113.53 109.84 3.69 9.80e-01 1.04e+00 1.42e+01 angle pdb=" C THR A 352 " pdb=" N CYS A 353 " pdb=" CA CYS A 353 " ideal model delta sigma weight residual 121.54 128.15 -6.61 1.91e+00 2.74e-01 1.20e+01 angle pdb=" N GLU A 351 " pdb=" CA GLU A 351 " pdb=" C GLU A 351 " ideal model delta sigma weight residual 113.18 108.89 4.29 1.33e+00 5.65e-01 1.04e+01 angle pdb=" C GLY A 162 " pdb=" N ASP A 163 " pdb=" CA ASP A 163 " ideal model delta sigma weight residual 121.14 115.63 5.51 1.75e+00 3.27e-01 9.93e+00 angle pdb=" C ASP A 163 " pdb=" N ARG A 164 " pdb=" CA ARG A 164 " ideal model delta sigma weight residual 122.09 116.49 5.60 1.79e+00 3.12e-01 9.78e+00 ... (remaining 4586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1664 17.82 - 35.65: 206 35.65 - 53.47: 60 53.47 - 71.30: 12 71.30 - 89.12: 4 Dihedral angle restraints: 1946 sinusoidal: 725 harmonic: 1221 Sorted by residual: dihedral pdb=" CA ALA A 350 " pdb=" C ALA A 350 " pdb=" N GLU A 351 " pdb=" CA GLU A 351 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG A 299 " pdb=" CD ARG A 299 " pdb=" NE ARG A 299 " pdb=" CZ ARG A 299 " ideal model delta sinusoidal sigma weight residual -180.00 -136.42 -43.58 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG A 138 " pdb=" CD ARG A 138 " pdb=" NE ARG A 138 " pdb=" CZ ARG A 138 " ideal model delta sinusoidal sigma weight residual 180.00 137.91 42.09 2 1.50e+01 4.44e-03 9.58e+00 ... (remaining 1943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 441 0.054 - 0.107: 78 0.107 - 0.161: 14 0.161 - 0.214: 1 0.214 - 0.268: 3 Chirality restraints: 537 Sorted by residual: chirality pdb=" CG LEU A 413 " pdb=" CB LEU A 413 " pdb=" CD1 LEU A 413 " pdb=" CD2 LEU A 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU A 499 " pdb=" CB LEU A 499 " pdb=" CD1 LEU A 499 " pdb=" CD2 LEU A 499 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB THR A 373 " pdb=" CA THR A 373 " pdb=" OG1 THR A 373 " pdb=" CG2 THR A 373 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 534 not shown) Planarity restraints: 563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.015 2.00e-02 2.50e+03 1.44e-02 5.16e+00 pdb=" CG TRP A 178 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 136 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LYS A 136 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS A 136 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 137 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 214 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 215 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.024 5.00e-02 4.00e+02 ... (remaining 560 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 420 2.75 - 3.28: 3494 3.28 - 3.82: 5686 3.82 - 4.36: 5948 4.36 - 4.90: 10785 Nonbonded interactions: 26333 Sorted by model distance: nonbonded pdb=" O VAL A 346 " pdb=" OG1 THR A 349 " model vdw 2.208 3.040 nonbonded pdb=" O VAL A 537 " pdb=" ND2 ASN A 538 " model vdw 2.270 3.120 nonbonded pdb=" O MET A 448 " pdb=" NH1 ARG A 456 " model vdw 2.278 3.120 nonbonded pdb=" O ILE A 213 " pdb=" OG1 THR A 216 " model vdw 2.282 3.040 nonbonded pdb=" O TRP A 178 " pdb=" OG1 THR A 182 " model vdw 2.297 3.040 ... (remaining 26328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.007 0.151 3380 Z= 0.331 Angle : 0.744 9.441 4591 Z= 0.385 Chirality : 0.046 0.268 537 Planarity : 0.004 0.043 563 Dihedral : 17.688 89.123 1166 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.29 % Allowed : 35.26 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.42), residues: 426 helix: 1.60 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.44 (0.90), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 178 HIS 0.002 0.001 HIS A 132 PHE 0.010 0.001 PHE A 151 TYR 0.006 0.001 TYR A 246 ARG 0.002 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.09728 ( 281) hydrogen bonds : angle 5.31661 ( 834) covalent geometry : bond 0.00657 ( 3380) covalent geometry : angle 0.74389 ( 4591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.347 Fit side-chains REVERT: A 306 MET cc_start: 0.8527 (mmm) cc_final: 0.7927 (mmm) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.1599 time to fit residues: 12.2534 Evaluate side-chains 64 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.155725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126000 restraints weight = 5023.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129909 restraints weight = 2806.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132418 restraints weight = 1978.013| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3380 Z= 0.160 Angle : 0.602 6.534 4591 Z= 0.322 Chirality : 0.042 0.179 537 Planarity : 0.004 0.041 563 Dihedral : 6.667 53.754 479 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.20 % Allowed : 28.61 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.43), residues: 426 helix: 1.81 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -1.00 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 178 HIS 0.002 0.001 HIS A 260 PHE 0.021 0.001 PHE A 510 TYR 0.026 0.001 TYR A 160 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.05127 ( 281) hydrogen bonds : angle 4.33359 ( 834) covalent geometry : bond 0.00344 ( 3380) covalent geometry : angle 0.60176 ( 4591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 532 ARG cc_start: 0.9123 (tpp80) cc_final: 0.8859 (tpp80) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 0.1563 time to fit residues: 17.1887 Evaluate side-chains 82 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.155828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127857 restraints weight = 4779.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131772 restraints weight = 2581.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134350 restraints weight = 1788.402| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3380 Z= 0.178 Angle : 0.607 7.354 4591 Z= 0.327 Chirality : 0.043 0.193 537 Planarity : 0.004 0.040 563 Dihedral : 6.387 46.504 479 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.49 % Allowed : 28.03 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.43), residues: 426 helix: 1.80 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.88 (0.98), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 178 HIS 0.002 0.001 HIS A 260 PHE 0.012 0.001 PHE A 327 TYR 0.012 0.001 TYR A 160 ARG 0.001 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.05387 ( 281) hydrogen bonds : angle 4.29215 ( 834) covalent geometry : bond 0.00402 ( 3380) covalent geometry : angle 0.60676 ( 4591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.361 Fit side-chains REVERT: A 332 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8497 (mm) REVERT: A 532 ARG cc_start: 0.9065 (tpp80) cc_final: 0.8834 (tpp80) outliers start: 19 outliers final: 13 residues processed: 88 average time/residue: 0.1536 time to fit residues: 16.4304 Evaluate side-chains 77 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.159124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131205 restraints weight = 4856.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135147 restraints weight = 2621.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137745 restraints weight = 1818.235| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3380 Z= 0.145 Angle : 0.581 6.769 4591 Z= 0.313 Chirality : 0.042 0.203 537 Planarity : 0.004 0.037 563 Dihedral : 6.193 47.323 479 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 6.65 % Allowed : 26.30 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.42), residues: 426 helix: 1.84 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.74 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 178 HIS 0.001 0.001 HIS A 260 PHE 0.029 0.001 PHE A 510 TYR 0.010 0.001 TYR A 192 ARG 0.002 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 281) hydrogen bonds : angle 4.17367 ( 834) covalent geometry : bond 0.00300 ( 3380) covalent geometry : angle 0.58057 ( 4591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8462 (mm) REVERT: A 487 ARG cc_start: 0.7969 (tpp80) cc_final: 0.7747 (tpp80) REVERT: A 532 ARG cc_start: 0.9079 (tpp80) cc_final: 0.8840 (tpp80) outliers start: 23 outliers final: 14 residues processed: 91 average time/residue: 0.1526 time to fit residues: 17.0232 Evaluate side-chains 79 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.158894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130793 restraints weight = 4880.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134743 restraints weight = 2629.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137385 restraints weight = 1819.693| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3380 Z= 0.148 Angle : 0.610 8.603 4591 Z= 0.321 Chirality : 0.042 0.197 537 Planarity : 0.004 0.035 563 Dihedral : 6.136 52.261 479 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.07 % Allowed : 27.75 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.42), residues: 426 helix: 1.82 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.79 (1.00), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 178 HIS 0.002 0.001 HIS A 260 PHE 0.012 0.001 PHE A 498 TYR 0.015 0.002 TYR A 160 ARG 0.001 0.000 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 281) hydrogen bonds : angle 4.15396 ( 834) covalent geometry : bond 0.00312 ( 3380) covalent geometry : angle 0.60985 ( 4591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8468 (mm) REVERT: A 497 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8089 (mt-10) REVERT: A 532 ARG cc_start: 0.9056 (tpp80) cc_final: 0.8836 (tpp80) outliers start: 21 outliers final: 16 residues processed: 85 average time/residue: 0.1549 time to fit residues: 15.9811 Evaluate side-chains 80 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 3 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.159467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131425 restraints weight = 4938.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.135435 restraints weight = 2632.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138049 restraints weight = 1810.949| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3380 Z= 0.146 Angle : 0.605 7.591 4591 Z= 0.321 Chirality : 0.042 0.205 537 Planarity : 0.004 0.036 563 Dihedral : 6.135 58.802 479 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.78 % Allowed : 28.61 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.42), residues: 426 helix: 1.81 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.82 (0.99), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 178 HIS 0.002 0.001 HIS A 260 PHE 0.030 0.001 PHE A 510 TYR 0.011 0.001 TYR A 192 ARG 0.001 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 281) hydrogen bonds : angle 4.17265 ( 834) covalent geometry : bond 0.00311 ( 3380) covalent geometry : angle 0.60522 ( 4591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 332 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8474 (mm) REVERT: A 487 ARG cc_start: 0.7971 (tpp80) cc_final: 0.7742 (tpp80) outliers start: 20 outliers final: 15 residues processed: 82 average time/residue: 0.1719 time to fit residues: 16.8470 Evaluate side-chains 81 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.162155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132652 restraints weight = 4771.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136686 restraints weight = 2669.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139300 restraints weight = 1875.482| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3380 Z= 0.144 Angle : 0.609 7.127 4591 Z= 0.322 Chirality : 0.042 0.208 537 Planarity : 0.004 0.033 563 Dihedral : 5.871 51.666 479 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 6.07 % Allowed : 28.03 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.42), residues: 426 helix: 1.84 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.89 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 178 HIS 0.002 0.001 HIS A 260 PHE 0.010 0.001 PHE A 498 TYR 0.016 0.001 TYR A 160 ARG 0.001 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 281) hydrogen bonds : angle 4.14829 ( 834) covalent geometry : bond 0.00304 ( 3380) covalent geometry : angle 0.60877 ( 4591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 332 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8430 (mm) REVERT: A 514 LEU cc_start: 0.8924 (mm) cc_final: 0.8704 (mm) outliers start: 21 outliers final: 16 residues processed: 78 average time/residue: 0.1586 time to fit residues: 15.0133 Evaluate side-chains 79 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.158971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129511 restraints weight = 4742.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133444 restraints weight = 2669.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135993 restraints weight = 1889.035| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3380 Z= 0.169 Angle : 0.632 6.916 4591 Z= 0.337 Chirality : 0.043 0.195 537 Planarity : 0.004 0.033 563 Dihedral : 5.745 46.122 479 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.20 % Allowed : 28.90 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.42), residues: 426 helix: 1.77 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.86 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 178 HIS 0.002 0.001 HIS A 260 PHE 0.028 0.001 PHE A 510 TYR 0.011 0.001 TYR A 192 ARG 0.002 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 281) hydrogen bonds : angle 4.23863 ( 834) covalent geometry : bond 0.00382 ( 3380) covalent geometry : angle 0.63219 ( 4591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8245 (tt) REVERT: A 332 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8465 (mm) REVERT: A 514 LEU cc_start: 0.9003 (mm) cc_final: 0.8736 (mm) outliers start: 18 outliers final: 16 residues processed: 75 average time/residue: 0.1551 time to fit residues: 14.3361 Evaluate side-chains 81 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.159864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130488 restraints weight = 4798.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134486 restraints weight = 2666.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137095 restraints weight = 1870.329| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3380 Z= 0.161 Angle : 0.646 9.266 4591 Z= 0.340 Chirality : 0.043 0.218 537 Planarity : 0.004 0.033 563 Dihedral : 5.564 46.223 479 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.36 % Allowed : 28.32 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.43), residues: 426 helix: 1.77 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.80 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 178 HIS 0.002 0.001 HIS A 260 PHE 0.012 0.001 PHE A 498 TYR 0.018 0.002 TYR A 160 ARG 0.002 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.05030 ( 281) hydrogen bonds : angle 4.22040 ( 834) covalent geometry : bond 0.00355 ( 3380) covalent geometry : angle 0.64626 ( 4591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8249 (tt) REVERT: A 332 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8474 (mm) REVERT: A 497 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 510 PHE cc_start: 0.7611 (t80) cc_final: 0.7410 (t80) REVERT: A 514 LEU cc_start: 0.9026 (mm) cc_final: 0.8687 (mm) outliers start: 22 outliers final: 18 residues processed: 79 average time/residue: 0.1732 time to fit residues: 16.6049 Evaluate side-chains 83 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.0470 chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.160256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131270 restraints weight = 4730.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135232 restraints weight = 2627.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137835 restraints weight = 1842.427| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3380 Z= 0.157 Angle : 0.639 7.709 4591 Z= 0.341 Chirality : 0.043 0.216 537 Planarity : 0.004 0.033 563 Dihedral : 5.423 46.082 479 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.49 % Allowed : 29.19 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.43), residues: 426 helix: 1.76 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.78 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 178 HIS 0.002 0.001 HIS A 260 PHE 0.013 0.001 PHE A 519 TYR 0.010 0.001 TYR A 192 ARG 0.005 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 281) hydrogen bonds : angle 4.25566 ( 834) covalent geometry : bond 0.00344 ( 3380) covalent geometry : angle 0.63947 ( 4591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8456 (mm) REVERT: A 510 PHE cc_start: 0.7654 (t80) cc_final: 0.7454 (t80) REVERT: A 514 LEU cc_start: 0.9012 (mm) cc_final: 0.8666 (mm) outliers start: 19 outliers final: 17 residues processed: 75 average time/residue: 0.1659 time to fit residues: 15.1122 Evaluate side-chains 79 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.161658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133684 restraints weight = 4826.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137676 restraints weight = 2600.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140282 restraints weight = 1790.644| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3380 Z= 0.146 Angle : 0.638 9.862 4591 Z= 0.337 Chirality : 0.042 0.207 537 Planarity : 0.004 0.045 563 Dihedral : 5.242 45.756 479 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.49 % Allowed : 28.90 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.43), residues: 426 helix: 1.81 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.78 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.001 0.001 HIS A 260 PHE 0.011 0.001 PHE A 498 TYR 0.026 0.002 TYR A 160 ARG 0.004 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 281) hydrogen bonds : angle 4.24213 ( 834) covalent geometry : bond 0.00305 ( 3380) covalent geometry : angle 0.63783 ( 4591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1390.45 seconds wall clock time: 25 minutes 16.23 seconds (1516.23 seconds total)