Starting phenix.real_space_refine on Thu Jul 2 05:07:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh8_40036/07_2026/8gh8_40036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh8_40036/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gh8_40036/07_2026/8gh8_40036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh8_40036/07_2026/8gh8_40036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gh8_40036/07_2026/8gh8_40036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh8_40036/07_2026/8gh8_40036.map" } 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-dev-6108/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: 1.28, per 1000 atoms: 0.18 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: 0.56 Conformation dependent library (CDL) restraints added in 271.2 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: 0.48 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: 0.57 Time building geometry restraints manager: 0.74 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: 10008 2.03 - 4.06: 523 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: 0.990 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.960 Find NCS groups from input model: 0.110 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.550 ------------------------------------------------------------------------------- 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 : 0.905 10.142 10585 Z= 0.709 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 0.90472 / 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 : 0.183 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: 0.0593 time to fit residues: 4.9344 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 : 0.176 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 50.0000 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.5307 r_free = 0.5307 target = 0.310604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.255234 restraints weight = 80052.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.260632 restraints weight = 33887.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.259130 restraints weight = 27723.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.258748 restraints weight = 28229.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.258549 restraints weight = 24963.810| |-----------------------------------------------------------------------------| r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7399 Z= 0.221 Angle : 0.809 14.174 10585 Z= 0.443 Chirality : 0.046 0.297 1227 Planarity : 0.006 0.068 871 Dihedral : 30.169 172.514 2143 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.61 % Favored : 86.03 % Rotamer: Outliers : 0.23 % Allowed : 9.51 % Favored : 90.26 % 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: -3.93 (0.32), residues: 551 helix: -2.27 (0.60), residues: 69 sheet: -3.03 (2.10), residues: 6 loop : -2.98 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 3 TYR 0.021 0.004 TYR C 60 PHE 0.026 0.004 PHE C 17 HIS 0.006 0.001 HIS D 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 ( 7399) covalent geometry : angle 0.80886 / 0.44 (10585) hydrogen bonds : bond 0.05308 / 3.52 ( 94) hydrogen bonds : angle 5.27382 / 3.36 ( 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 46 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.249 Fit side-chains REVERT: A 60 TYR cc_start: 0.6312 (m-80) cc_final: 0.6059 (m-80) REVERT: B 12 LYS cc_start: 0.8160 (tttm) cc_final: 0.7892 (ttpt) REVERT: C 1 MET cc_start: 0.4906 (tpt) cc_final: 0.3753 (tpt) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.0635 time to fit residues: 4.4032 Evaluate side-chains 41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 0.0010 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 0.0070 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 40.0000 chunk 45 optimal weight: 0.5980 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 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 = 0.5346 r_free = 0.5346 target = 0.317517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.270795 restraints weight = 79925.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.276098 restraints weight = 31663.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.273839 restraints weight = 29273.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.274060 restraints weight = 26539.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.273067 restraints weight = 25734.637| |-----------------------------------------------------------------------------| r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7399 Z= 0.153 Angle : 0.728 13.488 10585 Z= 0.407 Chirality : 0.043 0.311 1227 Planarity : 0.006 0.070 871 Dihedral : 30.108 171.728 2143 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.07 % Favored : 88.57 % 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: -3.78 (0.33), residues: 551 helix: -2.24 (0.60), residues: 69 sheet: -2.42 (0.92), residues: 22 loop : -2.84 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.015 0.002 TYR A 60 PHE 0.016 0.002 PHE D 62 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 ( 7399) covalent geometry : angle 0.72776 / 0.41 (10585) hydrogen bonds : bond 0.04753 / 3.24 ( 94) hydrogen bonds : angle 5.00944 / 3.28 ( 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: 0 poor density : 48 time to evaluate : 0.192 Fit side-chains REVERT: B 12 LYS cc_start: 0.8146 (tttm) cc_final: 0.7846 (ttpt) REVERT: C 1 MET cc_start: 0.4710 (tpt) cc_final: 0.3667 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0671 time to fit residues: 4.8353 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 : 0.206 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 0.3980 chunk 61 optimal weight: 50.0000 chunk 56 optimal weight: 40.0000 chunk 66 optimal weight: 50.0000 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.5330 r_free = 0.5330 target = 0.314410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.262439 restraints weight = 79545.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.265520 restraints weight = 31809.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.265422 restraints weight = 27762.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.264609 restraints weight = 25623.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.264051 restraints weight = 25512.512| |-----------------------------------------------------------------------------| r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5262 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7399 Z= 0.176 Angle : 0.742 13.891 10585 Z= 0.411 Chirality : 0.044 0.318 1227 Planarity : 0.006 0.068 871 Dihedral : 30.094 171.401 2143 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.07 % Favored : 86.57 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % 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: -3.87 (0.33), residues: 551 helix: -2.09 (0.63), residues: 69 sheet: -2.66 (1.13), residues: 18 loop : -2.95 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.016 0.003 TYR A 60 PHE 0.021 0.003 PHE C 17 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 ( 7399) covalent geometry : angle 0.74200 / 0.41 (10585) hydrogen bonds : bond 0.04631 / 3.12 ( 94) hydrogen bonds : angle 5.13022 / 3.34 ( 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 45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.200 Fit side-chains REVERT: B 12 LYS cc_start: 0.8068 (tttm) cc_final: 0.7831 (ttpt) REVERT: C 1 MET cc_start: 0.4928 (tpt) cc_final: 0.3679 (tpt) REVERT: D 60 TYR cc_start: 0.4406 (m-80) cc_final: 0.3933 (m-80) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0567 time to fit residues: 4.0122 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 : 0.183 ------------------------------------------------------------------------------- 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: 6.9990 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 0.0170 chunk 24 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 57 optimal weight: 40.0000 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5345 r_free = 0.5345 target = 0.317244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.278138 restraints weight = 80011.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.281321 restraints weight = 32565.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.281870 restraints weight = 28028.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.280570 restraints weight = 29369.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.279838 restraints weight = 27454.653| |-----------------------------------------------------------------------------| r_work (final): 0.4751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5021 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7399 Z= 0.143 Angle : 0.706 13.301 10585 Z= 0.393 Chirality : 0.042 0.319 1227 Planarity : 0.006 0.068 871 Dihedral : 30.069 170.599 2143 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.62 % Favored : 88.20 % 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: -3.75 (0.33), residues: 551 helix: -2.06 (0.63), residues: 69 sheet: -2.56 (0.92), residues: 22 loop : -2.85 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.023 0.002 TYR C 4 PHE 0.016 0.002 PHE D 62 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 ( 7399) covalent geometry : angle 0.70553 / 0.39 (10585) hydrogen bonds : bond 0.04168 / 2.92 ( 94) hydrogen bonds : angle 4.95343 / 3.30 ( 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 : 0.194 Fit side-chains REVERT: B 12 LYS cc_start: 0.8037 (tttm) cc_final: 0.7808 (ttpt) REVERT: C 1 MET cc_start: 0.4959 (tpt) cc_final: 0.3776 (tpt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0567 time to fit residues: 4.0388 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 : 0.171 ------------------------------------------------------------------------------- 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: 6.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.5334 r_free = 0.5334 target = 0.315783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.277820 restraints weight = 79979.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.280293 restraints weight = 30778.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.279271 restraints weight = 28510.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.278371 restraints weight = 26941.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.278130 restraints weight = 26658.283| |-----------------------------------------------------------------------------| r_work (final): 0.4713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5101 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7399 Z= 0.150 Angle : 0.708 12.903 10585 Z= 0.393 Chirality : 0.042 0.326 1227 Planarity : 0.006 0.069 871 Dihedral : 30.060 170.286 2143 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.34 % Favored : 87.48 % 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: -3.87 (0.33), residues: 551 helix: -2.09 (0.63), residues: 69 sheet: -3.67 (0.68), residues: 36 loop : -2.82 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 95 TYR 0.014 0.003 TYR D 60 PHE 0.021 0.002 PHE D 17 HIS 0.014 0.002 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 7399) covalent geometry : angle 0.70771 / 0.39 (10585) hydrogen bonds : bond 0.04193 / 2.89 ( 94) hydrogen bonds : angle 4.93481 / 3.26 ( 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 43 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.194 Fit side-chains REVERT: B 12 LYS cc_start: 0.8074 (tttm) cc_final: 0.7818 (ttpt) REVERT: C 1 MET cc_start: 0.4638 (tpt) cc_final: 0.3432 (tpt) REVERT: C 128 LYS cc_start: 0.6939 (tttm) cc_final: 0.6728 (tttt) REVERT: D 1 MET cc_start: 0.4874 (tpt) cc_final: 0.3417 (tpt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0499 time to fit residues: 3.3872 Evaluate side-chains 38 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 30 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.5341 r_free = 0.5341 target = 0.317374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.277760 restraints weight = 81608.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.280226 restraints weight = 36027.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.280478 restraints weight = 29483.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.280753 restraints weight = 28766.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.280635 restraints weight = 26717.736| |-----------------------------------------------------------------------------| r_work (final): 0.4859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4746 moved from start: 0.1994 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 : 0.698 12.556 10585 Z= 0.386 Chirality : 0.042 0.327 1227 Planarity : 0.006 0.069 871 Dihedral : 30.040 170.159 2143 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.89 % Favored : 88.93 % 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: -3.84 (0.33), residues: 551 helix: -2.14 (0.63), residues: 69 sheet: -4.28 (0.73), residues: 24 loop : -2.79 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 95 TYR 0.015 0.002 TYR D 60 PHE 0.015 0.002 PHE C 62 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 ( 7399) covalent geometry : angle 0.69797 / 0.39 (10585) hydrogen bonds : bond 0.03933 / 2.77 ( 94) hydrogen bonds : angle 4.90302 / 3.25 ( 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 45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.192 Fit side-chains REVERT: B 12 LYS cc_start: 0.8117 (tttm) cc_final: 0.7866 (ttpt) REVERT: C 1 MET cc_start: 0.4560 (tpt) cc_final: 0.3569 (tpt) REVERT: D 1 MET cc_start: 0.4694 (tpt) cc_final: 0.3263 (tpt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0556 time to fit residues: 3.9397 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 : 0.191 ------------------------------------------------------------------------------- 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: 30.0000 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.0270 chunk 35 optimal weight: 8.9990 chunk 66 optimal weight: 50.0000 chunk 30 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.316203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.274512 restraints weight = 80932.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.276905 restraints weight = 37481.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.277227 restraints weight = 30663.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.277917 restraints weight = 30592.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.277957 restraints weight = 27364.706| |-----------------------------------------------------------------------------| r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4806 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7399 Z= 0.146 Angle : 0.698 12.823 10585 Z= 0.386 Chirality : 0.042 0.330 1227 Planarity : 0.006 0.075 871 Dihedral : 30.016 170.149 2143 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.25 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -3.87 (0.33), residues: 551 helix: -2.10 (0.64), residues: 69 sheet: -4.39 (0.71), residues: 24 loop : -2.82 (0.28), residues: 458 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 0.015 0.002 PHE D 17 HIS 0.004 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 ( 7399) covalent geometry : angle 0.69792 / 0.39 (10585) hydrogen bonds : bond 0.03948 / 2.77 ( 94) hydrogen bonds : angle 4.90731 / 3.25 ( 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 : 0.178 Fit side-chains REVERT: B 12 LYS cc_start: 0.8045 (tttm) cc_final: 0.7800 (ttpt) REVERT: C 1 MET cc_start: 0.4551 (tpt) cc_final: 0.3471 (tpt) REVERT: D 1 MET cc_start: 0.4779 (tpt) cc_final: 0.3403 (tpt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0515 time to fit residues: 3.5798 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 : 0.180 ------------------------------------------------------------------------------- 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: 0.3980 chunk 57 optimal weight: 40.0000 chunk 63 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.5309 r_free = 0.5309 target = 0.310979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.267921 restraints weight = 78321.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.272095 restraints weight = 35531.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.270544 restraints weight = 28487.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.271045 restraints weight = 29444.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.270741 restraints weight = 26204.359| |-----------------------------------------------------------------------------| r_work (final): 0.4762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4994 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7399 Z= 0.198 Angle : 0.779 12.661 10585 Z= 0.419 Chirality : 0.044 0.330 1227 Planarity : 0.007 0.078 871 Dihedral : 30.052 170.075 2143 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.25 % Favored : 84.57 % 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: -4.02 (0.33), residues: 551 helix: -2.22 (0.63), residues: 71 sheet: -2.97 (0.76), residues: 42 loop : -2.99 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 3 TYR 0.021 0.003 TYR D 60 PHE 0.025 0.003 PHE C 34 HIS 0.008 0.002 HIS D 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 7399) covalent geometry : angle 0.77949 / 0.42 (10585) hydrogen bonds : bond 0.04605 / 3.02 ( 94) hydrogen bonds : angle 5.37350 / 3.47 ( 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 47 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.196 Fit side-chains REVERT: B 12 LYS cc_start: 0.8153 (tttm) cc_final: 0.7827 (ttpt) REVERT: C 1 MET cc_start: 0.4675 (tpt) cc_final: 0.3460 (tpt) REVERT: D 1 MET cc_start: 0.5022 (tpt) cc_final: 0.3289 (tpt) REVERT: D 2 ILE cc_start: 0.6501 (mt) cc_final: 0.5409 (pt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0579 time to fit residues: 4.2125 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 : 0.191 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 47 optimal weight: 0.0050 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.3772 ------------------------------------------------------------------------------- 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 = 0.317814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.276766 restraints weight = 81158.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.281855 restraints weight = 34384.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.280452 restraints weight = 28320.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.280674 restraints weight = 28833.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.280375 restraints weight = 27528.095| |-----------------------------------------------------------------------------| r_work (final): 0.4776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4937 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7399 Z= 0.139 Angle : 0.701 12.294 10585 Z= 0.385 Chirality : 0.042 0.320 1227 Planarity : 0.006 0.080 871 Dihedral : 29.967 170.215 2143 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.25 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.86 (0.34), residues: 551 helix: -2.07 (0.64), residues: 69 sheet: -3.76 (0.70), residues: 34 loop : -2.82 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 95 TYR 0.011 0.001 TYR C 4 PHE 0.025 0.002 PHE C 26 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 ( 7399) covalent geometry : angle 0.70118 / 0.38 (10585) hydrogen bonds : bond 0.03790 / 2.69 ( 94) hydrogen bonds : angle 5.01546 / 3.35 ( 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 : 0.185 Fit side-chains REVERT: B 12 LYS cc_start: 0.8135 (tttm) cc_final: 0.7825 (ttpt) REVERT: C 1 MET cc_start: 0.4550 (tpt) cc_final: 0.3642 (tpt) REVERT: D 1 MET cc_start: 0.4598 (tpt) cc_final: 0.3224 (tpt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0467 time to fit residues: 3.2439 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 : 0.193 ------------------------------------------------------------------------------- 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: 0.0010 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.0040 chunk 50 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.0936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 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 = 0.5353 r_free = 0.5353 target = 0.319620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.282523 restraints weight = 80027.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.286183 restraints weight = 31214.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.285689 restraints weight = 28129.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.284338 restraints weight = 26246.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.284045 restraints weight = 26132.446| |-----------------------------------------------------------------------------| r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4980 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7399 Z= 0.136 Angle : 0.682 12.072 10585 Z= 0.375 Chirality : 0.041 0.320 1227 Planarity : 0.006 0.077 871 Dihedral : 29.907 170.305 2143 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.53 % Favored : 89.29 % 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: -3.69 (0.33), residues: 551 helix: -2.08 (0.63), residues: 69 sheet: -2.77 (0.93), residues: 22 loop : -2.77 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 95 TYR 0.009 0.001 TYR A 60 PHE 0.023 0.002 PHE C 62 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 ( 7399) covalent geometry : angle 0.68206 / 0.38 (10585) hydrogen bonds : bond 0.03784 / 2.73 ( 94) hydrogen bonds : angle 4.91271 / 3.33 ( 211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1134.47 seconds wall clock time: 20 minutes 17.65 seconds (1217.65 seconds total)