Starting phenix.real_space_refine on Wed Jul 1 21:06:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w35_43762/07_2026/8w35_43762.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w35_43762/07_2026/8w35_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 { model { file = "/net/cci-nas-00/data/ceres_data/8w35_43762/07_2026/8w35_43762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w35_43762/07_2026/8w35_43762.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w35_43762/07_2026/8w35_43762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w35_43762/07_2026/8w35_43762.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 0.75, per 1000 atoms: 0.29 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: 0.25 Conformation dependent library (CDL) restraints added in 69.7 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: 0.36 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: 0.36 Time building geometry restraints manager: 0.33 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=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sigma weight residual 1.397 1.424 -0.027 1.00e-02 1.00e+04 7.06e+00 bond pdb=" N1 C C 27 " pdb=" C2 C C 27 " ideal model delta sigma weight residual 1.397 1.422 -0.025 1.00e-02 1.00e+04 6.22e+00 bond pdb=" N1 C C 3 " pdb=" C2 C C 3 " ideal model delta sigma weight residual 1.397 1.421 -0.024 1.00e-02 1.00e+04 5.92e+00 bond pdb=" N9 A C 10 " pdb=" C4 A C 10 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.45e+00 bond pdb=" N9 A C 21 " pdb=" C4 A C 21 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.43e+00 ... (remaining 2724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 3646 1.86 - 3.71: 176 3.71 - 5.57: 26 5.57 - 7.43: 3 7.43 - 9.29: 1 Bond angle restraints: 3852 Sorted by residual: angle pdb=" C1' C C 8 " pdb=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sigma weight residual 118.80 124.07 -5.27 1.10e+00 8.26e-01 2.29e+01 angle pdb=" C2 C C 8 " pdb=" N1 C C 8 " pdb=" C6 C C 8 " ideal model delta sigma weight residual 120.30 118.43 1.87 4.00e-01 6.25e+00 2.18e+01 angle pdb=" C1' C C 27 " pdb=" N1 C C 27 " pdb=" C2 C C 27 " ideal model delta sigma weight residual 118.80 123.89 -5.09 1.10e+00 8.26e-01 2.14e+01 angle pdb=" N1 C C 25 " pdb=" C2 C C 25 " pdb=" O2 C C 25 " ideal model delta sigma weight residual 118.90 121.67 -2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" N1 C C 27 " pdb=" C2 C C 27 " pdb=" O2 C C 27 " ideal model delta sigma weight residual 118.90 121.67 -2.77 6.00e-01 2.78e+00 2.12e+01 ... (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: 0.140 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:5.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 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= 0.326 Angle : 0.907 9.287 3852 Z= 0.734 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.001 ARG A 73 TYR 0.026 0.003 TYR A 34 PHE 0.006 0.002 PHE B 78 TRP 0.020 0.003 TRP B 35 HIS 0.002 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.33 ( 2729) covalent geometry : angle 0.90715 / 0.73 ( 3852) hydrogen bonds : bond 0.16728 / 10.67 ( 147) hydrogen bonds : angle 5.55636 / 4.03 ( 406) *********************** 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 : 0.048 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: 0.6050 time to fit residues: 30.1337 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 : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.217994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.183078 restraints weight = 2445.278| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 0.92 r_work: 0.3724 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2729 Z= 0.142 Angle : 0.500 4.246 3852 Z= 0.292 Chirality : 0.037 0.201 450 Planarity : 0.005 0.041 372 Dihedral : 19.337 89.710 794 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.00 % Allowed : 15.50 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.52), residues: 230 helix: 0.43 (0.37), residues: 174 sheet: None (None), residues: 0 loop : -1.66 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 67 TYR 0.013 0.002 TYR A 34 PHE 0.005 0.002 PHE A 78 TRP 0.010 0.002 TRP B 97 HIS 0.002 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 ( 2729) covalent geometry : angle 0.50014 / 0.29 ( 3852) hydrogen bonds : bond 0.07153 / 4.65 ( 147) hydrogen bonds : angle 4.24773 / 3.04 ( 406) *********************** 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 49 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.083 Fit side-chains REVERT: B 75 LYS cc_start: 0.7222 (mtpp) cc_final: 0.7016 (mtmm) REVERT: B 77 ARG cc_start: 0.7016 (tpt90) cc_final: 0.6423 (tpp80) outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.8368 time to fit residues: 39.9368 Evaluate side-chains 43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER 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 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.217637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.182581 restraints weight = 2455.449| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 0.92 r_work: 0.3731 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2729 Z= 0.116 Angle : 0.436 4.312 3852 Z= 0.256 Chirality : 0.034 0.121 450 Planarity : 0.005 0.049 372 Dihedral : 19.196 91.401 794 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.00 % Allowed : 15.50 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.55), residues: 230 helix: 1.02 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.70 (0.79), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 67 TYR 0.009 0.002 TYR A 34 PHE 0.005 0.002 PHE A 78 TRP 0.007 0.001 TRP B 35 HIS 0.002 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.12 ( 2729) covalent geometry : angle 0.43615 / 0.26 ( 3852) hydrogen bonds : bond 0.05810 / 3.76 ( 147) hydrogen bonds : angle 3.90459 / 2.78 ( 406) *********************** 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 48 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.084 Fit side-chains REVERT: B 67 ARG cc_start: 0.6090 (mtm110) cc_final: 0.5553 (ttm110) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.7726 time to fit residues: 35.3398 Evaluate side-chains 43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.214842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.183071 restraints weight = 2411.064| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 0.72 r_work: 0.3701 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2729 Z= 0.137 Angle : 0.455 3.081 3852 Z= 0.266 Chirality : 0.035 0.125 450 Planarity : 0.005 0.051 372 Dihedral : 19.210 91.716 794 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.50 % Allowed : 15.00 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.55), residues: 230 helix: 1.10 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.52 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 73 TYR 0.010 0.002 TYR A 107 PHE 0.008 0.002 PHE A 78 TRP 0.009 0.002 TRP B 97 HIS 0.002 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 2729) covalent geometry : angle 0.45545 / 0.27 ( 3852) hydrogen bonds : bond 0.06448 / 4.21 ( 147) hydrogen bonds : angle 3.93328 / 2.81 ( 406) *********************** 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 53 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.084 Fit side-chains REVERT: B 61 MET cc_start: 0.5671 (OUTLIER) cc_final: 0.4860 (ttm) REVERT: B 67 ARG cc_start: 0.6181 (mtm110) cc_final: 0.5692 (ttm110) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 0.6886 time to fit residues: 32.9698 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 : 0.080 ------------------------------------------------------------------------------- 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 61 MET 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 15 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 0.0010 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.218155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.186644 restraints weight = 2425.621| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 0.75 r_work: 0.3730 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2729 Z= 0.096 Angle : 0.385 3.203 3852 Z= 0.226 Chirality : 0.032 0.122 450 Planarity : 0.004 0.046 372 Dihedral : 19.123 90.983 794 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.00 % Allowed : 16.50 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.56), residues: 230 helix: 1.36 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.45 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.009 0.001 TYR A 108 PHE 0.003 0.001 PHE A 78 TRP 0.005 0.001 TRP A 35 HIS 0.002 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.10 ( 2729) covalent geometry : angle 0.38462 / 0.23 ( 3852) hydrogen bonds : bond 0.04868 / 3.16 ( 147) hydrogen bonds : angle 3.67092 / 2.61 ( 406) *********************** 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 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.084 Fit side-chains REVERT: A 77 ARG cc_start: 0.7580 (mmt180) cc_final: 0.6933 (mmm-85) REVERT: B 67 ARG cc_start: 0.6185 (mtm110) cc_final: 0.5786 (ttm110) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.7363 time to fit residues: 32.1984 Evaluate side-chains 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.215091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.181531 restraints weight = 2421.423| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 0.85 r_work: 0.3713 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1855 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= 0.126 Angle : 0.427 3.142 3852 Z= 0.249 Chirality : 0.033 0.122 450 Planarity : 0.005 0.047 372 Dihedral : 19.152 91.275 794 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.56), residues: 230 helix: 1.29 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.48 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.010 0.002 TYR A 107 PHE 0.007 0.002 PHE A 78 TRP 0.008 0.002 TRP B 97 HIS 0.001 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 ( 2729) covalent geometry : angle 0.42667 / 0.25 ( 3852) hydrogen bonds : bond 0.05807 / 3.79 ( 147) hydrogen bonds : angle 3.76812 / 2.69 ( 406) *********************** 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 51 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.093 Fit side-chains REVERT: A 22 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: B 61 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.5583 (mtm) REVERT: B 67 ARG cc_start: 0.6174 (mtm110) cc_final: 0.5758 (ttm110) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.4826 time to fit residues: 22.1337 Evaluate side-chains 50 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.047 ------------------------------------------------------------------------------- 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 61 MET 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 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.218646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.186660 restraints weight = 2426.212| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 0.77 r_work: 0.3746 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2729 Z= 0.094 Angle : 0.376 3.052 3852 Z= 0.221 Chirality : 0.031 0.121 450 Planarity : 0.004 0.043 372 Dihedral : 19.084 90.464 794 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.00 % Allowed : 16.50 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.56), residues: 230 helix: 1.43 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.47 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.009 0.001 TYR A 108 PHE 0.003 0.001 PHE A 78 TRP 0.004 0.001 TRP B 97 HIS 0.001 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.09 ( 2729) covalent geometry : angle 0.37639 / 0.22 ( 3852) hydrogen bonds : bond 0.04688 / 3.05 ( 147) hydrogen bonds : angle 3.60878 / 2.57 ( 406) *********************** 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 49 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.077 Fit side-chains REVERT: A 22 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6938 (tt0) REVERT: A 77 ARG cc_start: 0.7578 (mmt180) cc_final: 0.6956 (mmm-85) REVERT: B 67 ARG cc_start: 0.6120 (mtm110) cc_final: 0.5768 (ttm110) REVERT: B 75 LYS cc_start: 0.7218 (mtpp) cc_final: 0.6950 (mtmm) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 0.5877 time to fit residues: 26.3016 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 : 0.048 ------------------------------------------------------------------------------- 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 100 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 19 optimal weight: 0.0670 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.219131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.188379 restraints weight = 2488.959| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 0.75 r_work: 0.3756 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2729 Z= 0.094 Angle : 0.374 3.188 3852 Z= 0.219 Chirality : 0.031 0.120 450 Planarity : 0.004 0.040 372 Dihedral : 19.095 90.018 794 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.00 % Allowed : 17.50 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.56), residues: 230 helix: 1.48 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.38 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.008 0.001 TYR A 108 PHE 0.003 0.001 PHE A 78 TRP 0.005 0.001 TRP B 32 HIS 0.001 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.09 ( 2729) covalent geometry : angle 0.37445 / 0.22 ( 3852) hydrogen bonds : bond 0.04510 / 2.93 ( 147) hydrogen bonds : angle 3.56572 / 2.56 ( 406) *********************** 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 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.046 Fit side-chains REVERT: A 22 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6853 (tp30) REVERT: A 77 ARG cc_start: 0.7538 (mmt180) cc_final: 0.6942 (mmm-85) REVERT: B 67 ARG cc_start: 0.6060 (mtm110) cc_final: 0.5650 (ttm110) REVERT: B 75 LYS cc_start: 0.7224 (mtpp) cc_final: 0.6967 (mtmm) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.5917 time to fit residues: 25.8900 Evaluate side-chains 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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 100 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.0470 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.220241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.188723 restraints weight = 2477.472| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 0.74 r_work: 0.3774 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2729 Z= 0.092 Angle : 0.374 3.236 3852 Z= 0.217 Chirality : 0.031 0.120 450 Planarity : 0.004 0.037 372 Dihedral : 19.091 89.250 794 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.00 % Allowed : 18.00 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.56), residues: 230 helix: 1.51 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.31 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.008 0.001 TYR A 108 PHE 0.003 0.001 PHE A 78 TRP 0.005 0.001 TRP B 32 HIS 0.001 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.09 ( 2729) covalent geometry : angle 0.37428 / 0.22 ( 3852) hydrogen bonds : bond 0.04312 / 2.81 ( 147) hydrogen bonds : angle 3.53883 / 2.54 ( 406) *********************** 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: 6 poor density : 39 time to evaluate : 0.083 Fit side-chains REVERT: A 22 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7067 (tp30) REVERT: A 77 ARG cc_start: 0.7606 (mmt180) cc_final: 0.6941 (mmm-85) REVERT: B 67 ARG cc_start: 0.6086 (mtm110) cc_final: 0.5663 (ttm110) REVERT: B 75 LYS cc_start: 0.7128 (mtpp) cc_final: 0.6860 (mtmm) REVERT: B 81 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.6913 (mtpp) outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.6193 time to fit residues: 26.4528 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 : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.218000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.184958 restraints weight = 2505.634| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 0.80 r_work: 0.3756 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2193 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= 0.109 Angle : 0.408 4.046 3852 Z= 0.235 Chirality : 0.032 0.122 450 Planarity : 0.004 0.036 372 Dihedral : 19.117 89.192 794 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.00 % Allowed : 18.00 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.56), residues: 230 helix: 1.46 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.31 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.009 0.001 TYR A 108 PHE 0.005 0.001 PHE A 78 TRP 0.006 0.001 TRP B 32 HIS 0.001 0.000 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 2729) covalent geometry : angle 0.40806 / 0.24 ( 3852) hydrogen bonds : bond 0.04910 / 3.21 ( 147) hydrogen bonds : angle 3.64986 / 2.63 ( 406) ********************** 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 43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.079 Fit side-chains REVERT: A 22 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: A 77 ARG cc_start: 0.7516 (mmt180) cc_final: 0.6930 (mmm-85) REVERT: B 67 ARG cc_start: 0.6111 (mtm110) cc_final: 0.5719 (ttm110) REVERT: B 81 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.6822 (mtpp) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 0.7393 time to fit residues: 30.8613 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.212171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.178778 restraints weight = 2461.977| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 0.89 r_work: 0.3649 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2729 Z= 0.217 Angle : 0.585 4.650 3852 Z= 0.332 Chirality : 0.040 0.128 450 Planarity : 0.006 0.044 372 Dihedral : 19.328 90.692 794 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.00 % Allowed : 17.00 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.55), residues: 230 helix: 0.94 (0.38), residues: 174 sheet: None (None), residues: 0 loop : -1.51 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 57 TYR 0.019 0.003 TYR A 107 PHE 0.014 0.004 PHE A 78 TRP 0.018 0.004 TRP A 35 HIS 0.003 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 ( 2729) covalent geometry : angle 0.58506 / 0.33 ( 3852) hydrogen bonds : bond 0.08154 / 5.34 ( 147) hydrogen bonds : angle 4.13724 / 2.99 ( 406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1087.44 seconds wall clock time: 19 minutes 12.43 seconds (1152.43 seconds total)