Starting phenix.real_space_refine on Mon Jan 13 14:12:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w35_43762/01_2025/8w35_43762.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w35_43762/01_2025/8w35_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/cci-nas-00/data/ceres_data/8w35_43762/01_2025/8w35_43762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w35_43762/01_2025/8w35_43762.map" model { file = "/net/cci-nas-00/data/ceres_data/8w35_43762/01_2025/8w35_43762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w35_43762/01_2025/8w35_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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 2.47, per 1000 atoms: 0.95 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 349.2 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: 1.05 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: 0.68 Time building geometry restraints manager: 0.80 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: 0.00 - 1.86: 3647 1.86 - 3.71: 175 3.71 - 5.57: 26 5.57 - 7.43: 3 7.43 - 9.29: 1 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: 0.120 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.320 Find NCS groups from input model: 0.070 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:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.254 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: 1.7173 time to fit residues: 85.6059 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.214814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.179639 restraints weight = 2419.824| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 0.92 r_work: 0.3677 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.223 Fit side-chains REVERT: B 61 MET cc_start: 0.5653 (mtm) cc_final: 0.5332 (mtm) REVERT: B 67 ARG cc_start: 0.6122 (mtm110) cc_final: 0.5662 (ttm110) REVERT: B 81 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7305 (mtpp) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 1.6277 time to fit residues: 79.5194 Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.213276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.180667 restraints weight = 2417.056| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 0.77 r_work: 0.3705 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1872 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= 0.202 Angle : 0.530 3.723 3852 Z= 0.286 Chirality : 0.036 0.121 450 Planarity : 0.005 0.045 372 Dihedral : 19.145 90.446 794 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.00 % Allowed : 15.00 % Favored : 80.00 % 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: 0.19 (0.54), residues: 230 helix: 0.71 (0.38), residues: 174 sheet: None (None), residues: 0 loop : -1.55 (0.80), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 97 HIS 0.002 0.001 HIS A 23 PHE 0.007 0.002 PHE A 78 TYR 0.011 0.002 TYR A 107 ARG 0.004 0.001 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 51 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.235 Fit side-chains REVERT: B 67 ARG cc_start: 0.6245 (mtm110) cc_final: 0.5836 (ttm110) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 1.5455 time to fit residues: 74.0598 Evaluate side-chains 48 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER 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 7 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.216264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.184446 restraints weight = 2437.998| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 0.77 r_work: 0.3717 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2729 Z= 0.144 Angle : 0.452 3.157 3852 Z= 0.244 Chirality : 0.033 0.122 450 Planarity : 0.004 0.044 372 Dihedral : 19.118 90.783 794 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: 0.67 (0.55), residues: 230 helix: 1.07 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.44 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 97 HIS 0.002 0.001 HIS B 23 PHE 0.005 0.002 PHE A 78 TYR 0.010 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 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.239 Fit side-chains REVERT: B 67 ARG cc_start: 0.6118 (mtm110) cc_final: 0.5702 (ttm110) outliers start: 9 outliers final: 5 residues processed: 44 average time/residue: 1.6752 time to fit residues: 75.0129 Evaluate side-chains 43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 88 ASP Chi-restraints excluded: chain B residue 94 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.218416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.190261 restraints weight = 2432.068| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 0.74 r_work: 0.3770 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2262 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= 0.122 Angle : 0.413 3.122 3852 Z= 0.221 Chirality : 0.031 0.121 450 Planarity : 0.004 0.042 372 Dihedral : 19.145 90.536 794 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.00 % Allowed : 19.50 % 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: 1.04 (0.56), residues: 230 helix: 1.35 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.36 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 97 HIS 0.002 0.001 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 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.231 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 1.5922 time to fit residues: 66.4870 Evaluate side-chains 37 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 0.0020 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.215434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.182639 restraints weight = 2472.256| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 0.77 r_work: 0.3714 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2250 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= 0.162 Angle : 0.461 3.322 3852 Z= 0.247 Chirality : 0.033 0.122 450 Planarity : 0.004 0.042 372 Dihedral : 19.208 90.272 794 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.00 % Allowed : 16.00 % 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: 0.99 (0.56), residues: 230 helix: 1.31 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.35 (0.84), 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 0.007 0.002 PHE A 78 TYR 0.010 0.002 TYR A 107 ARG 0.001 0.000 ARG B 57 *********************** 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 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.295 Fit side-chains REVERT: A 22 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7030 (tt0) REVERT: B 67 ARG cc_start: 0.6162 (mtm110) cc_final: 0.5782 (ttm110) REVERT: B 81 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7122 (mtpp) outliers start: 12 outliers final: 6 residues processed: 42 average time/residue: 1.5949 time to fit residues: 68.2594 Evaluate side-chains 43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU 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 81 LYS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.214108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.180269 restraints weight = 2537.414| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 0.86 r_work: 0.3615 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2729 Z= 0.174 Angle : 0.476 3.464 3852 Z= 0.256 Chirality : 0.034 0.122 450 Planarity : 0.004 0.041 372 Dihedral : 19.135 91.599 794 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.11 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: 0.91 (0.56), residues: 230 helix: 1.22 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.27 (0.86), 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 0.007 0.002 PHE A 78 TYR 0.011 0.002 TYR A 107 ARG 0.001 0.000 ARG A 39 *********************** 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 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.269 Fit side-chains REVERT: A 22 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7072 (tp30) REVERT: B 67 ARG cc_start: 0.6142 (mtm110) cc_final: 0.5661 (ttm110) REVERT: B 75 LYS cc_start: 0.7248 (mtpp) cc_final: 0.6910 (mtmm) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 1.5474 time to fit residues: 67.8545 Evaluate side-chains 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU 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 94 VAL 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 11 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 0.0040 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.220990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.190762 restraints weight = 2480.750| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 0.81 r_work: 0.3750 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2554 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= 0.107 Angle : 0.390 3.383 3852 Z= 0.209 Chirality : 0.030 0.120 450 Planarity : 0.004 0.035 372 Dihedral : 19.013 92.715 794 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.50 % Allowed : 20.00 % 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: 1.35 (0.57), residues: 230 helix: 1.57 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.22 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 35 HIS 0.001 0.000 HIS B 23 PHE 0.002 0.001 PHE A 78 TYR 0.008 0.001 TYR A 108 ARG 0.002 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 38 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.316 Fit side-chains REVERT: B 75 LYS cc_start: 0.7107 (mtpp) cc_final: 0.6839 (mtmm) outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 1.7142 time to fit residues: 63.0789 Evaluate side-chains 35 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.217430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.183229 restraints weight = 2476.618| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 0.90 r_work: 0.3689 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2729 Z= 0.136 Angle : 0.429 3.329 3852 Z= 0.229 Chirality : 0.031 0.127 450 Planarity : 0.004 0.034 372 Dihedral : 19.047 91.969 794 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.00 % Allowed : 20.50 % 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: 1.27 (0.57), residues: 230 helix: 1.48 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.10 (0.87), residues: 56 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 0.004 0.001 PHE A 78 TYR 0.009 0.001 TYR A 108 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 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 37 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.231 Fit side-chains REVERT: B 75 LYS cc_start: 0.7208 (mtpp) cc_final: 0.6900 (mtmm) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 1.6973 time to fit residues: 64.0616 Evaluate side-chains 36 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.219531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.190576 restraints weight = 2444.986| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 0.78 r_work: 0.3744 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2729 Z= 0.126 Angle : 0.420 4.034 3852 Z= 0.223 Chirality : 0.031 0.131 450 Planarity : 0.004 0.032 372 Dihedral : 19.045 90.599 794 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.00 % Allowed : 20.50 % 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: 1.54 (0.58), residues: 230 helix: 1.58 (0.40), residues: 172 sheet: None (None), residues: 0 loop : -0.59 (0.92), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 32 HIS 0.001 0.001 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 38 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.242 Fit side-chains REVERT: B 75 LYS cc_start: 0.7176 (mtpp) cc_final: 0.6893 (mtmm) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 1.6944 time to fit residues: 63.8581 Evaluate side-chains 37 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.218719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.185122 restraints weight = 2488.931| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 0.85 r_work: 0.3687 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2729 Z= 0.126 Angle : 0.422 4.027 3852 Z= 0.224 Chirality : 0.031 0.129 450 Planarity : 0.004 0.032 372 Dihedral : 19.059 89.737 794 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.50 % Allowed : 21.00 % 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: 1.54 (0.57), residues: 230 helix: 1.58 (0.40), residues: 172 sheet: None (None), residues: 0 loop : -0.61 (0.90), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 97 HIS 0.001 0.000 HIS A 23 PHE 0.003 0.001 PHE A 78 TYR 0.008 0.001 TYR A 108 ARG 0.001 0.000 ARG A 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.51 seconds wall clock time: 39 minutes 44.84 seconds (2384.84 seconds total)