Starting phenix.real_space_refine on Wed Sep 17 03:05:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w35_43762/09_2025/8w35_43762.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w35_43762/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8w35_43762/09_2025/8w35_43762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w35_43762/09_2025/8w35_43762.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w35_43762/09_2025/8w35_43762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w35_43762/09_2025/8w35_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-2.0-5805/lib/python3.9/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: 1.05, per 1000 atoms: 0.40 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: 0.35 Conformation dependent library (CDL) restraints added in 99.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 0.38 Time building geometry restraints manager: 0.36 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.520 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00486 ( 2729) covalent geometry : angle 0.90687 ( 3852) hydrogen bonds : bond 0.16728 ( 147) hydrogen bonds : angle 5.55636 ( 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 : 0.086 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: 0.8709 time to fit residues: 43.3184 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 : 0.083 ------------------------------------------------------------------------------- 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... 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 = 0.4311 r_free = 0.4311 target = 0.216678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.184938 restraints weight = 2440.771| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 0.72 r_work: 0.3743 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2729 Z= 0.130 Angle : 0.503 4.109 3852 Z= 0.275 Chirality : 0.035 0.141 450 Planarity : 0.005 0.040 372 Dihedral : 19.141 91.226 794 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.50 % Allowed : 15.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.53), residues: 230 helix: 0.47 (0.38), residues: 174 sheet: None (None), residues: 0 loop : -1.65 (0.75), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.012 0.002 TYR A 34 PHE 0.005 0.002 PHE B 78 TRP 0.011 0.002 TRP B 35 HIS 0.002 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2729) covalent geometry : angle 0.50340 ( 3852) hydrogen bonds : bond 0.06085 ( 147) hydrogen bonds : angle 4.02890 ( 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 52 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.091 Fit side-chains REVERT: B 61 MET cc_start: 0.5664 (mtm) cc_final: 0.5454 (mtm) REVERT: B 67 ARG cc_start: 0.6119 (mtm110) cc_final: 0.5642 (ttm110) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.8619 time to fit residues: 42.9292 Evaluate side-chains 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.217590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.185909 restraints weight = 2433.886| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 0.74 r_work: 0.3777 rms_B_bonded: 2.97 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: 0.7411 moved from start: 0.1893 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= 0.112 Angle : 0.444 3.073 3852 Z= 0.240 Chirality : 0.033 0.119 450 Planarity : 0.004 0.038 372 Dihedral : 19.075 90.277 794 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.00 % Allowed : 14.50 % 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 aren not related in a simple way. whole: 0.62 (0.55), residues: 230 helix: 1.06 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.57 (0.79), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.010 0.002 TYR A 108 PHE 0.004 0.002 PHE A 78 TRP 0.007 0.002 TRP B 97 HIS 0.002 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 2729) covalent geometry : angle 0.44444 ( 3852) hydrogen bonds : bond 0.05108 ( 147) hydrogen bonds : angle 3.66050 ( 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 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.125 Fit side-chains REVERT: B 67 ARG cc_start: 0.6099 (mtm110) cc_final: 0.5765 (ttm110) outliers start: 8 outliers final: 3 residues processed: 45 average time/residue: 0.7692 time to fit residues: 35.2224 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 = 0.4279 r_free = 0.4279 target = 0.213283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.180687 restraints weight = 2418.846| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 0.78 r_work: 0.3689 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2729 Z= 0.154 Angle : 0.514 3.673 3852 Z= 0.276 Chirality : 0.036 0.121 450 Planarity : 0.005 0.043 372 Dihedral : 19.195 90.755 794 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.32 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 aren not related in a simple way. whole: 0.56 (0.55), residues: 230 helix: 1.00 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.50 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.011 0.002 TYR A 107 PHE 0.008 0.002 PHE A 78 TRP 0.010 0.002 TRP B 97 HIS 0.002 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2729) covalent geometry : angle 0.51401 ( 3852) hydrogen bonds : bond 0.06813 ( 147) hydrogen bonds : angle 3.91405 ( 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 51 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.086 Fit side-chains REVERT: A 22 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: B 67 ARG cc_start: 0.6145 (mtm110) cc_final: 0.5764 (ttm110) REVERT: B 81 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7183 (mtpp) outliers start: 11 outliers final: 5 residues processed: 46 average time/residue: 0.7697 time to fit residues: 36.0049 Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.0020 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5406 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.220686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.190408 restraints weight = 2461.753| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 0.81 r_work: 0.3763 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2729 Z= 0.089 Angle : 0.390 3.184 3852 Z= 0.210 Chirality : 0.030 0.120 450 Planarity : 0.004 0.035 372 Dihedral : 19.103 89.167 794 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.50 % Allowed : 19.00 % 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 aren not related in a simple way. whole: 1.11 (0.56), residues: 230 helix: 1.43 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.44 (0.81), 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 0.002 0.001 PHE B 78 TRP 0.005 0.001 TRP A 35 HIS 0.001 0.000 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 2729) covalent geometry : angle 0.38967 ( 3852) hydrogen bonds : bond 0.03693 ( 147) hydrogen bonds : angle 3.38324 ( 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 41 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.085 Fit side-chains REVERT: B 75 LYS cc_start: 0.7119 (mtpp) cc_final: 0.6898 (mtmm) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.7050 time to fit residues: 28.7281 Evaluate side-chains 36 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 22 optimal weight: 9.9990 chunk 19 optimal weight: 0.1980 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.220547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.188364 restraints weight = 2472.534| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 0.77 r_work: 0.3784 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2435 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= 0.088 Angle : 0.389 3.222 3852 Z= 0.207 Chirality : 0.030 0.120 450 Planarity : 0.004 0.034 372 Dihedral : 19.095 87.518 794 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.50 % Allowed : 19.00 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.57), residues: 230 helix: 1.59 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.37 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 0.002 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00172 ( 2729) covalent geometry : angle 0.38879 ( 3852) hydrogen bonds : bond 0.03884 ( 147) hydrogen bonds : angle 3.34083 ( 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 40 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.087 Fit side-chains REVERT: A 81 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7441 (mttt) REVERT: B 75 LYS cc_start: 0.7068 (mtpp) cc_final: 0.6817 (mtmm) outliers start: 5 outliers final: 2 residues processed: 37 average time/residue: 0.6289 time to fit residues: 23.7301 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 : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain B residue 88 ASP 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: 0.0670 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.219170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.190565 restraints weight = 2466.897| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 0.77 r_work: 0.3737 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2483 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= 0.097 Angle : 0.404 3.287 3852 Z= 0.215 Chirality : 0.031 0.119 450 Planarity : 0.004 0.032 372 Dihedral : 19.094 86.293 794 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.00 % Allowed : 19.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.57), residues: 230 helix: 1.57 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.29 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.009 0.001 TYR A 108 PHE 0.004 0.001 PHE A 78 TRP 0.006 0.001 TRP B 97 HIS 0.002 0.000 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 2729) covalent geometry : angle 0.40400 ( 3852) hydrogen bonds : bond 0.04374 ( 147) hydrogen bonds : angle 3.40106 ( 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 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.085 Fit side-chains REVERT: A 81 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7384 (mttt) REVERT: B 75 LYS cc_start: 0.7106 (mtpp) cc_final: 0.6889 (mtmm) REVERT: B 81 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.6900 (mtpp) outliers start: 6 outliers final: 1 residues processed: 39 average time/residue: 0.7829 time to fit residues: 31.0745 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 : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain B residue 81 LYS 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: 0.3980 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.220498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.188474 restraints weight = 2530.732| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 0.77 r_work: 0.3778 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2612 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= 0.091 Angle : 0.394 3.290 3852 Z= 0.209 Chirality : 0.030 0.120 450 Planarity : 0.003 0.030 372 Dihedral : 19.050 84.007 794 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.00 % Allowed : 18.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.57), residues: 230 helix: 1.65 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.27 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 A 23 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 2729) covalent geometry : angle 0.39408 ( 3852) hydrogen bonds : bond 0.03900 ( 147) hydrogen bonds : angle 3.33739 ( 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 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.090 Fit side-chains REVERT: A 22 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7072 (tp30) REVERT: A 81 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7356 (mttt) REVERT: B 75 LYS cc_start: 0.7081 (mtpp) cc_final: 0.6816 (mtmm) REVERT: B 81 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.6940 (mtpp) outliers start: 8 outliers final: 2 residues processed: 40 average time/residue: 0.7526 time to fit residues: 30.6575 Evaluate side-chains 41 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.0980 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.215237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.182049 restraints weight = 2485.687| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 0.81 r_work: 0.3719 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2729 Z= 0.146 Angle : 0.493 3.485 3852 Z= 0.264 Chirality : 0.034 0.131 450 Planarity : 0.004 0.037 372 Dihedral : 19.204 84.569 794 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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 aren not related in a simple way. whole: 1.12 (0.57), residues: 230 helix: 1.39 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.23 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.012 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 23 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2729) covalent geometry : angle 0.49324 ( 3852) hydrogen bonds : bond 0.06285 ( 147) hydrogen bonds : angle 3.78751 ( 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 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.088 Fit side-chains REVERT: A 22 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6845 (tp30) REVERT: A 81 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7314 (mttt) REVERT: B 67 ARG cc_start: 0.6159 (mtm110) cc_final: 0.5770 (ttm110) REVERT: B 75 LYS cc_start: 0.7264 (mtpp) cc_final: 0.6972 (mtmm) REVERT: B 81 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.6870 (mtpp) outliers start: 8 outliers final: 3 residues processed: 44 average time/residue: 0.8194 time to fit residues: 36.7078 Evaluate side-chains 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 0.0980 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.216237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.183099 restraints weight = 2507.807| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 0.77 r_work: 0.3740 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2602 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= 0.131 Angle : 0.477 4.917 3852 Z= 0.254 Chirality : 0.033 0.127 450 Planarity : 0.004 0.037 372 Dihedral : 19.209 84.206 794 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.00 % Allowed : 18.50 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.57), residues: 230 helix: 1.41 (0.40), residues: 172 sheet: None (None), residues: 0 loop : -0.62 (0.91), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.011 0.002 TYR A 107 PHE 0.007 0.002 PHE A 78 TRP 0.008 0.002 TRP B 97 HIS 0.002 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2729) covalent geometry : angle 0.47704 ( 3852) hydrogen bonds : bond 0.05618 ( 147) hydrogen bonds : angle 3.79133 ( 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 : 0.091 Fit side-chains REVERT: A 22 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: A 81 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7338 (mttt) REVERT: B 67 ARG cc_start: 0.6130 (mtm110) cc_final: 0.5723 (ttm110) REVERT: B 75 LYS cc_start: 0.7251 (mtpp) cc_final: 0.6982 (mtmm) REVERT: B 81 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.6869 (mtpp) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 0.8259 time to fit residues: 34.4137 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 overall best weight: 1.2344 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.217798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.184371 restraints weight = 2487.307| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 0.80 r_work: 0.3743 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2667 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= 0.116 Angle : 0.456 5.234 3852 Z= 0.242 Chirality : 0.032 0.125 450 Planarity : 0.004 0.036 372 Dihedral : 19.170 82.884 794 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.50 % Allowed : 18.00 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.57), residues: 230 helix: 1.46 (0.40), residues: 172 sheet: None (None), residues: 0 loop : -0.56 (0.91), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 57 TYR 0.009 0.002 TYR A 108 PHE 0.005 0.001 PHE A 78 TRP 0.007 0.001 TRP B 97 HIS 0.002 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 2729) covalent geometry : angle 0.45585 ( 3852) hydrogen bonds : bond 0.05009 ( 147) hydrogen bonds : angle 3.72550 ( 406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1273.37 seconds wall clock time: 22 minutes 22.12 seconds (1342.12 seconds total)