Starting phenix.real_space_refine on Fri Aug 2 13:27:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w35_43762/08_2024/8w35_43762.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w35_43762/08_2024/8w35_43762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w35_43762/08_2024/8w35_43762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w35_43762/08_2024/8w35_43762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w35_43762/08_2024/8w35_43762.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w35_43762/08_2024/8w35_43762.cif" } resolution = 2.61 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= 0.009 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: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 10 5.16 5 C 1500 2.51 5 N 462 2.21 5 O 605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 16": "OD1" <-> "OD2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 114": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2611 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 942 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 942 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "C" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 727 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna2p': 3, 'rna3p': 30} Chain breaks: 1 Time building chain proxies: 2.31, per 1000 atoms: 0.88 Number of scatterers: 2611 At special positions: 0 Unit cell: (69.017, 65.8316, 76.4496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 34 15.00 O 605 8.00 N 462 7.00 C 1500 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: 1.04 Conformation dependent library (CDL) restraints added in 498.4 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 448 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 73.1% alpha, 1.7% beta 12 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 43 through 69 removed outlier: 3.534A pdb=" N GLU A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.656A pdb=" N ASP A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 110 removed outlier: 3.699A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 43 through 69 removed outlier: 3.760A pdb=" N GLU B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.585A pdb=" N ASP B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 76 116 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 611 1.34 - 1.46: 745 1.46 - 1.57: 1287 1.57 - 1.69: 66 1.69 - 1.81: 20 Bond restraints: 2729 Sorted by residual: bond pdb=" N ILE B 58 " pdb=" CA ILE B 58 " ideal model delta sigma weight residual 1.461 1.478 -0.018 1.19e-02 7.06e+03 2.19e+00 bond pdb=" CB ARG B 77 " pdb=" CG ARG B 77 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sigma weight residual 1.397 1.424 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CB ASP B 83 " pdb=" CG ASP B 83 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.61e+00 bond pdb=" C ASN B 89 " pdb=" N PRO B 90 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.58e+00 ... (remaining 2724 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.53: 241 106.53 - 113.39: 1479 113.39 - 120.26: 1061 120.26 - 127.13: 973 127.13 - 134.00: 98 Bond angle restraints: 3852 Sorted by residual: angle pdb=" CB ARG B 77 " pdb=" CG ARG B 77 " pdb=" CD ARG B 77 " ideal model delta sigma weight residual 111.30 120.59 -9.29 2.30e+00 1.89e-01 1.63e+01 angle pdb=" C ASN A 93 " pdb=" CA ASN A 93 " pdb=" CB ASN A 93 " ideal model delta sigma weight residual 110.42 117.67 -7.25 1.99e+00 2.53e-01 1.33e+01 angle pdb=" CA GLU B 72 " pdb=" CB GLU B 72 " pdb=" CG GLU B 72 " ideal model delta sigma weight residual 114.10 120.73 -6.63 2.00e+00 2.50e-01 1.10e+01 angle pdb=" C LEU B 13 " pdb=" N MET B 14 " pdb=" CA MET B 14 " ideal model delta sigma weight residual 122.40 127.20 -4.80 1.45e+00 4.76e-01 1.10e+01 angle pdb=" C LEU A 13 " pdb=" N MET A 14 " pdb=" CA MET A 14 " ideal model delta sigma weight residual 122.19 126.07 -3.88 1.41e+00 5.03e-01 7.58e+00 ... (remaining 3847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 1448 18.16 - 36.33: 148 36.33 - 54.49: 56 54.49 - 72.66: 41 72.66 - 90.82: 11 Dihedral angle restraints: 1704 sinusoidal: 1014 harmonic: 690 Sorted by residual: dihedral pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " pdb=" CD GLU A 110 " pdb=" OE1 GLU A 110 " ideal model delta sinusoidal sigma weight residual 0.00 -90.82 90.82 1 3.00e+01 1.11e-03 1.08e+01 dihedral pdb=" C ASN A 93 " pdb=" N ASN A 93 " pdb=" CA ASN A 93 " pdb=" CB ASN A 93 " ideal model delta harmonic sigma weight residual -122.60 -130.55 7.95 0 2.50e+00 1.60e-01 1.01e+01 dihedral pdb=" CB LYS B 75 " pdb=" CG LYS B 75 " pdb=" CD LYS B 75 " pdb=" CE LYS B 75 " ideal model delta sinusoidal sigma weight residual 60.00 118.22 -58.22 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 296 0.036 - 0.071: 101 0.071 - 0.106: 40 0.106 - 0.142: 10 0.142 - 0.177: 3 Chirality restraints: 450 Sorted by residual: chirality pdb=" CA ASN A 93 " pdb=" N ASN A 93 " pdb=" C ASN A 93 " pdb=" CB ASN A 93 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CB VAL B 94 " pdb=" CA VAL B 94 " pdb=" CG1 VAL B 94 " pdb=" CG2 VAL B 94 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA TYR B 107 " pdb=" N TYR B 107 " pdb=" C TYR B 107 " pdb=" CB TYR B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 447 not shown) Planarity restraints: 372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 89 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO A 90 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 109 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C THR A 109 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 109 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 110 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 73 " 0.027 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO A 74 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.023 5.00e-02 4.00e+02 ... (remaining 369 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 795 2.86 - 3.37: 2176 3.37 - 3.88: 4491 3.88 - 4.39: 5203 4.39 - 4.90: 7944 Nonbonded interactions: 20609 Sorted by model distance: nonbonded pdb=" OD1 ASP B 65 " pdb=" OH TYR B 107 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASN A 80 " pdb=" NE2 GLN B 7 " model vdw 2.397 3.120 nonbonded pdb=" OG SER A 18 " pdb=" OP1 G C 5 " model vdw 2.400 3.040 nonbonded pdb=" NE1 TRP B 32 " pdb=" OE2 GLU B 36 " model vdw 2.437 3.120 nonbonded pdb=" OE2 GLU A 5 " pdb=" OH TYR B 108 " model vdw 2.505 3.040 ... (remaining 20604 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.160 Find NCS groups from input model: 0.050 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:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 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 0.041 2729 Z= 0.307 Angle : 0.907 9.287 3852 Z= 0.491 Chirality : 0.045 0.177 450 Planarity : 0.007 0.050 372 Dihedral : 19.538 90.823 1256 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.00 % Allowed : 12.50 % Favored : 86.50 % 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: -1.65 (0.45), residues: 230 helix: -0.74 (0.34), residues: 166 sheet: None (None), residues: 0 loop : -1.68 (0.62), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 35 HIS 0.002 0.001 HIS A 23 PHE 0.006 0.002 PHE B 78 TYR 0.026 0.003 TYR A 34 ARG 0.010 0.001 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.238 Fit side-chains REVERT: A 4 LYS cc_start: 0.6660 (mttm) cc_final: 0.6442 (mttt) REVERT: A 49 GLU cc_start: 0.6105 (tp30) cc_final: 0.5531 (mt-10) REVERT: A 73 ARG cc_start: 0.4959 (ttt-90) cc_final: 0.4706 (ttt90) REVERT: B 30 ARG cc_start: 0.6693 (ttm170) cc_final: 0.6454 (ttp-170) REVERT: B 49 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5922 (mm-30) REVERT: B 61 MET cc_start: 0.4441 (mtm) cc_final: 0.4211 (mtm) REVERT: B 75 LYS cc_start: 0.6137 (mtpp) cc_final: 0.5726 (mtmm) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 1.5864 time to fit residues: 79.0708 Evaluate side-chains 42 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2729 Z= 0.208 Angle : 0.558 3.671 3852 Z= 0.305 Chirality : 0.038 0.139 450 Planarity : 0.006 0.042 372 Dihedral : 19.218 91.016 794 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.00 % Allowed : 14.00 % Favored : 81.00 % 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: -0.31 (0.53), residues: 230 helix: 0.31 (0.38), residues: 174 sheet: None (None), residues: 0 loop : -1.60 (0.77), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 97 HIS 0.002 0.001 HIS A 23 PHE 0.007 0.003 PHE B 78 TYR 0.013 0.002 TYR A 34 ARG 0.004 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.235 Fit side-chains REVERT: A 49 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5477 (mt-10) REVERT: B 61 MET cc_start: 0.4703 (mtm) cc_final: 0.4402 (mtm) REVERT: B 67 ARG cc_start: 0.4879 (mtm110) cc_final: 0.4642 (ttm110) REVERT: B 77 ARG cc_start: 0.6279 (tpt90) cc_final: 0.6016 (tpt90) REVERT: B 81 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.5866 (mtpp) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 1.4879 time to fit residues: 72.7613 Evaluate side-chains 48 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 overall best weight: 2.3382 ------------------------------------------------------------------------------- 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: 0.6041 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2729 Z= 0.220 Angle : 0.553 3.982 3852 Z= 0.299 Chirality : 0.038 0.122 450 Planarity : 0.005 0.046 372 Dihedral : 19.182 90.488 794 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.50 % Allowed : 15.00 % Favored : 79.50 % 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 (0.54), residues: 230 helix: 0.63 (0.38), residues: 174 sheet: None (None), residues: 0 loop : -1.59 (0.81), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 97 HIS 0.002 0.001 HIS A 23 PHE 0.008 0.002 PHE A 78 TYR 0.012 0.002 TYR A 107 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.215 Fit side-chains REVERT: A 49 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5479 (mt-10) REVERT: B 67 ARG cc_start: 0.4741 (mtm110) cc_final: 0.4521 (ttm110) REVERT: B 77 ARG cc_start: 0.6324 (tpt90) cc_final: 0.5978 (tpt90) outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 1.4485 time to fit residues: 69.3908 Evaluate side-chains 49 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.6013 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2729 Z= 0.172 Angle : 0.484 3.437 3852 Z= 0.261 Chirality : 0.034 0.122 450 Planarity : 0.005 0.046 372 Dihedral : 19.163 91.100 794 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.50 % Allowed : 16.00 % Favored : 78.50 % 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: 0.44 (0.55), residues: 230 helix: 0.91 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.54 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 97 HIS 0.002 0.001 HIS A 23 PHE 0.006 0.002 PHE A 78 TYR 0.011 0.002 TYR A 108 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.215 Fit side-chains REVERT: A 37 SER cc_start: 0.6063 (OUTLIER) cc_final: 0.5748 (p) REVERT: A 49 GLU cc_start: 0.5915 (tp30) cc_final: 0.5470 (mt-10) REVERT: B 67 ARG cc_start: 0.4942 (mtm110) cc_final: 0.4684 (ttm110) REVERT: B 77 ARG cc_start: 0.6290 (tpt90) cc_final: 0.5959 (tpt90) outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 1.5125 time to fit residues: 72.3943 Evaluate side-chains 48 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.5968 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2729 Z= 0.120 Angle : 0.413 3.108 3852 Z= 0.222 Chirality : 0.031 0.121 450 Planarity : 0.004 0.042 372 Dihedral : 19.147 90.948 794 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.00 % Allowed : 18.50 % Favored : 77.50 % 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: 0.99 (0.56), residues: 230 helix: 1.30 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.35 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 97 HIS 0.002 0.000 HIS B 23 PHE 0.003 0.001 PHE A 78 TYR 0.009 0.001 TYR A 108 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.234 Fit side-chains REVERT: A 22 GLU cc_start: 0.5594 (OUTLIER) cc_final: 0.4681 (tp30) REVERT: A 37 SER cc_start: 0.5792 (OUTLIER) cc_final: 0.5531 (p) REVERT: A 49 GLU cc_start: 0.5880 (tp30) cc_final: 0.5473 (mt-10) REVERT: B 77 ARG cc_start: 0.6264 (tpt90) cc_final: 0.5885 (tpt90) outliers start: 8 outliers final: 3 residues processed: 43 average time/residue: 1.4737 time to fit residues: 64.6392 Evaluate side-chains 41 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 88 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.0170 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 0.0870 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2729 Z= 0.105 Angle : 0.385 3.272 3852 Z= 0.205 Chirality : 0.030 0.121 450 Planarity : 0.003 0.035 372 Dihedral : 19.043 90.094 794 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.50 % Allowed : 19.50 % Favored : 78.00 % 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: 1.31 (0.57), residues: 230 helix: 1.56 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.30 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 32 HIS 0.002 0.000 HIS B 23 PHE 0.002 0.001 PHE A 78 TYR 0.008 0.001 TYR A 108 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.209 Fit side-chains REVERT: A 37 SER cc_start: 0.5728 (OUTLIER) cc_final: 0.5438 (p) REVERT: A 49 GLU cc_start: 0.5791 (tp30) cc_final: 0.5375 (mt-10) REVERT: B 77 ARG cc_start: 0.6190 (tpt90) cc_final: 0.5854 (tpt90) outliers start: 5 outliers final: 1 residues processed: 37 average time/residue: 1.5348 time to fit residues: 57.9843 Evaluate side-chains 37 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 60 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2729 Z= 0.136 Angle : 0.426 3.328 3852 Z= 0.226 Chirality : 0.031 0.122 450 Planarity : 0.004 0.034 372 Dihedral : 18.988 91.924 794 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.00 % Allowed : 18.50 % Favored : 78.50 % 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: 1.30 (0.57), residues: 230 helix: 1.52 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.19 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 97 HIS 0.002 0.000 HIS A 23 PHE 0.005 0.001 PHE A 78 TYR 0.009 0.001 TYR A 108 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.241 Fit side-chains REVERT: A 37 SER cc_start: 0.5816 (OUTLIER) cc_final: 0.5521 (p) REVERT: A 49 GLU cc_start: 0.5836 (tp30) cc_final: 0.5391 (mt-10) REVERT: B 67 ARG cc_start: 0.5181 (mtm110) cc_final: 0.4971 (ttm110) REVERT: B 77 ARG cc_start: 0.6235 (tpt90) cc_final: 0.5892 (tpt90) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 1.5003 time to fit residues: 59.7194 Evaluate side-chains 40 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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: 0.5985 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2729 Z= 0.141 Angle : 0.435 3.309 3852 Z= 0.233 Chirality : 0.032 0.121 450 Planarity : 0.004 0.034 372 Dihedral : 19.045 92.097 794 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.50 % Allowed : 17.00 % Favored : 78.50 % 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: 1.47 (0.58), residues: 230 helix: 1.53 (0.40), residues: 172 sheet: None (None), residues: 0 loop : -0.61 (0.91), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 97 HIS 0.002 0.001 HIS A 23 PHE 0.005 0.001 PHE A 78 TYR 0.010 0.002 TYR A 108 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.243 Fit side-chains REVERT: A 37 SER cc_start: 0.5809 (OUTLIER) cc_final: 0.5509 (p) REVERT: A 49 GLU cc_start: 0.5840 (tp30) cc_final: 0.5399 (mt-10) REVERT: A 81 LYS cc_start: 0.6598 (OUTLIER) cc_final: 0.5623 (mttt) REVERT: B 67 ARG cc_start: 0.5062 (mtm110) cc_final: 0.4848 (ttm110) REVERT: B 77 ARG cc_start: 0.6219 (tpt90) cc_final: 0.5878 (tpt90) REVERT: B 81 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.5107 (mtpp) outliers start: 9 outliers final: 4 residues processed: 41 average time/residue: 1.5107 time to fit residues: 63.2017 Evaluate side-chains 41 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.5966 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2729 Z= 0.122 Angle : 0.416 3.380 3852 Z= 0.221 Chirality : 0.031 0.131 450 Planarity : 0.003 0.031 372 Dihedral : 19.026 91.120 794 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.50 % Allowed : 18.50 % Favored : 78.00 % 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: 1.58 (0.58), residues: 230 helix: 1.60 (0.40), residues: 172 sheet: None (None), residues: 0 loop : -0.54 (0.91), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 97 HIS 0.001 0.000 HIS B 23 PHE 0.004 0.001 PHE A 78 TYR 0.008 0.001 TYR A 108 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.255 Fit side-chains REVERT: A 37 SER cc_start: 0.5772 (OUTLIER) cc_final: 0.5489 (p) REVERT: A 49 GLU cc_start: 0.5843 (tp30) cc_final: 0.5365 (mt-10) REVERT: A 81 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.5594 (mttt) REVERT: B 77 ARG cc_start: 0.6217 (tpt90) cc_final: 0.5880 (tpt90) outliers start: 7 outliers final: 3 residues processed: 39 average time/residue: 1.5199 time to fit residues: 60.5072 Evaluate side-chains 39 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.5966 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2729 Z= 0.129 Angle : 0.421 3.775 3852 Z= 0.224 Chirality : 0.031 0.131 450 Planarity : 0.004 0.031 372 Dihedral : 19.050 90.173 794 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.50 % Allowed : 19.00 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.57), residues: 230 helix: 1.58 (0.40), residues: 172 sheet: None (None), residues: 0 loop : -0.52 (0.90), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 97 HIS 0.001 0.000 HIS A 23 PHE 0.004 0.001 PHE A 78 TYR 0.009 0.001 TYR A 108 ARG 0.001 0.000 ARG A 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.211 Fit side-chains REVERT: A 22 GLU cc_start: 0.5629 (OUTLIER) cc_final: 0.4708 (tp30) REVERT: A 37 SER cc_start: 0.5784 (OUTLIER) cc_final: 0.5491 (p) REVERT: A 49 GLU cc_start: 0.5823 (tp30) cc_final: 0.5365 (mt-10) REVERT: A 81 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.5623 (mttt) REVERT: B 75 LYS cc_start: 0.5973 (mtpp) cc_final: 0.5529 (mtmm) REVERT: B 77 ARG cc_start: 0.6217 (tpt90) cc_final: 0.5885 (tpt90) outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 1.3966 time to fit residues: 54.1544 Evaluate side-chains 39 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.216054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.182686 restraints weight = 2445.258| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 0.79 r_work: 0.3726 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2729 Z= 0.190 Angle : 0.503 4.568 3852 Z= 0.269 Chirality : 0.034 0.136 450 Planarity : 0.004 0.036 372 Dihedral : 19.180 90.087 794 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.50 % Allowed : 19.00 % Favored : 77.50 % 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: 1.24 (0.57), residues: 230 helix: 1.31 (0.39), residues: 172 sheet: None (None), residues: 0 loop : -0.50 (0.93), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 97 HIS 0.002 0.001 HIS A 23 PHE 0.008 0.002 PHE A 78 TYR 0.012 0.002 TYR A 107 ARG 0.001 0.000 ARG B 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1483.02 seconds wall clock time: 26 minutes 26.56 seconds (1586.56 seconds total)