Starting phenix.real_space_refine on Tue Aug 4 21:12:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh8_40036/08_2026/8gh8_40036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh8_40036/08_2026/8gh8_40036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gh8_40036/08_2026/8gh8_40036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh8_40036/08_2026/8gh8_40036.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh8_40036/08_2026/8gh8_40036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh8_40036/08_2026/8gh8_40036.cif" } resolution = 4.3 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= 0.001 sd= 0.063 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 136 5.49 5 S 4 5.16 5 C 4084 2.51 5 N 1216 2.21 5 O 1551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6991 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1053 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "B" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1044 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "C" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1053 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "D" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1053 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 131} Chain: "E" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "F" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "H" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Time building chain proxies: 1.82, per 1000 atoms: 0.26 Number of scatterers: 6991 At special positions: 0 Unit cell: (164.35, 167.2, 69.35, 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 4 16.00 P 136 15.00 O 1551 8.00 N 1216 7.00 C 4084 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: 0.50 Conformation dependent library (CDL) restraints added in 401.8 milliseconds 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 23.4% alpha, 5.2% beta 16 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.558A pdb=" N GLN A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 96 through 102 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 124 through 129 removed outlier: 4.400A pdb=" N LYS A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 129' Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.910A pdb=" N LEU B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.978A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.507A pdb=" N GLY B 129 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.630A pdb=" N GLN C 36 " --> pdb=" O PRO C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 74 removed outlier: 3.936A pdb=" N PHE C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 86 removed outlier: 3.856A pdb=" N ALA C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 86 " --> pdb=" O PRO C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 81 through 86' Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.936A pdb=" N LYS C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 67 through 75 removed outlier: 3.788A pdb=" N PHE D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.788A pdb=" N THR D 110 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.906A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.602A pdb=" N PHE B 26 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE B 27 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 18 through 20 removed outlier: 3.619A pdb=" N LEU C 59 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN C 29 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.675A pdb=" N GLY D 7 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 44 " --> pdb=" O GLY D 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 17 through 19 removed outlier: 5.622A pdb=" N PHE D 27 " --> pdb=" O LEU D 59 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 0.59 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1417 1.33 - 1.45: 2040 1.45 - 1.57: 3666 1.57 - 1.68: 268 1.68 - 1.80: 8 Bond restraints: 7399 Sorted by residual: bond pdb=" N ALA B 91 " pdb=" CA ALA B 91 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.32e+01 bond pdb=" N LEU B 89 " pdb=" CA LEU B 89 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.18e+01 bond pdb=" C3' DA F 15 " pdb=" C2' DA F 15 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DA E 14 " pdb=" C2' DA E 14 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT E 32 " pdb=" C2' DT E 32 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 7394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 10006 2.03 - 4.06: 525 4.06 - 6.09: 42 6.09 - 8.11: 10 8.11 - 10.14: 2 Bond angle restraints: 10585 Sorted by residual: angle pdb=" N SER B 90 " pdb=" CA SER B 90 " pdb=" C SER B 90 " ideal model delta sigma weight residual 113.18 103.04 10.14 1.21e+00 6.83e-01 7.03e+01 angle pdb=" O4' DA F 26 " pdb=" C4' DA F 26 " pdb=" C3' DA F 26 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" O4' DT H 11 " pdb=" C4' DT H 11 " pdb=" C3' DT H 11 " ideal model delta sigma weight residual 106.00 103.35 2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT F 32 " pdb=" C4 DT F 32 " pdb=" O4 DT F 32 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" C GLU D 66 " pdb=" CA GLU D 66 " pdb=" CB GLU D 66 " ideal model delta sigma weight residual 116.34 110.40 5.94 1.40e+00 5.10e-01 1.80e+01 ... (remaining 10580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 3523 34.99 - 69.97: 580 69.97 - 104.96: 23 104.96 - 139.94: 1 139.94 - 174.93: 6 Dihedral angle restraints: 4133 sinusoidal: 2588 harmonic: 1545 Sorted by residual: dihedral pdb=" CA SER B 90 " pdb=" C SER B 90 " pdb=" N ALA B 91 " pdb=" CA ALA B 91 " ideal model delta harmonic sigma weight residual -180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA TYR A 60 " pdb=" C TYR A 60 " pdb=" N GLY A 61 " pdb=" CA GLY A 61 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA PRO D 93 " pdb=" C PRO D 93 " pdb=" N PRO D 94 " pdb=" CA PRO D 94 " ideal model delta harmonic sigma weight residual -180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 4130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1203 0.115 - 0.230: 21 0.230 - 0.345: 0 0.345 - 0.459: 0 0.459 - 0.574: 3 Chirality restraints: 1227 Sorted by residual: chirality pdb=" P DG F 28 " pdb=" OP1 DG F 28 " pdb=" OP2 DG F 28 " pdb=" O5' DG F 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" P DA F 30 " pdb=" OP1 DA F 30 " pdb=" OP2 DA F 30 " pdb=" O5' DA F 30 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" P DA F 29 " pdb=" OP1 DA F 29 " pdb=" OP2 DA F 29 " pdb=" O5' DA F 29 " both_signs ideal model delta sigma weight residual True 2.34 -2.82 -0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 1224 not shown) Planarity restraints: 871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 89 " -0.018 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C LEU C 89 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU C 89 " -0.021 2.00e-02 2.50e+03 pdb=" N SER C 90 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 93 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO D 94 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 94 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 94 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 93 " -0.038 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO B 94 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " -0.032 5.00e-02 4.00e+02 ... (remaining 868 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 835 2.76 - 3.29: 6239 3.29 - 3.83: 11306 3.83 - 4.36: 12441 4.36 - 4.90: 19026 Nonbonded interactions: 49847 Sorted by model distance: nonbonded pdb=" O ILE C 2 " pdb=" OG1 THR C 48 " model vdw 2.219 3.040 nonbonded pdb=" O ALA A 106 " pdb=" OG1 THR A 110 " model vdw 2.248 3.040 nonbonded pdb=" N LEU A 8 " pdb=" O LEU A 20 " model vdw 2.294 3.120 nonbonded pdb=" O LEU A 88 " pdb=" NH1 ARG A 117 " model vdw 2.323 3.120 nonbonded pdb=" NH2 ARG B 6 " pdb=" OE1 GLU B 43 " model vdw 2.327 3.120 ... (remaining 49842 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' and resid 1 through 139) selection = chain 'B' selection = (chain 'C' and resid 1 through 139) selection = (chain 'D' and resid 1 through 139) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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 group one per residue 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: 1.240 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 7.940 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4381 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 : 0.006 0.047 7399 Z= 0.491 Angle : 0.909 10.142 10585 Z= 0.714 Chirality : 0.053 0.574 1227 Planarity : 0.006 0.068 871 Dihedral : 26.603 174.929 3151 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.70 % Favored : 86.75 % Rotamer: Outliers : 0.23 % Allowed : 0.00 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.65 (0.33), residues: 551 helix: -2.08 (0.62), residues: 70 sheet: -2.03 (1.10), residues: 18 loop : -2.78 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 122 TYR 0.017 0.002 TYR A 60 PHE 0.021 0.002 PHE C 17 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.49 ( 7399) covalent geometry : angle 0.90922 / 0.71 (10585) hydrogen bonds : bond 0.18757 / 11.11 ( 94) hydrogen bonds : angle 5.41283 / 3.58 ( 211) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.117 Fit side-chains REVERT: B 12 LYS cc_start: 0.8310 (tttm) cc_final: 0.7868 (ttpt) REVERT: C 1 MET cc_start: 0.4402 (tpt) cc_final: 0.3078 (tpt) REVERT: D 1 MET cc_start: 0.4949 (tpt) cc_final: 0.3107 (tpt) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.0706 time to fit residues: 5.6630 Evaluate side-chains 40 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 40.0000 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5322 r_free = 0.5322 target = 0.311749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.259678 restraints weight = 81652.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.264769 restraints weight = 34460.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.263397 restraints weight = 28194.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.263760 restraints weight = 27450.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.263364 restraints weight = 26316.590| |-----------------------------------------------------------------------------| r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5398 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7399 Z= 0.241 Angle : 0.849 14.271 10585 Z= 0.459 Chirality : 0.048 0.322 1227 Planarity : 0.007 0.068 871 Dihedral : 30.177 173.266 2143 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.36 % Allowed : 14.34 % Favored : 85.30 % Rotamer: Outliers : 0.23 % Allowed : 10.67 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.02 (0.32), residues: 551 helix: -2.32 (0.60), residues: 69 sheet: -3.31 (2.12), residues: 6 loop : -3.04 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 3 TYR 0.021 0.004 TYR C 60 PHE 0.030 0.004 PHE C 17 HIS 0.008 0.002 HIS D 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 ( 7399) covalent geometry : angle 0.84915 / 0.46 (10585) hydrogen bonds : bond 0.05846 / 3.82 ( 94) hydrogen bonds : angle 5.34201 / 3.38 ( 211) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.124 Fit side-chains REVERT: A 60 TYR cc_start: 0.6438 (m-80) cc_final: 0.6185 (m-80) REVERT: B 12 LYS cc_start: 0.8163 (tttm) cc_final: 0.7885 (ttpt) REVERT: C 1 MET cc_start: 0.4949 (tpt) cc_final: 0.3760 (tpt) REVERT: D 1 MET cc_start: 0.5276 (tpt) cc_final: 0.3270 (tpt) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.0484 time to fit residues: 3.0743 Evaluate side-chains 38 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 64 optimal weight: 50.0000 chunk 17 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.314068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.264022 restraints weight = 79636.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.267966 restraints weight = 31955.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.266995 restraints weight = 28869.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.266282 restraints weight = 26142.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.265568 restraints weight = 24827.315| |-----------------------------------------------------------------------------| r_work (final): 0.4672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5228 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 0.040 7399 Z= 0.170 Angle : 0.757 13.746 10585 Z= 0.419 Chirality : 0.045 0.337 1227 Planarity : 0.006 0.070 871 Dihedral : 30.118 172.193 2143 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.43 % Favored : 88.20 % Rotamer: Outliers : 0.23 % Allowed : 5.10 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.97 (0.32), residues: 551 helix: -2.29 (0.60), residues: 70 sheet: -2.48 (0.89), residues: 28 loop : -3.00 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 99 TYR 0.015 0.002 TYR A 60 PHE 0.020 0.002 PHE D 62 HIS 0.005 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 ( 7399) covalent geometry : angle 0.75710 / 0.42 (10585) hydrogen bonds : bond 0.04986 / 3.33 ( 94) hydrogen bonds : angle 5.15865 / 3.34 ( 211) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.117 Fit side-chains REVERT: B 12 LYS cc_start: 0.8113 (tttm) cc_final: 0.7815 (ttpt) REVERT: C 1 MET cc_start: 0.4906 (tpt) cc_final: 0.3792 (tpt) REVERT: D 60 TYR cc_start: 0.4631 (m-80) cc_final: 0.4061 (m-80) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0462 time to fit residues: 3.3133 Evaluate side-chains 40 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 55 optimal weight: 50.0000 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 40.0000 chunk 56 optimal weight: 40.0000 chunk 66 optimal weight: 50.0000 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5333 r_free = 0.5333 target = 0.315127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.263232 restraints weight = 79580.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.266777 restraints weight = 32672.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.266163 restraints weight = 27635.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.265704 restraints weight = 25932.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.265242 restraints weight = 26505.714| |-----------------------------------------------------------------------------| r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5231 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7399 Z= 0.161 Angle : 0.740 13.966 10585 Z= 0.408 Chirality : 0.045 0.349 1227 Planarity : 0.006 0.067 871 Dihedral : 30.076 171.475 2143 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.25 % Favored : 86.39 % Rotamer: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.88 (0.33), residues: 551 helix: -2.05 (0.63), residues: 69 sheet: -2.54 (0.94), residues: 22 loop : -2.96 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 99 TYR 0.014 0.002 TYR A 60 PHE 0.017 0.002 PHE C 17 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 ( 7399) covalent geometry : angle 0.74006 / 0.41 (10585) hydrogen bonds : bond 0.04391 / 3.00 ( 94) hydrogen bonds : angle 5.11902 / 3.32 ( 211) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.197 Fit side-chains REVERT: B 12 LYS cc_start: 0.8112 (tttm) cc_final: 0.7857 (ttpt) REVERT: C 1 MET cc_start: 0.4995 (tpt) cc_final: 0.3752 (tpt) REVERT: D 1 MET cc_start: 0.4805 (tpt) cc_final: 0.3216 (tpt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0476 time to fit residues: 3.2705 Evaluate side-chains 40 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 30.0000 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.0000 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 40.0000 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.315928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.266779 restraints weight = 79326.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.269786 restraints weight = 32629.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.268592 restraints weight = 28330.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.268828 restraints weight = 27388.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.268077 restraints weight = 25724.871| |-----------------------------------------------------------------------------| r_work (final): 0.4693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5172 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7399 Z= 0.157 Angle : 0.730 13.414 10585 Z= 0.402 Chirality : 0.044 0.354 1227 Planarity : 0.006 0.068 871 Dihedral : 30.073 171.128 2143 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.80 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.89 (0.33), residues: 551 helix: -2.09 (0.63), residues: 69 sheet: -2.62 (0.86), residues: 24 loop : -2.96 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 95 TYR 0.014 0.002 TYR A 60 PHE 0.018 0.002 PHE D 17 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 ( 7399) covalent geometry : angle 0.73016 / 0.40 (10585) hydrogen bonds : bond 0.04361 / 2.98 ( 94) hydrogen bonds : angle 5.07458 / 3.32 ( 211) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.175 Fit side-chains REVERT: B 12 LYS cc_start: 0.8101 (tttm) cc_final: 0.7813 (ttpt) REVERT: C 1 MET cc_start: 0.4945 (tpt) cc_final: 0.3802 (tpt) REVERT: D 1 MET cc_start: 0.4990 (tpt) cc_final: 0.3445 (tpt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0450 time to fit residues: 3.2660 Evaluate side-chains 42 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5329 r_free = 0.5329 target = 0.314913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.276857 restraints weight = 79834.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.279275 restraints weight = 30463.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.278758 restraints weight = 29719.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.277718 restraints weight = 26943.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.277343 restraints weight = 26343.150| |-----------------------------------------------------------------------------| r_work (final): 0.4702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5123 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7399 Z= 0.147 Angle : 0.721 13.083 10585 Z= 0.398 Chirality : 0.043 0.356 1227 Planarity : 0.006 0.068 871 Dihedral : 30.060 170.736 2143 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.52 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.84 (0.33), residues: 551 helix: -2.17 (0.62), residues: 69 sheet: -2.49 (0.96), residues: 22 loop : -2.91 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 95 TYR 0.015 0.002 TYR D 60 PHE 0.019 0.002 PHE D 17 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 ( 7399) covalent geometry : angle 0.72124 / 0.40 (10585) hydrogen bonds : bond 0.04096 / 2.84 ( 94) hydrogen bonds : angle 5.06880 / 3.32 ( 211) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.118 Fit side-chains REVERT: B 12 LYS cc_start: 0.8130 (tttm) cc_final: 0.7871 (ttpt) REVERT: C 1 MET cc_start: 0.4722 (tpt) cc_final: 0.3535 (tpt) REVERT: D 1 MET cc_start: 0.4934 (tpt) cc_final: 0.3459 (tpt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0538 time to fit residues: 3.6144 Evaluate side-chains 39 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 40.0000 chunk 11 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5315 r_free = 0.5315 target = 0.313631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.259970 restraints weight = 80890.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.264344 restraints weight = 32698.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.263757 restraints weight = 26791.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.263626 restraints weight = 26097.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.262917 restraints weight = 24623.606| |-----------------------------------------------------------------------------| r_work (final): 0.4629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5309 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 : 0.004 0.044 7399 Z= 0.180 Angle : 0.770 13.531 10585 Z= 0.415 Chirality : 0.045 0.361 1227 Planarity : 0.006 0.072 871 Dihedral : 30.081 170.974 2143 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.34 % Favored : 85.48 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.00 (0.33), residues: 551 helix: -2.13 (0.63), residues: 70 sheet: -2.54 (0.79), residues: 36 loop : -3.05 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 122 TYR 0.029 0.004 TYR C 4 PHE 0.020 0.003 PHE D 17 HIS 0.009 0.002 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 7399) covalent geometry : angle 0.77039 / 0.42 (10585) hydrogen bonds : bond 0.04422 / 2.95 ( 94) hydrogen bonds : angle 5.27055 / 3.40 ( 211) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.157 Fit side-chains REVERT: B 12 LYS cc_start: 0.8224 (tttm) cc_final: 0.7912 (ttpt) REVERT: C 1 MET cc_start: 0.4844 (tpt) cc_final: 0.3866 (tpt) REVERT: D 1 MET cc_start: 0.4869 (tpt) cc_final: 0.3063 (tpt) REVERT: D 2 ILE cc_start: 0.6255 (mt) cc_final: 0.5162 (pt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0412 time to fit residues: 2.9697 Evaluate side-chains 42 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 60 optimal weight: 40.0000 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 19 optimal weight: 0.0980 chunk 4 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 50.0000 chunk 30 optimal weight: 0.4980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5337 r_free = 0.5337 target = 0.316787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.278218 restraints weight = 81479.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.281668 restraints weight = 33268.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.281087 restraints weight = 29677.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.280928 restraints weight = 27952.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.280199 restraints weight = 27194.739| |-----------------------------------------------------------------------------| r_work (final): 0.4729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5079 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7399 Z= 0.138 Angle : 0.706 12.279 10585 Z= 0.389 Chirality : 0.043 0.357 1227 Planarity : 0.006 0.073 871 Dihedral : 30.023 170.855 2143 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.25 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.80 (0.33), residues: 551 helix: -2.11 (0.62), residues: 69 sheet: -2.61 (0.93), residues: 22 loop : -2.88 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 95 TYR 0.016 0.002 TYR C 4 PHE 0.019 0.002 PHE C 26 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 ( 7399) covalent geometry : angle 0.70605 / 0.39 (10585) hydrogen bonds : bond 0.03826 / 2.72 ( 94) hydrogen bonds : angle 5.03627 / 3.34 ( 211) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.185 Fit side-chains REVERT: B 12 LYS cc_start: 0.8103 (tttm) cc_final: 0.7780 (ttpt) REVERT: C 1 MET cc_start: 0.4631 (tpt) cc_final: 0.3702 (tpt) REVERT: D 1 MET cc_start: 0.4622 (tpt) cc_final: 0.3246 (tpt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0413 time to fit residues: 2.9863 Evaluate side-chains 41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 40.0000 chunk 63 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.5321 r_free = 0.5321 target = 0.314316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.259740 restraints weight = 78791.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.265142 restraints weight = 33632.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.263398 restraints weight = 27013.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.263258 restraints weight = 26085.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.263012 restraints weight = 25595.691| |-----------------------------------------------------------------------------| r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7399 Z= 0.189 Angle : 0.771 12.808 10585 Z= 0.414 Chirality : 0.045 0.361 1227 Planarity : 0.007 0.077 871 Dihedral : 30.036 170.805 2143 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.88 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.98 (0.33), residues: 551 helix: -2.20 (0.63), residues: 71 sheet: -2.28 (0.82), residues: 36 loop : -3.05 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 95 TYR 0.023 0.003 TYR D 60 PHE 0.036 0.004 PHE C 26 HIS 0.007 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 7399) covalent geometry : angle 0.77053 / 0.41 (10585) hydrogen bonds : bond 0.04425 / 2.97 ( 94) hydrogen bonds : angle 5.29051 / 3.41 ( 211) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.179 Fit side-chains REVERT: B 12 LYS cc_start: 0.8140 (tttm) cc_final: 0.7792 (ttpt) REVERT: C 1 MET cc_start: 0.4806 (tpt) cc_final: 0.3616 (tpt) REVERT: D 1 MET cc_start: 0.4911 (tpt) cc_final: 0.3262 (tpt) REVERT: D 2 ILE cc_start: 0.6314 (mt) cc_final: 0.5173 (pt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0534 time to fit residues: 3.7644 Evaluate side-chains 42 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.5317 r_free = 0.5317 target = 0.313152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.270304 restraints weight = 81141.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.275832 restraints weight = 34927.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.274369 restraints weight = 28702.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.274204 restraints weight = 28495.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.273382 restraints weight = 26622.811| |-----------------------------------------------------------------------------| r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5094 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7399 Z= 0.163 Angle : 0.737 12.264 10585 Z= 0.399 Chirality : 0.044 0.354 1227 Planarity : 0.006 0.080 871 Dihedral : 30.014 171.025 2143 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.52 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.91 (0.33), residues: 551 helix: -2.15 (0.63), residues: 70 sheet: -2.23 (1.06), residues: 22 loop : -2.99 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 95 TYR 0.014 0.002 TYR D 60 PHE 0.038 0.003 PHE C 26 HIS 0.004 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 7399) covalent geometry : angle 0.73693 / 0.40 (10585) hydrogen bonds : bond 0.04050 / 2.79 ( 94) hydrogen bonds : angle 5.24371 / 3.42 ( 211) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.183 Fit side-chains REVERT: B 12 LYS cc_start: 0.8188 (tttm) cc_final: 0.7808 (ttpt) REVERT: C 1 MET cc_start: 0.4718 (tpt) cc_final: 0.3607 (tpt) REVERT: D 1 MET cc_start: 0.4969 (tpt) cc_final: 0.3480 (tpt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0468 time to fit residues: 3.2218 Evaluate side-chains 41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 0.0040 chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.317982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.279056 restraints weight = 80201.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.287451 restraints weight = 31678.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.283623 restraints weight = 29468.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.282601 restraints weight = 27679.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.281933 restraints weight = 26385.139| |-----------------------------------------------------------------------------| r_work (final): 0.4746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5044 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7399 Z= 0.140 Angle : 0.704 12.190 10585 Z= 0.384 Chirality : 0.042 0.349 1227 Planarity : 0.006 0.080 871 Dihedral : 29.977 171.092 2143 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.43 % Favored : 88.38 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.77 (0.33), residues: 551 helix: -2.18 (0.63), residues: 69 sheet: -2.67 (1.27), residues: 12 loop : -2.85 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 95 TYR 0.014 0.002 TYR C 4 PHE 0.021 0.002 PHE C 26 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 ( 7399) covalent geometry : angle 0.70440 / 0.38 (10585) hydrogen bonds : bond 0.03823 / 2.72 ( 94) hydrogen bonds : angle 5.09200 / 3.41 ( 211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 960.75 seconds wall clock time: 17 minutes 4.65 seconds (1024.65 seconds total)