Starting phenix.real_space_refine on Mon Feb 10 23:39:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvj_34129/02_2025/7yvj_34129.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvj_34129/02_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_34129/02_2025/7yvj_34129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvj_34129/02_2025/7yvj_34129.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvj_34129/02_2025/7yvj_34129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvj_34129/02_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-5592/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: 5.39, per 1000 atoms: 1.65 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: 0.79 Conformation dependent library (CDL) restraints added in 424.3 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: 0.43 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: 0.92 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.060 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- 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 : 0.426 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: 0.2095 time to fit residues: 30.0356 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 : 0.383 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.091079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.081052 restraints weight = 8467.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.083402 restraints weight = 3894.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084962 restraints weight = 2219.295| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3352 Z= 0.239 Angle : 0.681 8.486 4560 Z= 0.351 Chirality : 0.046 0.140 484 Planarity : 0.005 0.040 594 Dihedral : 5.551 57.214 479 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.50 % Favored : 95.02 % Rotamer: Outliers : 3.46 % Allowed : 17.58 % Favored : 78.96 % 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: -3.53 (0.34), residues: 422 helix: -5.19 (0.22), residues: 22 sheet: -1.51 (0.37), residues: 154 loop : -2.72 (0.33), 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 0.023 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 118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8014 (p90) cc_final: 0.7265 (p90) REVERT: A 55 ASN cc_start: 0.7922 (t0) cc_final: 0.7357 (t0) REVERT: C 13 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8504 (mmmt) REVERT: C 98 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7182 (tmt170) REVERT: B 386 LYS cc_start: 0.7741 (mttt) cc_final: 0.7299 (ttpt) REVERT: B 403 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8338 (ttm-80) REVERT: B 508 TYR cc_start: 0.8441 (m-80) cc_final: 0.8000 (m-80) outliers start: 12 outliers final: 8 residues processed: 112 average time/residue: 0.1944 time to fit residues: 25.1846 Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL 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: 4.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.089715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.079567 restraints weight = 8402.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081944 restraints weight = 3930.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083510 restraints weight = 2254.372| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3352 Z= 0.258 Angle : 0.662 6.308 4560 Z= 0.339 Chirality : 0.045 0.145 484 Planarity : 0.006 0.075 594 Dihedral : 5.389 56.020 479 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.45 % Favored : 94.31 % Rotamer: Outliers : 4.61 % Allowed : 20.75 % 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: -2.93 (0.36), residues: 422 helix: -4.74 (0.40), residues: 16 sheet: -1.10 (0.38), residues: 158 loop : -2.40 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 353 HIS 0.002 0.000 HIS A 41 PHE 0.012 0.001 PHE B 400 TYR 0.025 0.002 TYR C 80 ARG 0.010 0.001 ARG C 19 *********************** 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: 16 poor density : 102 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8078 (p90) cc_final: 0.7490 (p90) REVERT: A 55 ASN cc_start: 0.7891 (t0) cc_final: 0.7377 (t0) REVERT: C 13 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8430 (mmmt) REVERT: C 98 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7793 (ttp-170) REVERT: C 100 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7776 (tp-100) REVERT: B 358 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9172 (tp) REVERT: B 386 LYS cc_start: 0.7291 (mttt) cc_final: 0.6930 (ttpt) REVERT: B 498 ARG cc_start: 0.8236 (mtt90) cc_final: 0.7949 (mtt-85) REVERT: B 508 TYR cc_start: 0.8399 (m-80) cc_final: 0.8076 (m-80) outliers start: 16 outliers final: 13 residues processed: 110 average time/residue: 0.1940 time to fit residues: 24.9305 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 : 0.350 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.089865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.079903 restraints weight = 8484.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082297 restraints weight = 3858.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.083871 restraints weight = 2179.260| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3352 Z= 0.211 Angle : 0.662 9.654 4560 Z= 0.329 Chirality : 0.044 0.143 484 Planarity : 0.005 0.042 594 Dihedral : 5.182 54.459 479 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.50 % Favored : 95.26 % Rotamer: Outliers : 6.63 % Allowed : 20.75 % 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: -2.48 (0.37), residues: 422 helix: -4.62 (0.47), residues: 16 sheet: -0.66 (0.39), residues: 158 loop : -2.20 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 353 HIS 0.002 0.000 HIS A 41 PHE 0.013 0.001 PHE B 400 TYR 0.011 0.001 TYR C 80 ARG 0.008 0.001 ARG A 56 *********************** 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 130 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8054 (p90) cc_final: 0.7451 (p90) REVERT: A 55 ASN cc_start: 0.7910 (t0) cc_final: 0.7333 (t0) REVERT: C 13 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8537 (mmmt) REVERT: C 43 LYS cc_start: 0.8999 (mmtp) cc_final: 0.8786 (mmtp) REVERT: C 100 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7945 (tp-100) REVERT: B 386 LYS cc_start: 0.7241 (mttt) cc_final: 0.6895 (ttpt) REVERT: B 498 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7938 (mtt-85) REVERT: B 508 TYR cc_start: 0.8320 (m-80) cc_final: 0.8075 (m-80) outliers start: 23 outliers final: 18 residues processed: 116 average time/residue: 0.1959 time to fit residues: 26.6303 Evaluate side-chains 116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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 119 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU 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: 3.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.0010 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076814 restraints weight = 8660.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.079123 restraints weight = 4042.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.080637 restraints weight = 2300.405| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3352 Z= 0.357 Angle : 0.711 9.323 4560 Z= 0.363 Chirality : 0.045 0.148 484 Planarity : 0.006 0.074 594 Dihedral : 5.591 55.925 479 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.35 % Favored : 92.42 % Rotamer: Outliers : 5.48 % Allowed : 23.34 % Favored : 71.18 % 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: -2.45 (0.37), residues: 422 helix: -4.54 (0.49), residues: 23 sheet: -0.47 (0.41), residues: 152 loop : -2.17 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 115 HIS 0.003 0.001 HIS A 41 PHE 0.013 0.002 PHE C 68 TYR 0.017 0.002 TYR C 80 ARG 0.010 0.001 ARG C 19 *********************** 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 112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8164 (p90) cc_final: 0.7316 (p90) REVERT: A 55 ASN cc_start: 0.8105 (t0) cc_final: 0.7802 (t0) REVERT: C 100 GLN cc_start: 0.8303 (tp-100) cc_final: 0.8031 (tp-100) REVERT: B 498 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7917 (mtt-85) outliers start: 19 outliers final: 18 residues processed: 104 average time/residue: 0.1841 time to fit residues: 22.5603 Evaluate side-chains 105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 119 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR 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: 1.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 41 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 = 0.3377 r_free = 0.3377 target = 0.088896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078959 restraints weight = 8787.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081385 restraints weight = 3980.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082991 restraints weight = 2225.930| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3755 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 : 0.669 8.030 4560 Z= 0.333 Chirality : 0.044 0.155 484 Planarity : 0.004 0.034 594 Dihedral : 5.294 53.823 479 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.45 % Favored : 94.31 % Rotamer: Outliers : 6.05 % Allowed : 23.34 % Favored : 70.61 % 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: -2.30 (0.38), residues: 422 helix: -4.44 (0.64), residues: 16 sheet: -0.33 (0.42), residues: 152 loop : -2.20 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS A 41 PHE 0.013 0.001 PHE C 68 TYR 0.023 0.001 TYR C 80 ARG 0.010 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 117 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8109 (p90) cc_final: 0.7582 (p90) REVERT: A 55 ASN cc_start: 0.8115 (t0) cc_final: 0.7583 (t0) REVERT: C 13 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8521 (mmmt) REVERT: C 43 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8775 (mmtp) REVERT: C 100 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7941 (tp-100) REVERT: B 498 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7944 (mtt-85) outliers start: 21 outliers final: 20 residues processed: 107 average time/residue: 0.1670 time to fit residues: 21.3299 Evaluate side-chains 113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR 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=2.50 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.088028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.078290 restraints weight = 8492.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.080642 restraints weight = 3916.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082201 restraints weight = 2215.612| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3352 Z= 0.274 Angle : 0.688 9.086 4560 Z= 0.342 Chirality : 0.044 0.146 484 Planarity : 0.004 0.034 594 Dihedral : 5.338 53.109 479 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.64 % Favored : 93.13 % Rotamer: Outliers : 6.34 % Allowed : 24.21 % Favored : 69.45 % 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: -2.19 (0.38), residues: 422 helix: -4.45 (0.61), residues: 16 sheet: -0.24 (0.42), residues: 152 loop : -2.12 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 115 HIS 0.002 0.001 HIS A 41 PHE 0.011 0.001 PHE B 400 TYR 0.019 0.001 TYR C 80 ARG 0.011 0.001 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 115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8176 (p90) cc_final: 0.7365 (p90) REVERT: A 55 ASN cc_start: 0.8242 (t0) cc_final: 0.7964 (t0) REVERT: C 13 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8578 (mmmt) REVERT: C 34 MET cc_start: 0.9024 (mmp) cc_final: 0.8811 (mmp) REVERT: C 100 GLN cc_start: 0.8303 (tp-100) cc_final: 0.8027 (tp-100) REVERT: B 498 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7917 (mtt-85) outliers start: 22 outliers final: 22 residues processed: 104 average time/residue: 0.1714 time to fit residues: 21.3502 Evaluate side-chains 113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP 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: 0.9980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.087598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.077808 restraints weight = 8657.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.080197 restraints weight = 4004.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081781 restraints weight = 2261.610| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3352 Z= 0.295 Angle : 0.709 8.359 4560 Z= 0.351 Chirality : 0.045 0.154 484 Planarity : 0.004 0.033 594 Dihedral : 5.408 53.107 479 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.87 % Favored : 92.89 % Rotamer: Outliers : 6.92 % Allowed : 24.50 % Favored : 68.59 % 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 (0.38), residues: 422 helix: -4.03 (0.69), residues: 22 sheet: -0.28 (0.42), residues: 152 loop : -2.05 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 115 HIS 0.002 0.001 HIS A 41 PHE 0.011 0.001 PHE C 68 TYR 0.015 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: 24 poor density : 96 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8198 (p90) cc_final: 0.7388 (p90) REVERT: A 55 ASN cc_start: 0.8317 (t0) cc_final: 0.8111 (t0) REVERT: C 13 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8574 (mmmt) REVERT: C 65 LYS cc_start: 0.8497 (tppp) cc_final: 0.8139 (tppt) REVERT: C 100 GLN cc_start: 0.8354 (tp-100) cc_final: 0.8067 (tp-100) REVERT: B 498 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7939 (mtt-85) outliers start: 24 outliers final: 23 residues processed: 108 average time/residue: 0.1698 time to fit residues: 21.9212 Evaluate side-chains 116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP 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: 0.5980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.090000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080440 restraints weight = 8615.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082781 restraints weight = 3950.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084337 restraints weight = 2222.297| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3352 Z= 0.192 Angle : 0.691 8.528 4560 Z= 0.335 Chirality : 0.044 0.153 484 Planarity : 0.004 0.029 594 Dihedral : 5.110 50.376 479 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.92 % Favored : 93.84 % Rotamer: Outliers : 6.63 % Allowed : 24.78 % Favored : 68.59 % 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: -1.89 (0.39), residues: 422 helix: -3.60 (1.12), residues: 16 sheet: -0.09 (0.42), residues: 152 loop : -1.92 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.001 0.000 HIS A 41 PHE 0.013 0.001 PHE B 400 TYR 0.016 0.001 TYR C 80 ARG 0.005 0.000 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 122 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8092 (p90) cc_final: 0.7457 (p90) REVERT: A 55 ASN cc_start: 0.8274 (t0) cc_final: 0.7826 (t0) REVERT: C 13 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8623 (mmmt) REVERT: C 34 MET cc_start: 0.8866 (mmp) cc_final: 0.8634 (mmp) REVERT: C 65 LYS cc_start: 0.8449 (tppp) cc_final: 0.8141 (tppt) REVERT: B 466 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.8220 (ptm-80) REVERT: B 498 ARG cc_start: 0.8129 (mtt90) cc_final: 0.7905 (mtt-85) outliers start: 23 outliers final: 21 residues processed: 111 average time/residue: 0.1564 time to fit residues: 21.0083 Evaluate side-chains 115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP 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 483 VAL Chi-restraints excluded: chain B residue 511 VAL 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: 0.7980 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN C 100 GLN B 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079915 restraints weight = 8491.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082239 restraints weight = 3936.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083740 restraints weight = 2224.497| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3352 Z= 0.234 Angle : 0.730 9.806 4560 Z= 0.355 Chirality : 0.045 0.146 484 Planarity : 0.004 0.029 594 Dihedral : 5.098 49.451 479 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.64 % Favored : 93.13 % Rotamer: Outliers : 6.92 % Allowed : 24.50 % Favored : 68.59 % 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: -1.76 (0.40), residues: 422 helix: -3.94 (0.85), residues: 16 sheet: 0.07 (0.43), residues: 152 loop : -1.86 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 353 HIS 0.002 0.001 HIS A 41 PHE 0.013 0.001 PHE C 68 TYR 0.014 0.001 TYR C 80 ARG 0.005 0.000 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 122 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8074 (p90) cc_final: 0.7421 (p90) REVERT: A 55 ASN cc_start: 0.8299 (t0) cc_final: 0.7869 (t0) REVERT: C 13 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8622 (mmmt) REVERT: C 34 MET cc_start: 0.8906 (mmp) cc_final: 0.8643 (mmp) REVERT: C 65 LYS cc_start: 0.8468 (tppp) cc_final: 0.8124 (tppt) REVERT: B 466 ARG cc_start: 0.8628 (ptm-80) cc_final: 0.8279 (ptm-80) REVERT: B 498 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7915 (mtt-85) outliers start: 24 outliers final: 22 residues processed: 110 average time/residue: 0.1556 time to fit residues: 20.6446 Evaluate side-chains 117 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 32 SER 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 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP 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 483 VAL Chi-restraints excluded: chain B residue 511 VAL 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: 2.9990 chunk 26 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.9342 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.089580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080042 restraints weight = 8553.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.082357 restraints weight = 3956.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083878 restraints weight = 2243.222| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3352 Z= 0.235 Angle : 0.732 10.073 4560 Z= 0.357 Chirality : 0.045 0.145 484 Planarity : 0.004 0.029 594 Dihedral : 5.149 48.377 479 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.40 % Favored : 93.36 % Rotamer: Outliers : 6.63 % Allowed : 24.50 % Favored : 68.88 % 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: -1.72 (0.40), residues: 422 helix: -4.11 (0.73), residues: 16 sheet: 0.13 (0.43), residues: 152 loop : -1.84 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 353 HIS 0.002 0.000 HIS A 41 PHE 0.015 0.001 PHE C 68 TYR 0.012 0.001 TYR C 80 ARG 0.005 0.001 ARG C 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.03 seconds wall clock time: 32 minutes 42.21 seconds (1962.21 seconds total)