Starting phenix.real_space_refine on Tue Feb 13 07:09:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/02_2024/7yho_33832_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/02_2024/7yho_33832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/02_2024/7yho_33832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/02_2024/7yho_33832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/02_2024/7yho_33832_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/02_2024/7yho_33832_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 49 5.49 5 S 23 5.16 5 C 2348 2.51 5 N 697 2.21 5 O 802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3923 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2910 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 22, 'TRANS': 338} Chain breaks: 5 Chain: "B" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 539 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 466 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1826 SG CYS A1045 53.403 54.606 40.943 1.00 78.34 S ATOM 1774 SG CYS A1038 50.038 53.672 46.312 1.00 73.18 S ATOM 1845 SG CYS A1048 55.115 57.801 46.484 1.00 81.69 S ATOM 1888 SG CYS A1054 55.624 51.262 45.560 1.00 83.08 S Time building chain proxies: 2.94, per 1000 atoms: 0.75 Number of scatterers: 3923 At special positions: 0 Unit cell: (73.03, 105.19, 89.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 23 16.00 P 49 15.00 O 802 8.00 N 697 7.00 C 2348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 522.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1401 " pdb="FE4 SF4 A1401 " - pdb=" SG CYS A1054 " pdb="FE3 SF4 A1401 " - pdb=" SG CYS A1048 " pdb="FE1 SF4 A1401 " - pdb=" SG CYS A1045 " pdb="FE2 SF4 A1401 " - pdb=" SG CYS A1038 " Number of angles added : 12 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 48.8% alpha, 5.0% beta 19 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 561 through 583 removed outlier: 3.577A pdb=" N VAL A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 611 through 624 Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 906 through 922 Processing helix chain 'A' and resid 930 through 933 Processing helix chain 'A' and resid 937 through 946 Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 1007 through 1015 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1020 through 1036 Processing helix chain 'A' and resid 1049 through 1051 No H-bonds generated for 'chain 'A' and resid 1049 through 1051' Processing helix chain 'A' and resid 1055 through 1060 Processing helix chain 'A' and resid 1213 through 1216 Processing helix chain 'A' and resid 1286 through 1290 Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1310 through 1314 Processing helix chain 'A' and resid 1338 through 1341 No H-bonds generated for 'chain 'A' and resid 1338 through 1341' Processing helix chain 'A' and resid 1347 through 1356 Processing sheet with id= A, first strand: chain 'A' and resid 1204 through 1206 Processing sheet with id= B, first strand: chain 'A' and resid 1230 through 1232 104 hydrogen bonds defined for protein. 300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 1676 1.41 - 1.63: 2406 1.63 - 1.84: 30 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 4124 Sorted by residual: bond pdb=" CA LEU A1026 " pdb=" C LEU A1026 " ideal model delta sigma weight residual 1.523 1.432 0.092 1.30e-02 5.92e+03 4.97e+01 bond pdb=" CA HIS A1027 " pdb=" C HIS A1027 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.39e-02 5.18e+03 3.25e+01 bond pdb=" C THR A1022 " pdb=" O THR A1022 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.15e-02 7.56e+03 1.90e+01 bond pdb=" N TYR A1028 " pdb=" CA TYR A1028 " ideal model delta sigma weight residual 1.459 1.407 0.053 1.21e-02 6.83e+03 1.89e+01 bond pdb=" CA HIS A1027 " pdb=" CB HIS A1027 " ideal model delta sigma weight residual 1.530 1.457 0.073 1.68e-02 3.54e+03 1.87e+01 ... (remaining 4119 not shown) Histogram of bond angle deviations from ideal: 73.67 - 85.73: 12 85.73 - 97.79: 0 97.79 - 109.86: 1019 109.86 - 121.92: 3919 121.92 - 133.98: 846 Bond angle restraints: 5796 Sorted by residual: angle pdb=" N TYR A1028 " pdb=" CA TYR A1028 " pdb=" C TYR A1028 " ideal model delta sigma weight residual 111.28 98.69 12.59 1.09e+00 8.42e-01 1.34e+02 angle pdb=" N HIS A1027 " pdb=" CA HIS A1027 " pdb=" C HIS A1027 " ideal model delta sigma weight residual 112.89 123.53 -10.64 1.24e+00 6.50e-01 7.36e+01 angle pdb=" N ILE A1031 " pdb=" CA ILE A1031 " pdb=" C ILE A1031 " ideal model delta sigma weight residual 110.62 103.40 7.22 1.02e+00 9.61e-01 5.00e+01 angle pdb=" N LEU A1026 " pdb=" CA LEU A1026 " pdb=" C LEU A1026 " ideal model delta sigma weight residual 111.28 103.77 7.51 1.09e+00 8.42e-01 4.74e+01 angle pdb=" CB HIS A1027 " pdb=" CG HIS A1027 " pdb=" CD2 HIS A1027 " ideal model delta sigma weight residual 131.20 123.55 7.65 1.30e+00 5.92e-01 3.46e+01 ... (remaining 5791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 2041 35.70 - 71.39: 273 71.39 - 107.09: 2 107.09 - 142.79: 0 142.79 - 178.48: 1 Dihedral angle restraints: 2317 sinusoidal: 1272 harmonic: 1045 Sorted by residual: dihedral pdb=" C HIS A1027 " pdb=" N HIS A1027 " pdb=" CA HIS A1027 " pdb=" CB HIS A1027 " ideal model delta harmonic sigma weight residual -122.60 -143.67 21.07 0 2.50e+00 1.60e-01 7.11e+01 dihedral pdb=" N HIS A1027 " pdb=" C HIS A1027 " pdb=" CA HIS A1027 " pdb=" CB HIS A1027 " ideal model delta harmonic sigma weight residual 122.80 143.77 -20.97 0 2.50e+00 1.60e-01 7.04e+01 dihedral pdb=" C4' DT C 17 " pdb=" C3' DT C 17 " pdb=" O3' DT C 17 " pdb=" P DT C 18 " ideal model delta sinusoidal sigma weight residual 220.00 41.52 178.48 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 2314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 634 0.231 - 0.462: 0 0.462 - 0.693: 2 0.693 - 0.924: 0 0.924 - 1.155: 1 Chirality restraints: 637 Sorted by residual: chirality pdb=" CA HIS A1027 " pdb=" N HIS A1027 " pdb=" C HIS A1027 " pdb=" CB HIS A1027 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" P DG B 6 " pdb=" OP1 DG B 6 " pdb=" OP2 DG B 6 " pdb=" O5' DG B 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.51e+00 chirality pdb=" P DG B 3 " pdb=" OP1 DG B 3 " pdb=" OP2 DG B 3 " pdb=" O5' DG B 3 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 634 not shown) Planarity restraints: 561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1028 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C TYR A1028 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR A1028 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A1029 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A1294 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A1295 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1295 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1295 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1023 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LEU A1023 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU A1023 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR A1024 " 0.008 2.00e-02 2.50e+03 ... (remaining 558 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 951 2.80 - 3.32: 3530 3.32 - 3.85: 7111 3.85 - 4.37: 7849 4.37 - 4.90: 12194 Nonbonded interactions: 31635 Sorted by model distance: nonbonded pdb=" NH1 ARG A 566 " pdb=" O PRO A1013 " model vdw 2.273 2.520 nonbonded pdb=" O GLN A 607 " pdb=" NH2 ARG A 903 " model vdw 2.286 2.520 nonbonded pdb=" N HIS A1310 " pdb=" O PHE A1364 " model vdw 2.338 2.520 nonbonded pdb=" NH1 ARG A 572 " pdb=" O GLY A 982 " model vdw 2.374 2.520 nonbonded pdb=" O MET A 580 " pdb=" N GLN A 584 " model vdw 2.376 2.520 ... (remaining 31630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 12.190 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.850 Find NCS groups from input model: 0.100 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.005 0.092 4124 Z= 0.311 Angle : 0.744 12.594 5796 Z= 0.488 Chirality : 0.067 1.155 637 Planarity : 0.004 0.040 561 Dihedral : 23.571 178.481 1637 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 8.78 % Allowed : 12.85 % Favored : 78.37 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.45), residues: 349 helix: 1.33 (0.40), residues: 178 sheet: 1.75 (1.40), residues: 12 loop : -1.04 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1012 HIS 0.003 0.001 HIS A 612 PHE 0.019 0.001 PHE A1033 TYR 0.012 0.001 TYR A1024 ARG 0.001 0.000 ARG A1204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 580 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.4232 (mpt) REVERT: A 607 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7320 (mt0) REVERT: A 1057 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7347 (t80) REVERT: A 1204 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6278 (mpp-170) outliers start: 28 outliers final: 12 residues processed: 95 average time/residue: 0.1830 time to fit residues: 20.8791 Evaluate side-chains 73 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1365 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4124 Z= 0.202 Angle : 0.592 8.039 5796 Z= 0.333 Chirality : 0.039 0.198 637 Planarity : 0.005 0.040 561 Dihedral : 27.357 179.750 962 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.64 % Allowed : 19.12 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.45), residues: 349 helix: 1.08 (0.39), residues: 177 sheet: 1.84 (1.32), residues: 12 loop : -1.21 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.013 0.002 HIS A1027 PHE 0.016 0.001 PHE A1033 TYR 0.010 0.001 TYR A1300 ARG 0.004 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 607 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7225 (mt0) REVERT: A 889 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7746 (tmm-80) REVERT: A 981 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 1057 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7407 (t80) REVERT: A 1204 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6305 (mpp-170) REVERT: A 1214 LEU cc_start: 0.7949 (mm) cc_final: 0.7669 (mt) REVERT: A 1281 THR cc_start: 0.6619 (OUTLIER) cc_final: 0.6344 (p) outliers start: 18 outliers final: 10 residues processed: 69 average time/residue: 0.1682 time to fit residues: 14.3860 Evaluate side-chains 69 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1365 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7182 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4124 Z= 0.195 Angle : 0.549 5.924 5796 Z= 0.310 Chirality : 0.038 0.182 637 Planarity : 0.004 0.039 561 Dihedral : 27.220 179.114 951 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.33 % Allowed : 22.57 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.45), residues: 349 helix: 1.03 (0.39), residues: 181 sheet: -0.50 (0.95), residues: 26 loop : -1.42 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.015 0.002 PHE A 604 TYR 0.011 0.001 TYR A1300 ARG 0.003 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 56 time to evaluate : 0.356 Fit side-chains REVERT: A 889 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7765 (tmm-80) REVERT: A 981 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7697 (mp) REVERT: A 1027 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.6988 (t-90) REVERT: A 1057 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7412 (t80) REVERT: A 1204 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6296 (mpp-170) REVERT: A 1214 LEU cc_start: 0.7995 (mm) cc_final: 0.7716 (mt) REVERT: A 1281 THR cc_start: 0.6651 (OUTLIER) cc_final: 0.6368 (p) outliers start: 17 outliers final: 10 residues processed: 67 average time/residue: 0.1854 time to fit residues: 15.1761 Evaluate side-chains 69 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1365 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7190 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4124 Z= 0.194 Angle : 0.555 6.672 5796 Z= 0.312 Chirality : 0.037 0.186 637 Planarity : 0.004 0.038 561 Dihedral : 27.102 179.059 947 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 7.21 % Allowed : 21.32 % Favored : 71.47 % 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: -0.13 (0.45), residues: 349 helix: 0.96 (0.39), residues: 187 sheet: -0.40 (0.94), residues: 26 loop : -1.49 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1012 HIS 0.004 0.001 HIS A 612 PHE 0.014 0.001 PHE A1033 TYR 0.011 0.001 TYR A1300 ARG 0.003 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 55 time to evaluate : 0.340 Fit side-chains REVERT: A 981 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7684 (mp) REVERT: A 1027 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.6916 (t-90) REVERT: A 1057 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7461 (t80) REVERT: A 1204 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6171 (mpp-170) REVERT: A 1214 LEU cc_start: 0.8042 (mm) cc_final: 0.7720 (mt) REVERT: A 1281 THR cc_start: 0.6694 (OUTLIER) cc_final: 0.6411 (p) outliers start: 23 outliers final: 12 residues processed: 70 average time/residue: 0.1683 time to fit residues: 14.5140 Evaluate side-chains 70 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1365 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 32 optimal weight: 0.0020 chunk 26 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 overall best weight: 0.2800 ------------------------------------------------------------------------------- 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: 0.7147 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4124 Z= 0.164 Angle : 0.547 5.542 5796 Z= 0.309 Chirality : 0.036 0.178 637 Planarity : 0.004 0.036 561 Dihedral : 26.999 179.397 945 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.33 % Allowed : 24.14 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.45), residues: 349 helix: 1.04 (0.40), residues: 189 sheet: 0.33 (1.14), residues: 19 loop : -1.47 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 983 HIS 0.004 0.001 HIS A1203 PHE 0.010 0.001 PHE A 604 TYR 0.010 0.001 TYR A1300 ARG 0.002 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 580 MET cc_start: 0.5064 (OUTLIER) cc_final: 0.4082 (mpt) REVERT: A 928 ASP cc_start: 0.7483 (p0) cc_final: 0.7263 (p0) REVERT: A 930 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6839 (pm20) REVERT: A 981 LEU cc_start: 0.7928 (tp) cc_final: 0.7667 (mp) REVERT: A 1027 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.6822 (t-90) REVERT: A 1057 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7421 (t80) REVERT: A 1214 LEU cc_start: 0.8005 (mm) cc_final: 0.7748 (mt) REVERT: A 1281 THR cc_start: 0.6617 (OUTLIER) cc_final: 0.6351 (p) outliers start: 17 outliers final: 6 residues processed: 66 average time/residue: 0.1704 time to fit residues: 13.9074 Evaluate side-chains 66 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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: 0.7162 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4124 Z= 0.183 Angle : 0.552 4.801 5796 Z= 0.311 Chirality : 0.036 0.176 637 Planarity : 0.004 0.036 561 Dihedral : 26.925 179.798 939 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.33 % Allowed : 24.45 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.45), residues: 349 helix: 1.17 (0.40), residues: 188 sheet: 0.24 (1.08), residues: 19 loop : -1.53 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 983 HIS 0.003 0.001 HIS A 612 PHE 0.012 0.001 PHE A 604 TYR 0.010 0.001 TYR A1300 ARG 0.005 0.000 ARG A1329 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 580 MET cc_start: 0.5098 (OUTLIER) cc_final: 0.4227 (mpt) REVERT: A 981 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7692 (mp) REVERT: A 1057 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7474 (t80) REVERT: A 1214 LEU cc_start: 0.8022 (mm) cc_final: 0.7759 (mt) REVERT: A 1281 THR cc_start: 0.6645 (OUTLIER) cc_final: 0.6386 (p) outliers start: 17 outliers final: 11 residues processed: 65 average time/residue: 0.1629 time to fit residues: 13.2442 Evaluate side-chains 67 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1291 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7178 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4124 Z= 0.192 Angle : 0.555 5.187 5796 Z= 0.313 Chirality : 0.036 0.172 637 Planarity : 0.004 0.036 561 Dihedral : 26.855 179.799 937 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.33 % Allowed : 25.08 % Favored : 69.59 % 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: 0.07 (0.45), residues: 349 helix: 1.17 (0.40), residues: 188 sheet: -0.09 (1.01), residues: 19 loop : -1.49 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 983 HIS 0.003 0.001 HIS A 612 PHE 0.012 0.001 PHE A 604 TYR 0.011 0.001 TYR A1300 ARG 0.004 0.000 ARG A1329 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 0.388 Fit side-chains REVERT: A 928 ASP cc_start: 0.7541 (p0) cc_final: 0.7336 (p0) REVERT: A 930 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6854 (pm20) REVERT: A 981 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7714 (mp) REVERT: A 1057 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7504 (t80) REVERT: A 1214 LEU cc_start: 0.8066 (mm) cc_final: 0.7790 (mt) outliers start: 17 outliers final: 11 residues processed: 63 average time/residue: 0.1455 time to fit residues: 11.5682 Evaluate side-chains 65 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1291 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4124 Z= 0.198 Angle : 0.569 6.342 5796 Z= 0.318 Chirality : 0.036 0.170 637 Planarity : 0.004 0.036 561 Dihedral : 26.809 179.964 934 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.02 % Allowed : 25.71 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.45), residues: 349 helix: 1.03 (0.40), residues: 187 sheet: -0.28 (1.00), residues: 19 loop : -1.51 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 983 HIS 0.004 0.001 HIS A 612 PHE 0.014 0.001 PHE A1033 TYR 0.011 0.001 TYR A1300 ARG 0.005 0.000 ARG A1329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.412 Fit side-chains REVERT: A 1057 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7515 (t80) REVERT: A 1214 LEU cc_start: 0.8070 (mm) cc_final: 0.7791 (mt) REVERT: A 1281 THR cc_start: 0.6675 (OUTLIER) cc_final: 0.6411 (p) outliers start: 16 outliers final: 12 residues processed: 64 average time/residue: 0.1506 time to fit residues: 12.3216 Evaluate side-chains 65 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1291 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.0030 chunk 25 optimal weight: 0.7980 overall best weight: 0.4648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4124 Z= 0.194 Angle : 0.569 6.625 5796 Z= 0.319 Chirality : 0.036 0.167 637 Planarity : 0.004 0.036 561 Dihedral : 26.712 179.776 934 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.70 % Allowed : 26.33 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.45), residues: 349 helix: 0.97 (0.39), residues: 188 sheet: -0.30 (1.01), residues: 19 loop : -1.44 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1012 HIS 0.003 0.001 HIS A 612 PHE 0.011 0.001 PHE A1364 TYR 0.010 0.001 TYR A1300 ARG 0.005 0.000 ARG A1329 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.354 Fit side-chains REVERT: A 1057 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 1214 LEU cc_start: 0.8067 (mm) cc_final: 0.7795 (mt) REVERT: A 1281 THR cc_start: 0.6682 (OUTLIER) cc_final: 0.6419 (p) REVERT: A 1290 MET cc_start: 0.6680 (mmm) cc_final: 0.6470 (mmm) outliers start: 15 outliers final: 11 residues processed: 63 average time/residue: 0.1529 time to fit residues: 12.2166 Evaluate side-chains 65 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.0070 chunk 32 optimal weight: 0.0030 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4124 Z= 0.189 Angle : 0.594 9.737 5796 Z= 0.327 Chirality : 0.036 0.163 637 Planarity : 0.004 0.039 561 Dihedral : 26.595 179.390 934 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.76 % Allowed : 28.21 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.45), residues: 349 helix: 1.07 (0.39), residues: 185 sheet: -0.30 (1.03), residues: 19 loop : -1.39 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1012 HIS 0.003 0.001 HIS A1212 PHE 0.010 0.001 PHE A1364 TYR 0.008 0.001 TYR A1300 ARG 0.005 0.000 ARG A1329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.388 Fit side-chains REVERT: A 980 ARG cc_start: 0.6874 (mpt180) cc_final: 0.5556 (tpt170) REVERT: A 1057 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7487 (t80) REVERT: A 1214 LEU cc_start: 0.8087 (mm) cc_final: 0.7811 (mt) REVERT: A 1281 THR cc_start: 0.6637 (OUTLIER) cc_final: 0.6394 (p) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.1633 time to fit residues: 12.0689 Evaluate side-chains 62 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1291 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.160732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.135004 restraints weight = 8183.457| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.36 r_work: 0.4045 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4124 Z= 0.294 Angle : 0.630 7.067 5796 Z= 0.350 Chirality : 0.038 0.169 637 Planarity : 0.005 0.040 561 Dihedral : 26.735 179.851 934 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.39 % Allowed : 26.96 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.45), residues: 349 helix: 0.57 (0.39), residues: 189 sheet: -0.51 (1.00), residues: 19 loop : -1.56 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 592 HIS 0.007 0.001 HIS A 612 PHE 0.018 0.002 PHE A 604 TYR 0.018 0.002 TYR A1300 ARG 0.005 0.000 ARG A1329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1514.91 seconds wall clock time: 27 minutes 45.73 seconds (1665.73 seconds total)