Starting phenix.real_space_refine on Wed Mar 5 18:40:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvj_34129/03_2025/7yvj_34129.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvj_34129/03_2025/7yvj_34129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvj_34129/03_2025/7yvj_34129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvj_34129/03_2025/7yvj_34129.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvj_34129/03_2025/7yvj_34129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvj_34129/03_2025/7yvj_34129.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 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 16 5.16 5 C 2073 2.51 5 N 552 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3267 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1491 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 4.06, per 1000 atoms: 1.24 Number of scatterers: 3267 At special positions: 0 Unit cell: (72.16, 68.88, 82, 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 16 16.00 O 626 8.00 N 552 7.00 C 2073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 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: 0.80 Conformation dependent library (CDL) restraints added in 416.3 milliseconds 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 7.0% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.697A pdb=" N ASP C 31 " --> pdb=" O MET C 28 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER C 32 " --> pdb=" O ILE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.571A pdb=" N ASP C 90 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 5.578A pdb=" N VAL A 10 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 removed outlier: 5.578A pdb=" N VAL A 10 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 22 Processing sheet with id=AA4, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.863A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.057A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 97 hydrogen bonds defined for protein. 216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 535 1.31 - 1.44: 1009 1.44 - 1.56: 1788 1.56 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3352 Sorted by residual: bond pdb=" CA ASN B 437 " pdb=" C ASN B 437 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.35e-02 5.49e+03 2.23e+01 bond pdb=" CA VAL B 350 " pdb=" C VAL B 350 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.22e-02 6.72e+03 2.04e+01 bond pdb=" C VAL B 350 " pdb=" O VAL B 350 " ideal model delta sigma weight residual 1.237 1.192 0.044 1.13e-02 7.83e+03 1.54e+01 bond pdb=" C ASN B 437 " pdb=" O ASN B 437 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.17e-02 7.31e+03 1.54e+01 bond pdb=" CA SER B 438 " pdb=" C SER B 438 " ideal model delta sigma weight residual 1.526 1.475 0.050 1.28e-02 6.10e+03 1.54e+01 ... (remaining 3347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 4249 1.99 - 3.98: 272 3.98 - 5.97: 29 5.97 - 7.96: 7 7.96 - 9.95: 3 Bond angle restraints: 4560 Sorted by residual: angle pdb=" C ALA B 372 " pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta sigma weight residual 119.64 125.83 -6.19 1.01e+00 9.80e-01 3.75e+01 angle pdb=" N TRP B 353 " pdb=" CA TRP B 353 " pdb=" C TRP B 353 " ideal model delta sigma weight residual 110.24 117.26 -7.02 1.30e+00 5.92e-01 2.91e+01 angle pdb=" N ASN B 354 " pdb=" CA ASN B 354 " pdb=" C ASN B 354 " ideal model delta sigma weight residual 109.59 118.06 -8.47 1.61e+00 3.86e-01 2.77e+01 angle pdb=" N ALA B 372 " pdb=" CA ALA B 372 " pdb=" C ALA B 372 " ideal model delta sigma weight residual 109.81 119.76 -9.95 2.21e+00 2.05e-01 2.03e+01 angle pdb=" N TYR B 351 " pdb=" CA TYR B 351 " pdb=" C TYR B 351 " ideal model delta sigma weight residual 113.19 118.37 -5.18 1.19e+00 7.06e-01 1.89e+01 ... (remaining 4555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 1720 15.89 - 31.78: 196 31.78 - 47.67: 38 47.67 - 63.56: 5 63.56 - 79.45: 2 Dihedral angle restraints: 1961 sinusoidal: 731 harmonic: 1230 Sorted by residual: dihedral pdb=" N ASN B 439 " pdb=" C ASN B 439 " pdb=" CA ASN B 439 " pdb=" CB ASN B 439 " ideal model delta harmonic sigma weight residual 122.80 113.87 8.93 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" CA GLN A 40 " pdb=" C GLN A 40 " pdb=" N HIS A 41 " pdb=" CA HIS A 41 " ideal model delta harmonic sigma weight residual 180.00 162.44 17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA THR A 72 " pdb=" C THR A 72 " pdb=" N ALA A 73 " pdb=" CA ALA A 73 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 1958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 392 0.080 - 0.160: 77 0.160 - 0.239: 8 0.239 - 0.319: 5 0.319 - 0.399: 2 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA TYR C 104 " pdb=" N TYR C 104 " pdb=" C TYR C 104 " pdb=" CB TYR C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CA ALA B 372 " pdb=" N ALA B 372 " pdb=" C ALA B 372 " pdb=" CB ALA B 372 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA TRP B 353 " pdb=" N TRP B 353 " pdb=" C TRP B 353 " pdb=" CB TRP B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 481 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 420 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.91e+00 pdb=" CG ASP B 420 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP B 420 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B 420 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 436 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C TRP B 436 " 0.050 2.00e-02 2.50e+03 pdb=" O TRP B 436 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN B 437 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 350 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C VAL B 350 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL B 350 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR B 351 " 0.013 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 22 2.42 - 3.04: 2156 3.04 - 3.66: 4751 3.66 - 4.28: 6698 4.28 - 4.90: 11578 Nonbonded interactions: 25205 Sorted by model distance: nonbonded pdb=" O GLN A 16 " pdb=" CD1 LEU A 80 " model vdw 1.805 3.460 nonbonded pdb=" OH TYR C 105 " pdb=" ND2 ASN B 354 " model vdw 2.023 3.120 nonbonded pdb=" O GLY B 476 " pdb=" OD1 ASN B 477 " model vdw 2.099 3.040 nonbonded pdb=" O SER C 30 " pdb=" OD1 ASP C 31 " model vdw 2.150 3.040 nonbonded pdb=" O GLY B 446 " pdb=" OH TYR B 449 " model vdw 2.190 3.040 ... (remaining 25200 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 6.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.300 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.008 0.064 3352 Z= 0.540 Angle : 1.049 9.948 4560 Z= 0.678 Chirality : 0.070 0.399 484 Planarity : 0.005 0.037 594 Dihedral : 13.624 79.449 1171 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 1.18 % Allowed : 8.29 % Favored : 90.52 % Rotamer: Outliers : 1.73 % Allowed : 9.80 % Favored : 88.47 % 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: -4.50 (0.32), residues: 422 helix: -5.27 (0.23), residues: 29 sheet: -2.27 (0.36), residues: 153 loop : -3.28 (0.31), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 353 HIS 0.003 0.002 HIS A 41 PHE 0.008 0.001 PHE A 102 TYR 0.021 0.002 TYR C 104 ARG 0.004 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7487 (t0) cc_final: 0.7170 (t0) REVERT: C 13 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8451 (mmmt) REVERT: C 98 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7424 (tmt170) REVERT: C 100 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7810 (tp-100) REVERT: B 386 LYS cc_start: 0.7757 (mttt) cc_final: 0.7221 (pttt) outliers start: 6 outliers final: 1 residues processed: 124 average time/residue: 0.2017 time to fit residues: 29.0242 Evaluate side-chains 99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 41 HIS B 354 ASN B 505 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080818 restraints weight = 8472.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083152 restraints weight = 3895.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084723 restraints weight = 2226.144| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3352 Z= 0.247 Angle : 0.678 7.915 4560 Z= 0.351 Chirality : 0.045 0.141 484 Planarity : 0.005 0.041 594 Dihedral : 5.534 57.233 479 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.50 % Favored : 95.02 % Rotamer: Outliers : 3.17 % Allowed : 18.16 % Favored : 78.67 % 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: -3.56 (0.34), residues: 422 helix: -5.20 (0.21), residues: 22 sheet: -1.53 (0.37), residues: 154 loop : -2.74 (0.32), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 353 HIS 0.003 0.001 HIS A 41 PHE 0.016 0.001 PHE C 68 TYR 0.022 0.002 TYR B 508 ARG 0.006 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8030 (p90) cc_final: 0.7276 (p90) REVERT: A 55 ASN cc_start: 0.7933 (t0) cc_final: 0.7337 (t0) REVERT: C 13 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8500 (mmmt) REVERT: C 98 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7184 (tmt170) REVERT: B 386 LYS cc_start: 0.7729 (mttt) cc_final: 0.7297 (ttpt) REVERT: B 403 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8347 (ttm-80) REVERT: B 508 TYR cc_start: 0.8449 (m-80) cc_final: 0.8203 (m-80) outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 0.1977 time to fit residues: 25.2297 Evaluate side-chains 103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.0020 chunk 38 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080530 restraints weight = 8343.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082897 restraints weight = 3875.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084419 restraints weight = 2218.994| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3352 Z= 0.225 Angle : 0.648 6.254 4560 Z= 0.332 Chirality : 0.045 0.145 484 Planarity : 0.005 0.044 594 Dihedral : 5.289 55.170 479 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.69 % Favored : 94.08 % Rotamer: Outliers : 4.32 % Allowed : 21.04 % Favored : 74.64 % 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: -2.84 (0.36), residues: 422 helix: -4.74 (0.40), residues: 16 sheet: -1.04 (0.38), residues: 156 loop : -2.34 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 353 HIS 0.001 0.000 HIS A 41 PHE 0.012 0.001 PHE B 400 TYR 0.013 0.001 TYR B 365 ARG 0.008 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8046 (p90) cc_final: 0.7239 (p90) REVERT: A 55 ASN cc_start: 0.7832 (t0) cc_final: 0.7195 (t0) REVERT: C 13 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8439 (mmmt) REVERT: C 34 MET cc_start: 0.9269 (mmt) cc_final: 0.9065 (mmp) REVERT: B 358 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9128 (tp) REVERT: B 386 LYS cc_start: 0.7474 (mttt) cc_final: 0.7091 (ttpt) REVERT: B 466 ARG cc_start: 0.8428 (ptm-80) cc_final: 0.8196 (ptm-80) REVERT: B 498 ARG cc_start: 0.8232 (mtt90) cc_final: 0.7942 (mtt-85) REVERT: B 508 TYR cc_start: 0.8389 (m-80) cc_final: 0.8061 (m-80) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 0.1898 time to fit residues: 24.6381 Evaluate side-chains 113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080767 restraints weight = 8444.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083181 restraints weight = 3941.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084788 restraints weight = 2251.813| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3352 Z= 0.190 Angle : 0.657 10.009 4560 Z= 0.323 Chirality : 0.044 0.143 484 Planarity : 0.004 0.040 594 Dihedral : 5.110 53.921 479 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.74 % Favored : 95.02 % Rotamer: Outliers : 5.48 % Allowed : 21.61 % Favored : 72.91 % 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: -2.40 (0.37), residues: 422 helix: -4.58 (0.51), residues: 16 sheet: -0.67 (0.39), residues: 156 loop : -2.08 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.001 0.000 HIS A 41 PHE 0.013 0.001 PHE B 400 TYR 0.024 0.001 TYR C 80 ARG 0.010 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8014 (p90) cc_final: 0.7382 (p90) REVERT: A 55 ASN cc_start: 0.7810 (t0) cc_final: 0.7220 (t0) REVERT: C 13 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8506 (mmmt) REVERT: B 386 LYS cc_start: 0.7251 (mttt) cc_final: 0.6932 (ttpt) REVERT: B 466 ARG cc_start: 0.8499 (ptm-80) cc_final: 0.8249 (ptm-80) REVERT: B 498 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7922 (mtt-85) REVERT: B 508 TYR cc_start: 0.8305 (m-80) cc_final: 0.8078 (m-80) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 0.1998 time to fit residues: 26.1891 Evaluate side-chains 117 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.084537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.074790 restraints weight = 8691.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.077115 restraints weight = 4013.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078658 restraints weight = 2271.260| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3352 Z= 0.488 Angle : 0.777 8.530 4560 Z= 0.405 Chirality : 0.048 0.155 484 Planarity : 0.006 0.048 594 Dihedral : 6.003 57.623 479 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.06 % Favored : 91.71 % Rotamer: Outliers : 6.34 % Allowed : 21.04 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.37), residues: 422 helix: -4.53 (0.51), residues: 23 sheet: -0.59 (0.41), residues: 153 loop : -2.32 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 115 HIS 0.003 0.001 HIS A 41 PHE 0.015 0.002 PHE C 68 TYR 0.019 0.002 TYR C 80 ARG 0.009 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8228 (p90) cc_final: 0.7792 (p90) REVERT: A 55 ASN cc_start: 0.8162 (t0) cc_final: 0.7693 (t0) REVERT: B 498 ARG cc_start: 0.8217 (mtt90) cc_final: 0.7951 (mtt-85) outliers start: 22 outliers final: 19 residues processed: 108 average time/residue: 0.1748 time to fit residues: 22.2451 Evaluate side-chains 111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078573 restraints weight = 8781.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.081006 restraints weight = 3969.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082609 restraints weight = 2221.644| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3352 Z= 0.208 Angle : 0.689 9.880 4560 Z= 0.345 Chirality : 0.044 0.144 484 Planarity : 0.004 0.033 594 Dihedral : 5.373 53.526 479 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.92 % Favored : 93.84 % Rotamer: Outliers : 5.19 % Allowed : 23.05 % Favored : 71.76 % 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: -2.41 (0.38), residues: 422 helix: -4.42 (0.58), residues: 23 sheet: -0.36 (0.41), residues: 152 loop : -2.22 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.001 0.000 HIS A 41 PHE 0.014 0.001 PHE B 400 TYR 0.016 0.001 TYR C 80 ARG 0.005 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8152 (p90) cc_final: 0.7651 (p90) REVERT: A 55 ASN cc_start: 0.8090 (t0) cc_final: 0.7547 (t0) REVERT: C 13 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8597 (mmmt) REVERT: C 65 LYS cc_start: 0.8468 (tppp) cc_final: 0.8139 (tppt) REVERT: B 498 ARG cc_start: 0.8200 (mtt90) cc_final: 0.7955 (mtt-85) outliers start: 18 outliers final: 16 residues processed: 107 average time/residue: 0.1649 time to fit residues: 21.0913 Evaluate side-chains 111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.0040 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.088757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.079118 restraints weight = 8378.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.081440 restraints weight = 3889.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082907 restraints weight = 2212.955| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3352 Z= 0.239 Angle : 0.689 9.795 4560 Z= 0.345 Chirality : 0.045 0.152 484 Planarity : 0.004 0.033 594 Dihedral : 5.200 51.781 479 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.64 % Favored : 93.13 % Rotamer: Outliers : 6.92 % Allowed : 22.77 % Favored : 70.32 % 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: -2.13 (0.39), residues: 422 helix: -4.47 (0.61), residues: 16 sheet: -0.15 (0.43), residues: 152 loop : -2.12 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 115 HIS 0.002 0.001 HIS A 41 PHE 0.012 0.001 PHE C 68 TYR 0.012 0.001 TYR C 80 ARG 0.003 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8171 (p90) cc_final: 0.7377 (p90) REVERT: A 55 ASN cc_start: 0.8189 (t0) cc_final: 0.7882 (t0) REVERT: C 13 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8589 (mmmt) REVERT: C 65 LYS cc_start: 0.8474 (tppp) cc_final: 0.8137 (tppt) REVERT: B 498 ARG cc_start: 0.8166 (mtt90) cc_final: 0.7932 (mtt-85) outliers start: 24 outliers final: 21 residues processed: 111 average time/residue: 0.1830 time to fit residues: 24.2385 Evaluate side-chains 117 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.089536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079686 restraints weight = 8527.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.082068 restraints weight = 3892.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083607 restraints weight = 2196.248| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3352 Z= 0.209 Angle : 0.689 9.123 4560 Z= 0.340 Chirality : 0.044 0.145 484 Planarity : 0.004 0.030 594 Dihedral : 5.064 49.846 479 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.16 % Favored : 93.60 % Rotamer: Outliers : 6.05 % Allowed : 23.92 % Favored : 70.03 % 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: -1.97 (0.39), residues: 422 helix: -4.28 (0.67), residues: 16 sheet: -0.06 (0.43), residues: 152 loop : -2.00 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.001 0.000 HIS A 41 PHE 0.012 0.001 PHE B 400 TYR 0.024 0.001 TYR C 80 ARG 0.007 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8161 (p90) cc_final: 0.7519 (p90) REVERT: A 55 ASN cc_start: 0.8289 (t0) cc_final: 0.7796 (t0) REVERT: C 13 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8610 (mmmt) REVERT: C 34 MET cc_start: 0.8995 (mmp) cc_final: 0.8768 (mmp) REVERT: C 65 LYS cc_start: 0.8434 (tppp) cc_final: 0.8113 (tppt) REVERT: B 466 ARG cc_start: 0.8585 (ptm-80) cc_final: 0.8198 (ptm-80) REVERT: B 498 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7909 (mtt-85) outliers start: 21 outliers final: 19 residues processed: 109 average time/residue: 0.1692 time to fit residues: 21.8997 Evaluate side-chains 114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.0170 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 chunk 4 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 overall best weight: 0.0710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.093423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083411 restraints weight = 8571.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085892 restraints weight = 3896.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087507 restraints weight = 2170.814| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3352 Z= 0.170 Angle : 0.696 9.086 4560 Z= 0.341 Chirality : 0.044 0.165 484 Planarity : 0.004 0.030 594 Dihedral : 4.598 45.027 479 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.21 % Favored : 94.55 % Rotamer: Outliers : 4.61 % Allowed : 25.65 % Favored : 69.74 % 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: -1.57 (0.40), residues: 422 helix: -3.83 (0.91), residues: 16 sheet: 0.33 (0.44), residues: 151 loop : -1.82 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.001 0.000 HIS B 519 PHE 0.013 0.001 PHE B 400 TYR 0.014 0.001 TYR C 80 ARG 0.009 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7988 (p90) cc_final: 0.7364 (p90) REVERT: A 55 ASN cc_start: 0.8167 (t0) cc_final: 0.7585 (t0) REVERT: C 13 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8617 (mmmt) REVERT: B 466 ARG cc_start: 0.8533 (ptm-80) cc_final: 0.8195 (ptm-80) outliers start: 16 outliers final: 14 residues processed: 108 average time/residue: 0.1592 time to fit residues: 20.6514 Evaluate side-chains 114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.0670 chunk 26 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.092078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.082076 restraints weight = 8401.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084495 restraints weight = 3898.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086070 restraints weight = 2203.325| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3352 Z= 0.197 Angle : 0.716 9.837 4560 Z= 0.348 Chirality : 0.045 0.155 484 Planarity : 0.004 0.029 594 Dihedral : 4.651 44.656 479 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.92 % Favored : 93.84 % Rotamer: Outliers : 3.75 % Allowed : 27.09 % Favored : 69.16 % 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: -1.53 (0.41), residues: 422 helix: -3.82 (0.92), residues: 16 sheet: 0.33 (0.44), residues: 152 loop : -1.77 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 36 HIS 0.001 0.000 HIS A 41 PHE 0.012 0.001 PHE B 400 TYR 0.014 0.001 TYR C 80 ARG 0.008 0.001 ARG C 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8042 (p90) cc_final: 0.7277 (p90) REVERT: A 55 ASN cc_start: 0.8253 (t0) cc_final: 0.7775 (t0) REVERT: C 13 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8615 (mmmt) REVERT: C 34 MET cc_start: 0.8823 (mmp) cc_final: 0.8572 (mmp) REVERT: C 65 LYS cc_start: 0.8326 (mmmm) cc_final: 0.7651 (mppt) REVERT: B 466 ARG cc_start: 0.8551 (ptm-80) cc_final: 0.8273 (ptm-80) REVERT: B 498 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7811 (mtt-85) outliers start: 13 outliers final: 13 residues processed: 106 average time/residue: 0.1686 time to fit residues: 21.3634 Evaluate side-chains 111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 0.0040 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 overall best weight: 1.4998 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.088809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.079104 restraints weight = 8617.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.081417 restraints weight = 4037.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082936 restraints weight = 2315.955| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3352 Z= 0.327 Angle : 0.768 9.811 4560 Z= 0.383 Chirality : 0.047 0.144 484 Planarity : 0.005 0.043 594 Dihedral : 5.204 47.105 479 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.11 % Favored : 92.65 % Rotamer: Outliers : 5.19 % Allowed : 26.51 % Favored : 68.30 % 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: -1.75 (0.40), residues: 422 helix: -3.97 (0.71), residues: 22 sheet: 0.12 (0.44), residues: 152 loop : -1.80 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 353 HIS 0.003 0.001 HIS A 41 PHE 0.010 0.001 PHE C 68 TYR 0.025 0.002 TYR C 56 ARG 0.011 0.001 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.68 seconds wall clock time: 31 minutes 56.42 seconds (1916.42 seconds total)