Starting phenix.real_space_refine on Tue Feb 11 23:42:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh8_40036/02_2025/8gh8_40036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh8_40036/02_2025/8gh8_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_40036/02_2025/8gh8_40036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh8_40036/02_2025/8gh8_40036.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh8_40036/02_2025/8gh8_40036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh8_40036/02_2025/8gh8_40036.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.32, per 1000 atoms: 0.62 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: 1.58 Conformation dependent library (CDL) restraints added in 671.9 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: 2.15 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: 1.73 Time building geometry restraints manager: 1.85 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=" N SER C 90 " pdb=" CA SER C 90 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.66e+00 bond pdb=" C PRO C 132 " pdb=" N PRO C 133 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.12e-02 7.97e+03 9.08e+00 bond pdb=" N ALA C 91 " pdb=" CA ALA C 91 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.31e-02 5.83e+03 8.89e+00 ... (remaining 7394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 10199 2.03 - 4.06: 335 4.06 - 6.09: 39 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=" 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 angle pdb=" O LEU C 89 " pdb=" C LEU C 89 " pdb=" N SER C 90 " ideal model delta sigma weight residual 121.79 117.64 4.15 9.80e-01 1.04e+00 1.79e+01 angle pdb=" N ALA C 91 " pdb=" CA ALA C 91 " pdb=" C ALA C 91 " ideal model delta sigma weight residual 113.18 108.06 5.12 1.21e+00 6.83e-01 1.79e+01 angle pdb=" CA ALA B 91 " pdb=" C ALA B 91 " pdb=" O ALA B 91 " ideal model delta sigma weight residual 120.51 115.14 5.37 1.43e+00 4.89e-01 1.41e+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 - 0.113: 1208 0.113 - 0.226: 16 0.226 - 0.338: 0 0.338 - 0.451: 0 0.451 - 0.564: 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 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.95e+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 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.37e+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 2.35 -2.82 -0.48 2.00e-01 2.50e+01 5.69e+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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.080 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4247 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 : 0.004 0.047 7399 Z= 0.254 Angle : 0.791 10.142 10585 Z= 0.443 Chirality : 0.046 0.564 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.004 0.001 HIS B 49 PHE 0.021 0.002 PHE C 17 TYR 0.017 0.002 TYR A 60 ARG 0.006 0.001 ARG A 122 *********************** 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 : 0.560 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: 0.1965 time to fit residues: 15.7667 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 : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.315478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.262549 restraints weight = 79974.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.267610 restraints weight = 33671.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.266819 restraints weight = 27694.482| |-----------------------------------------------------------------------------| r_work (final): 0.4671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5138 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7399 Z= 0.250 Angle : 0.726 11.999 10585 Z= 0.392 Chirality : 0.038 0.167 1227 Planarity : 0.006 0.069 871 Dihedral : 30.008 175.583 2143 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.89 % Favored : 88.75 % Rotamer: Outliers : 0.23 % Allowed : 8.35 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.32), residues: 551 helix: -2.22 (0.60), residues: 69 sheet: -3.04 (1.97), residues: 6 loop : -2.85 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 49 PHE 0.020 0.003 PHE C 62 TYR 0.019 0.003 TYR C 60 ARG 0.004 0.000 ARG A 117 *********************** 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 : 0.574 Fit side-chains REVERT: B 12 LYS cc_start: 0.8091 (tttm) cc_final: 0.7817 (ttpt) REVERT: C 1 MET cc_start: 0.4797 (tpt) cc_final: 0.3741 (tpt) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.1509 time to fit residues: 10.2630 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 : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.0000 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 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 = 0.5350 r_free = 0.5350 target = 0.318141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.267394 restraints weight = 80356.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.272849 restraints weight = 32374.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.271508 restraints weight = 27619.258| |-----------------------------------------------------------------------------| r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5017 moved from start: 0.1354 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= 0.209 Angle : 0.700 11.538 10585 Z= 0.380 Chirality : 0.037 0.153 1227 Planarity : 0.006 0.065 871 Dihedral : 29.894 175.206 2143 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.71 % Favored : 88.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.33), residues: 551 helix: -2.22 (0.61), residues: 69 sheet: -2.54 (0.87), residues: 24 loop : -2.79 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 49 PHE 0.015 0.002 PHE C 17 TYR 0.013 0.002 TYR A 60 ARG 0.009 0.001 ARG D 99 *********************** 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 44 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.498 Fit side-chains REVERT: B 12 LYS cc_start: 0.8172 (tttm) cc_final: 0.7897 (ttpt) REVERT: C 1 MET cc_start: 0.4804 (tpt) cc_final: 0.3638 (tpt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1296 time to fit residues: 8.8258 Evaluate side-chains 36 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 40 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 17 optimal weight: 0.0770 chunk 53 optimal weight: 0.0000 chunk 36 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.319071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.272139 restraints weight = 79756.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.274843 restraints weight = 32286.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.274475 restraints weight = 27863.720| |-----------------------------------------------------------------------------| r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5010 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7399 Z= 0.197 Angle : 0.686 10.928 10585 Z= 0.372 Chirality : 0.036 0.175 1227 Planarity : 0.006 0.068 871 Dihedral : 29.775 175.097 2143 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.71 % Favored : 89.11 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.33), residues: 551 helix: -2.09 (0.62), residues: 69 sheet: -3.65 (0.65), residues: 36 loop : -2.72 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 49 PHE 0.015 0.002 PHE C 17 TYR 0.015 0.002 TYR C 60 ARG 0.004 0.000 ARG D 99 *********************** 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 44 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.567 Fit side-chains REVERT: B 12 LYS cc_start: 0.8145 (tttm) cc_final: 0.7871 (ttpt) REVERT: C 1 MET cc_start: 0.4778 (tpt) cc_final: 0.3546 (tpt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1338 time to fit residues: 9.0871 Evaluate side-chains 36 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 chunk 58 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5345 r_free = 0.5345 target = 0.318609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.268476 restraints weight = 80121.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.271639 restraints weight = 32988.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.271276 restraints weight = 28058.022| |-----------------------------------------------------------------------------| r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4991 moved from start: 0.1887 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= 0.212 Angle : 0.687 11.146 10585 Z= 0.374 Chirality : 0.036 0.163 1227 Planarity : 0.006 0.067 871 Dihedral : 29.711 175.371 2143 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.25 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.33), residues: 551 helix: -2.11 (0.62), residues: 69 sheet: -3.71 (0.66), residues: 36 loop : -2.73 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 49 PHE 0.017 0.002 PHE C 17 TYR 0.024 0.002 TYR D 60 ARG 0.003 0.000 ARG B 99 *********************** 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 48 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.541 Fit side-chains REVERT: B 12 LYS cc_start: 0.8042 (tttm) cc_final: 0.7739 (ttpt) REVERT: C 1 MET cc_start: 0.4536 (tpt) cc_final: 0.3526 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1394 time to fit residues: 10.1322 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 : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.0770 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 30 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5318 r_free = 0.5318 target = 0.313353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.274802 restraints weight = 79694.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.277532 restraints weight = 31212.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.276762 restraints weight = 28837.735| |-----------------------------------------------------------------------------| r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5082 moved from start: 0.2133 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= 0.243 Angle : 0.709 11.451 10585 Z= 0.383 Chirality : 0.037 0.169 1227 Planarity : 0.006 0.067 871 Dihedral : 29.685 175.948 2143 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.80 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.33), residues: 551 helix: -2.19 (0.62), residues: 70 sheet: -3.74 (0.66), residues: 36 loop : -2.84 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.002 HIS A 49 PHE 0.019 0.002 PHE C 17 TYR 0.019 0.002 TYR D 60 ARG 0.003 0.000 ARG D 6 *********************** 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 50 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.529 Fit side-chains REVERT: B 12 LYS cc_start: 0.8230 (tttm) cc_final: 0.7887 (ttpt) REVERT: C 1 MET cc_start: 0.4531 (tpt) cc_final: 0.3370 (tpt) REVERT: D 1 MET cc_start: 0.4847 (tpt) cc_final: 0.3231 (tpt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1296 time to fit residues: 9.9208 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 : 0.553 ------------------------------------------------------------------------------- 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: 0.0970 chunk 54 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.0020 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5348 r_free = 0.5348 target = 0.318703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.280348 restraints weight = 81999.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.284751 restraints weight = 36172.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.283895 restraints weight = 28522.591| |-----------------------------------------------------------------------------| r_work (final): 0.4879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4543 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7399 Z= 0.187 Angle : 0.685 10.956 10585 Z= 0.369 Chirality : 0.036 0.158 1227 Planarity : 0.006 0.069 871 Dihedral : 29.613 175.235 2143 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.43 % Favored : 88.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.33), residues: 551 helix: -2.11 (0.61), residues: 69 sheet: -2.95 (1.60), residues: 6 loop : -2.78 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 47 PHE 0.014 0.001 PHE C 62 TYR 0.021 0.002 TYR C 4 ARG 0.003 0.000 ARG D 99 *********************** 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 49 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.552 Fit side-chains REVERT: B 12 LYS cc_start: 0.8118 (tttm) cc_final: 0.7881 (ttpt) REVERT: C 1 MET cc_start: 0.4459 (tpt) cc_final: 0.3659 (tpt) REVERT: D 1 MET cc_start: 0.4449 (tpt) cc_final: 0.3108 (tpt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1412 time to fit residues: 10.3702 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 : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 36 optimal weight: 0.0770 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5321 r_free = 0.5321 target = 0.313834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.273325 restraints weight = 81430.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.277635 restraints weight = 37148.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.276624 restraints weight = 30415.213| |-----------------------------------------------------------------------------| r_work (final): 0.4823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7399 Z= 0.213 Angle : 0.692 10.935 10585 Z= 0.371 Chirality : 0.036 0.155 1227 Planarity : 0.006 0.072 871 Dihedral : 29.581 175.687 2143 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.98 % Favored : 87.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.33), residues: 551 helix: -2.09 (0.62), residues: 69 sheet: -2.68 (0.88), residues: 24 loop : -2.81 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 49 PHE 0.017 0.002 PHE D 17 TYR 0.014 0.002 TYR C 4 ARG 0.004 0.000 ARG B 99 *********************** 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 : 0.555 Fit side-chains REVERT: B 12 LYS cc_start: 0.8062 (tttm) cc_final: 0.7803 (ttpt) REVERT: C 1 MET cc_start: 0.4588 (tpt) cc_final: 0.3497 (tpt) REVERT: D 1 MET cc_start: 0.4736 (tpt) cc_final: 0.3329 (tpt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1392 time to fit residues: 9.4972 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 : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 38 optimal weight: 0.0050 chunk 30 optimal weight: 0.0470 chunk 44 optimal weight: 0.0870 chunk 66 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 overall best weight: 0.5872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5341 r_free = 0.5341 target = 0.317003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.278142 restraints weight = 79388.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4992 r_free = 0.4992 target = 0.281622 restraints weight = 35008.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.280981 restraints weight = 29413.665| |-----------------------------------------------------------------------------| r_work (final): 0.4848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4624 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 : 0.004 0.058 7399 Z= 0.210 Angle : 0.682 11.067 10585 Z= 0.367 Chirality : 0.036 0.156 1227 Planarity : 0.006 0.072 871 Dihedral : 29.540 175.693 2143 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.25 % Favored : 88.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.33), residues: 551 helix: -2.10 (0.63), residues: 69 sheet: -2.77 (0.98), residues: 18 loop : -2.79 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 49 PHE 0.019 0.002 PHE C 26 TYR 0.015 0.002 TYR C 4 ARG 0.003 0.000 ARG B 95 *********************** 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 42 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.603 Fit side-chains REVERT: B 12 LYS cc_start: 0.7999 (tttm) cc_final: 0.7736 (ttpt) REVERT: C 1 MET cc_start: 0.4469 (tpt) cc_final: 0.3395 (tpt) REVERT: D 1 MET cc_start: 0.4712 (tpt) cc_final: 0.3321 (tpt) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1391 time to fit residues: 9.1030 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 : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5319 r_free = 0.5319 target = 0.314180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.262807 restraints weight = 80505.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.268274 restraints weight = 34550.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.267407 restraints weight = 27621.299| |-----------------------------------------------------------------------------| r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5112 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7399 Z= 0.255 Angle : 0.723 11.560 10585 Z= 0.385 Chirality : 0.038 0.175 1227 Planarity : 0.006 0.072 871 Dihedral : 29.502 176.559 2143 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.16 % Favored : 85.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.34), residues: 551 helix: -2.22 (0.62), residues: 70 sheet: -2.90 (0.87), residues: 24 loop : -2.85 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 47 PHE 0.037 0.003 PHE C 26 TYR 0.018 0.002 TYR C 4 ARG 0.003 0.000 ARG B 99 ********************** 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 43 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.674 Fit side-chains REVERT: B 12 LYS cc_start: 0.8242 (tttm) cc_final: 0.7895 (ttpt) REVERT: C 1 MET cc_start: 0.4653 (tpt) cc_final: 0.3546 (tpt) REVERT: D 1 MET cc_start: 0.4967 (tpt) cc_final: 0.3278 (tpt) REVERT: D 2 ILE cc_start: 0.6262 (mt) cc_final: 0.5379 (pt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1464 time to fit residues: 9.6180 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 : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.0060 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 0.0070 chunk 3 optimal weight: 0.0980 chunk 38 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5366 r_free = 0.5366 target = 0.320644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.274965 restraints weight = 82130.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.281606 restraints weight = 33226.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.278823 restraints weight = 29816.129| |-----------------------------------------------------------------------------| r_work (final): 0.4713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7399 Z= 0.193 Angle : 0.680 11.397 10585 Z= 0.365 Chirality : 0.036 0.153 1227 Planarity : 0.006 0.072 871 Dihedral : 29.431 175.727 2143 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.71 % Favored : 89.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.34), residues: 551 helix: -2.03 (0.64), residues: 69 sheet: -2.92 (1.43), residues: 6 loop : -2.78 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 47 PHE 0.020 0.002 PHE C 26 TYR 0.014 0.002 TYR C 4 ARG 0.003 0.000 ARG D 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.23 seconds wall clock time: 37 minutes 27.18 seconds (2247.18 seconds total)