Starting phenix.real_space_refine on Fri Dec 27 06:53:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvj_34129/12_2024/7yvj_34129.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvj_34129/12_2024/7yvj_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_34129/12_2024/7yvj_34129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvj_34129/12_2024/7yvj_34129.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvj_34129/12_2024/7yvj_34129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvj_34129/12_2024/7yvj_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-5532/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: 5.48, per 1000 atoms: 1.68 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: 0.81 Conformation dependent library (CDL) restraints added in 391.5 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: 0.90 Time building geometry restraints manager: 0.94 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: 6.430 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: 0.030 Set scattering table: 0.030 Process input model: 15.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.020 ------------------------------------------------------------------------------- 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 : 0.373 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: 0.2175 time to fit residues: 31.0983 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 : 0.388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8009 (p90) cc_final: 0.7265 (p90) REVERT: A 55 ASN cc_start: 0.7923 (t0) cc_final: 0.7317 (t0) REVERT: C 13 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8497 (mmmt) REVERT: C 98 ARG cc_start: 0.8031 (ttp-170) cc_final: 0.7177 (tmt170) REVERT: B 386 LYS cc_start: 0.7739 (mttt) cc_final: 0.7270 (ttpt) REVERT: B 403 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.8341 (ttm-80) REVERT: B 508 TYR cc_start: 0.8464 (m-80) cc_final: 0.8003 (m-80) outliers start: 12 outliers final: 8 residues processed: 112 average time/residue: 0.2064 time to fit residues: 26.7918 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 : 0.381 ------------------------------------------------------------------------------- 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 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.0030 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.4948 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3045 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= 0.181 Angle : 0.635 6.206 4560 Z= 0.322 Chirality : 0.044 0.147 484 Planarity : 0.005 0.049 594 Dihedral : 5.107 54.280 479 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.98 % Favored : 94.79 % 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: -2.76 (0.35), residues: 422 helix: -4.70 (0.43), residues: 16 sheet: -0.97 (0.38), residues: 156 loop : -2.29 (0.33), 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 0.028 0.001 TYR C 80 ARG 0.008 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 120 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7971 (p90) cc_final: 0.7229 (p90) REVERT: A 55 ASN cc_start: 0.7848 (t0) cc_final: 0.7158 (t0) REVERT: C 13 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8463 (mmmt) REVERT: C 43 LYS cc_start: 0.8968 (mmtp) cc_final: 0.8753 (mmtp) REVERT: B 358 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9113 (tp) REVERT: B 386 LYS cc_start: 0.7744 (mttt) cc_final: 0.7293 (ttpt) REVERT: B 498 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7916 (mtt-85) REVERT: B 508 TYR cc_start: 0.8363 (m-80) cc_final: 0.8050 (m-80) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.1993 time to fit residues: 25.8970 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 : 0.369 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.0870 chunk 0 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3383 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= 0.186 Angle : 0.657 9.822 4560 Z= 0.324 Chirality : 0.043 0.144 484 Planarity : 0.005 0.055 594 Dihedral : 4.961 53.066 479 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.27 % Favored : 95.50 % Rotamer: Outliers : 4.90 % Allowed : 22.48 % 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: -2.36 (0.37), residues: 422 helix: -4.53 (0.53), residues: 16 sheet: -0.62 (0.39), residues: 158 loop : -2.08 (0.34), residues: 248 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 0.030 0.001 TYR C 80 ARG 0.013 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 123 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7969 (p90) cc_final: 0.7142 (p90) REVERT: A 55 ASN cc_start: 0.7813 (t0) cc_final: 0.7097 (t0) REVERT: C 13 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8471 (mmmt) REVERT: C 98 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7565 (tmm-80) REVERT: B 386 LYS cc_start: 0.7654 (mttt) cc_final: 0.7204 (ttpt) REVERT: B 498 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7906 (mtt-85) REVERT: B 508 TYR cc_start: 0.8325 (m-80) cc_final: 0.8075 (m-80) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.1911 time to fit residues: 25.1400 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 : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 34 MET 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 30 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3352 Z= 0.266 Angle : 0.664 8.450 4560 Z= 0.338 Chirality : 0.044 0.154 484 Planarity : 0.005 0.045 594 Dihedral : 5.215 53.638 479 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.45 % Favored : 94.31 % Rotamer: Outliers : 4.90 % Allowed : 23.34 % 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: -2.17 (0.38), residues: 422 helix: -4.54 (0.52), residues: 16 sheet: -0.35 (0.40), residues: 157 loop : -2.03 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 115 HIS 0.002 0.001 HIS A 41 PHE 0.015 0.001 PHE C 68 TYR 0.011 0.001 TYR C 56 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 117 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8072 (p90) cc_final: 0.7257 (p90) REVERT: A 55 ASN cc_start: 0.7985 (t0) cc_final: 0.7616 (t0) REVERT: B 386 LYS cc_start: 0.7236 (mttt) cc_final: 0.6803 (ttpt) REVERT: B 498 ARG cc_start: 0.8217 (mtt90) cc_final: 0.7960 (mtt-85) outliers start: 17 outliers final: 16 residues processed: 107 average time/residue: 0.2029 time to fit residues: 25.2964 Evaluate side-chains 114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR 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 34 MET 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 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU 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 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.0050 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3796 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= 0.183 Angle : 0.651 7.592 4560 Z= 0.325 Chirality : 0.043 0.142 484 Planarity : 0.005 0.054 594 Dihedral : 4.997 51.345 479 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.74 % Favored : 95.02 % Rotamer: Outliers : 6.34 % Allowed : 22.77 % Favored : 70.89 % 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: -1.92 (0.38), residues: 422 helix: -4.37 (0.69), residues: 16 sheet: -0.04 (0.41), residues: 152 loop : -1.95 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.001 0.000 HIS A 41 PHE 0.013 0.001 PHE C 68 TYR 0.017 0.001 TYR B 508 ARG 0.012 0.001 ARG A 56 *********************** 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 125 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8051 (p90) cc_final: 0.7315 (p90) REVERT: A 55 ASN cc_start: 0.7936 (t0) cc_final: 0.7337 (t0) REVERT: C 13 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8525 (mmmt) REVERT: C 65 LYS cc_start: 0.8444 (tppp) cc_final: 0.8146 (tppt) REVERT: B 386 LYS cc_start: 0.7272 (mttt) cc_final: 0.6892 (ttpt) REVERT: B 498 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7934 (mtt-85) outliers start: 22 outliers final: 18 residues processed: 113 average time/residue: 0.1981 time to fit residues: 26.1687 Evaluate side-chains 114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 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 430 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 22 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3938 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= 0.259 Angle : 0.696 7.871 4560 Z= 0.346 Chirality : 0.044 0.151 484 Planarity : 0.005 0.055 594 Dihedral : 5.168 51.339 479 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.40 % Favored : 93.36 % Rotamer: Outliers : 5.48 % Allowed : 23.92 % 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: -1.85 (0.39), residues: 422 helix: -4.39 (0.64), residues: 16 sheet: 0.03 (0.42), residues: 152 loop : -1.91 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 353 HIS 0.002 0.001 HIS A 41 PHE 0.011 0.001 PHE C 68 TYR 0.009 0.001 TYR A 51 ARG 0.012 0.001 ARG A 56 *********************** 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 119 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8132 (p90) cc_final: 0.7307 (p90) REVERT: A 55 ASN cc_start: 0.8116 (t0) cc_final: 0.7733 (t0) REVERT: B 386 LYS cc_start: 0.7097 (mttt) cc_final: 0.6744 (ttpt) REVERT: B 498 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7928 (mtt-85) outliers start: 19 outliers final: 18 residues processed: 109 average time/residue: 0.1869 time to fit residues: 23.9682 Evaluate side-chains 111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.0000 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3352 Z= 0.270 Angle : 0.718 9.098 4560 Z= 0.351 Chirality : 0.045 0.144 484 Planarity : 0.005 0.057 594 Dihedral : 5.255 51.191 479 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.16 % Favored : 93.60 % Rotamer: Outliers : 5.76 % Allowed : 24.50 % 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: -1.81 (0.39), residues: 422 helix: -3.89 (0.88), residues: 16 sheet: -0.02 (0.42), residues: 152 loop : -1.86 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 353 HIS 0.002 0.001 HIS A 41 PHE 0.013 0.001 PHE C 68 TYR 0.016 0.001 TYR B 508 ARG 0.003 0.000 ARG B 355 *********************** 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 115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8166 (p90) cc_final: 0.7333 (p90) REVERT: A 55 ASN cc_start: 0.8197 (t0) cc_final: 0.7866 (t0) REVERT: C 65 LYS cc_start: 0.8429 (mmmm) cc_final: 0.7852 (mppt) REVERT: B 498 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7946 (mtt-85) outliers start: 20 outliers final: 19 residues processed: 105 average time/residue: 0.1854 time to fit residues: 23.0328 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 : 0.470 ------------------------------------------------------------------------------- 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 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 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 430 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4211 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= 0.217 Angle : 0.708 9.975 4560 Z= 0.342 Chirality : 0.044 0.147 484 Planarity : 0.004 0.055 594 Dihedral : 5.057 49.256 479 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.69 % Favored : 94.08 % Rotamer: Outliers : 5.48 % Allowed : 25.94 % 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: -1.73 (0.40), residues: 422 helix: -3.86 (0.90), residues: 16 sheet: 0.08 (0.43), residues: 152 loop : -1.83 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 353 HIS 0.002 0.000 HIS A 41 PHE 0.012 0.001 PHE C 68 TYR 0.008 0.001 TYR B 508 ARG 0.002 0.000 ARG B 355 *********************** 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 121 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8143 (p90) cc_final: 0.7451 (p90) REVERT: A 55 ASN cc_start: 0.8240 (t0) cc_final: 0.7776 (t0) REVERT: B 498 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7943 (mtt-85) outliers start: 19 outliers final: 18 residues processed: 111 average time/residue: 0.1729 time to fit residues: 22.9879 Evaluate side-chains 112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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 430 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 20 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4319 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= 0.207 Angle : 0.720 8.598 4560 Z= 0.354 Chirality : 0.044 0.147 484 Planarity : 0.005 0.064 594 Dihedral : 5.005 47.572 479 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.45 % Favored : 94.31 % Rotamer: Outliers : 5.48 % Allowed : 25.94 % 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: -1.64 (0.40), residues: 422 helix: -4.01 (0.79), residues: 16 sheet: 0.19 (0.43), residues: 152 loop : -1.79 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 353 HIS 0.001 0.000 HIS A 41 PHE 0.016 0.001 PHE C 68 TYR 0.014 0.001 TYR C 80 ARG 0.010 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 118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8112 (p90) cc_final: 0.7406 (p90) REVERT: A 55 ASN cc_start: 0.8262 (t0) cc_final: 0.7800 (t0) REVERT: C 34 MET cc_start: 0.8837 (mmp) cc_final: 0.8566 (mmp) REVERT: B 498 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7926 (mtt-85) outliers start: 19 outliers final: 19 residues processed: 108 average time/residue: 0.1644 time to fit residues: 21.7479 Evaluate side-chains 115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 430 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 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.091758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081951 restraints weight = 8372.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084301 restraints weight = 3860.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.085852 restraints weight = 2197.282| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4455 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= 0.192 Angle : 0.712 8.679 4560 Z= 0.348 Chirality : 0.044 0.146 484 Planarity : 0.004 0.027 594 Dihedral : 4.851 45.573 479 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.98 % Favored : 94.79 % Rotamer: Outliers : 5.48 % Allowed : 26.51 % Favored : 68.01 % 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: -1.48 (0.41), residues: 422 helix: -4.01 (0.80), residues: 16 sheet: 0.31 (0.44), residues: 151 loop : -1.68 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 353 HIS 0.001 0.000 HIS A 41 PHE 0.014 0.001 PHE C 68 TYR 0.018 0.001 TYR C 80 ARG 0.002 0.000 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.68 seconds wall clock time: 29 minutes 42.47 seconds (1782.47 seconds total)