Starting phenix.real_space_refine on Sat Apr 26 16:39:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w35_43762/04_2025/8w35_43762.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w35_43762/04_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_43762/04_2025/8w35_43762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w35_43762/04_2025/8w35_43762.map" model { file = "/net/cci-nas-00/data/ceres_data/8w35_43762/04_2025/8w35_43762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w35_43762/04_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-5669/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: 2.54, per 1000 atoms: 0.97 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: 0.75 Conformation dependent library (CDL) restraints added in 241.4 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: 1.08 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: 0.74 Time building geometry restraints manager: 0.88 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.420 Find NCS groups from input model: 0.060 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.420 ------------------------------------------------------------------------------- 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= 0.265 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 Details of bonding type rmsd hydrogen bonds : bond 0.16728 ( 147) hydrogen bonds : angle 5.55636 ( 406) covalent geometry : bond 0.00486 ( 2729) covalent geometry : angle 0.90687 ( 3852) *********************** 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 : 0.256 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: 1.6472 time to fit residues: 82.0984 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 : 0.227 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.214333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.179135 restraints weight = 2419.510| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 0.92 r_work: 0.3670 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1404 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= 0.166 Angle : 0.565 4.211 3852 Z= 0.309 Chirality : 0.038 0.137 450 Planarity : 0.006 0.042 372 Dihedral : 19.230 90.910 794 Min Nonbonded Distance : 2.541 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: -0.33 (0.53), residues: 230 helix: 0.30 (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 0.013 0.002 TRP B 97 HIS 0.002 0.001 HIS A 112 PHE 0.007 0.003 PHE A 78 TYR 0.015 0.002 TYR A 34 ARG 0.004 0.001 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.07389 ( 147) hydrogen bonds : angle 4.19282 ( 406) covalent geometry : bond 0.00336 ( 2729) covalent geometry : angle 0.56471 ( 3852) *********************** 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 53 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.277 Fit side-chains REVERT: B 61 MET cc_start: 0.5662 (mtm) cc_final: 0.5359 (mtm) REVERT: B 67 ARG cc_start: 0.6144 (mtm110) cc_final: 0.5662 (ttm110) outliers start: 10 outliers final: 5 residues processed: 47 average time/residue: 1.5984 time to fit residues: 76.5161 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.0560 ------------------------------------------------------------------------------- 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 = 0.217008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.184027 restraints weight = 2431.740| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 0.85 r_work: 0.3675 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1783 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= 0.110 Angle : 0.445 3.115 3852 Z= 0.242 Chirality : 0.033 0.119 450 Planarity : 0.004 0.041 372 Dihedral : 19.081 90.791 794 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.00 % Allowed : 16.00 % 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: 0.49 (0.55), residues: 230 helix: 0.95 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.54 (0.79), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 35 HIS 0.002 0.001 HIS B 23 PHE 0.004 0.001 PHE A 78 TYR 0.010 0.002 TYR A 108 ARG 0.003 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 147) hydrogen bonds : angle 3.74235 ( 406) covalent geometry : bond 0.00213 ( 2729) covalent geometry : angle 0.44546 ( 3852) *********************** 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 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.245 Fit side-chains REVERT: B 67 ARG cc_start: 0.6195 (mtm110) cc_final: 0.5810 (ttm110) outliers start: 6 outliers final: 1 residues processed: 43 average time/residue: 1.6869 time to fit residues: 73.8681 Evaluate side-chains 41 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.212328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.180241 restraints weight = 2431.147| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 0.77 r_work: 0.3700 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2037 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= 0.169 Angle : 0.544 3.940 3852 Z= 0.292 Chirality : 0.037 0.121 450 Planarity : 0.005 0.044 372 Dihedral : 19.247 91.227 794 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.00 % Allowed : 17.00 % 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: 0.39 (0.55), residues: 230 helix: 0.86 (0.38), residues: 174 sheet: None (None), residues: 0 loop : -1.49 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 97 HIS 0.003 0.001 HIS A 23 PHE 0.009 0.003 PHE A 78 TYR 0.012 0.002 TYR A 107 ARG 0.002 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.07340 ( 147) hydrogen bonds : angle 4.01369 ( 406) covalent geometry : bond 0.00349 ( 2729) covalent geometry : angle 0.54391 ( 3852) *********************** 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 to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.349 Fit side-chains REVERT: B 67 ARG cc_start: 0.6166 (mtm110) cc_final: 0.5727 (ttm110) REVERT: B 81 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7333 (mtpp) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 1.5159 time to fit residues: 72.6138 Evaluate side-chains 49 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 13 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.217185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.185803 restraints weight = 2424.823| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 0.76 r_work: 0.3746 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2184 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= 0.105 Angle : 0.426 3.131 3852 Z= 0.229 Chirality : 0.032 0.121 450 Planarity : 0.004 0.042 372 Dihedral : 19.153 90.843 794 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 0.87 (0.56), residues: 230 helix: 1.23 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.43 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 97 HIS 0.002 0.001 HIS B 23 PHE 0.004 0.001 PHE A 78 TYR 0.009 0.001 TYR A 108 ARG 0.002 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 147) hydrogen bonds : angle 3.61529 ( 406) covalent geometry : bond 0.00206 ( 2729) covalent geometry : angle 0.42569 ( 3852) *********************** 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 45 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.255 Fit side-chains REVERT: B 67 ARG cc_start: 0.6075 (mtm110) cc_final: 0.5652 (ttm110) outliers start: 6 outliers final: 2 residues processed: 42 average time/residue: 1.6994 time to fit residues: 72.6494 Evaluate side-chains 39 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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: 0.9980 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.214365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.181179 restraints weight = 2465.463| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 0.84 r_work: 0.3635 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2241 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= 0.130 Angle : 0.468 3.377 3852 Z= 0.251 Chirality : 0.033 0.122 450 Planarity : 0.005 0.044 372 Dihedral : 19.216 90.266 794 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.00 % Allowed : 18.00 % Favored : 77.00 % 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: 0.86 (0.56), residues: 230 helix: 1.21 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.39 (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 108 ARG 0.001 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.05805 ( 147) hydrogen bonds : angle 3.73458 ( 406) covalent geometry : bond 0.00263 ( 2729) covalent geometry : angle 0.46806 ( 3852) *********************** 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 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.257 Fit side-chains REVERT: A 22 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: B 67 ARG cc_start: 0.6180 (mtm110) cc_final: 0.5726 (ttm110) REVERT: B 75 LYS cc_start: 0.7287 (mtpp) cc_final: 0.6970 (mtmm) REVERT: B 81 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.6906 (mtpp) outliers start: 10 outliers final: 6 residues processed: 43 average time/residue: 1.5964 time to fit residues: 69.9529 Evaluate side-chains 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 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 81 LYS 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=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: 4.9990 chunk 4 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.216764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.188012 restraints weight = 2544.009| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 0.69 r_work: 0.3748 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2341 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= 0.111 Angle : 0.435 3.243 3852 Z= 0.233 Chirality : 0.032 0.122 450 Planarity : 0.004 0.042 372 Dihedral : 19.163 89.145 794 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.90 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: 1.03 (0.57), residues: 230 helix: 1.35 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.38 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 97 HIS 0.001 0.001 HIS A 23 PHE 0.005 0.001 PHE A 78 TYR 0.010 0.002 TYR A 108 ARG 0.002 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 147) hydrogen bonds : angle 3.60747 ( 406) covalent geometry : bond 0.00221 ( 2729) covalent geometry : angle 0.43452 ( 3852) *********************** 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 45 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.209 Fit side-chains REVERT: A 22 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7066 (tp30) REVERT: B 67 ARG cc_start: 0.6172 (mtm110) cc_final: 0.5736 (ttm110) REVERT: B 75 LYS cc_start: 0.7268 (mtpp) cc_final: 0.6965 (mtmm) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 1.5472 time to fit residues: 66.2070 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.220102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.191091 restraints weight = 2480.532| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 0.81 r_work: 0.3759 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2549 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= 0.090 Angle : 0.398 3.315 3852 Z= 0.212 Chirality : 0.030 0.121 450 Planarity : 0.004 0.035 372 Dihedral : 19.130 87.394 794 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.70 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: 1.26 (0.57), residues: 230 helix: 1.53 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.35 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 32 HIS 0.002 0.001 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 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 147) hydrogen bonds : angle 3.40221 ( 406) covalent geometry : bond 0.00177 ( 2729) covalent geometry : angle 0.39802 ( 3852) *********************** 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 40 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.248 Fit side-chains REVERT: B 75 LYS cc_start: 0.7116 (mtpp) cc_final: 0.6862 (mtmm) outliers start: 6 outliers final: 3 residues processed: 38 average time/residue: 1.4632 time to fit residues: 56.7829 Evaluate side-chains 37 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 94 VAL 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 9 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.212689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.177856 restraints weight = 2455.594| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 0.93 r_work: 0.3646 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2729 Z= 0.167 Angle : 0.532 3.774 3852 Z= 0.285 Chirality : 0.036 0.127 450 Planarity : 0.005 0.040 372 Dihedral : 19.335 87.391 794 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.00 % Allowed : 17.50 % 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: 1.03 (0.57), residues: 230 helix: 1.21 (0.39), residues: 172 sheet: None (None), residues: 0 loop : -0.74 (0.91), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 35 HIS 0.003 0.001 HIS A 112 PHE 0.010 0.002 PHE A 78 TYR 0.013 0.002 TYR A 107 ARG 0.001 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.06974 ( 147) hydrogen bonds : angle 3.91593 ( 406) covalent geometry : bond 0.00350 ( 2729) covalent geometry : angle 0.53210 ( 3852) *********************** 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 45 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.254 Fit side-chains REVERT: B 61 MET cc_start: 0.5550 (mtm) cc_final: 0.5273 (mtm) REVERT: B 67 ARG cc_start: 0.6203 (mtm110) cc_final: 0.5723 (ttm110) REVERT: B 75 LYS cc_start: 0.7229 (mtpp) cc_final: 0.6926 (mtmm) REVERT: B 81 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.6899 (mtpp) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 1.5975 time to fit residues: 71.6540 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.214847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.182263 restraints weight = 2426.758| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 0.78 r_work: 0.3711 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2729 Z= 0.128 Angle : 0.475 3.824 3852 Z= 0.255 Chirality : 0.033 0.126 450 Planarity : 0.004 0.040 372 Dihedral : 19.274 87.006 794 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.50 % Allowed : 20.50 % 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: 1.14 (0.57), residues: 230 helix: 1.28 (0.40), residues: 172 sheet: None (None), residues: 0 loop : -0.70 (0.92), 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 0.006 0.002 PHE A 78 TYR 0.011 0.002 TYR A 108 ARG 0.001 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.05627 ( 147) hydrogen bonds : angle 3.78659 ( 406) covalent geometry : bond 0.00262 ( 2729) covalent geometry : angle 0.47469 ( 3852) ********************** 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 39 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.223 Fit side-chains REVERT: B 67 ARG cc_start: 0.6097 (mtm110) cc_final: 0.5645 (ttm110) REVERT: B 75 LYS cc_start: 0.7235 (mtpp) cc_final: 0.6971 (mtmm) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 1.6958 time to fit residues: 67.3271 Evaluate side-chains 39 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 1 optimal weight: 0.0980 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 0.0670 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.4360 r_free = 0.4360 target = 0.222559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.192714 restraints weight = 2495.029| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 0.76 r_work: 0.3809 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2729 Z= 0.089 Angle : 0.416 6.225 3852 Z= 0.218 Chirality : 0.030 0.125 450 Planarity : 0.003 0.033 372 Dihedral : 19.136 85.408 794 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.50 % Allowed : 22.50 % Favored : 77.00 % 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: 1.47 (0.57), residues: 230 helix: 1.55 (0.40), residues: 172 sheet: None (None), residues: 0 loop : -0.70 (0.89), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 32 HIS 0.001 0.000 HIS A 23 PHE 0.002 0.000 PHE A 78 TYR 0.008 0.001 TYR A 108 ARG 0.002 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 147) hydrogen bonds : angle 3.42762 ( 406) covalent geometry : bond 0.00177 ( 2729) covalent geometry : angle 0.41626 ( 3852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2600.88 seconds wall clock time: 44 minutes 55.32 seconds (2695.32 seconds total)