Starting phenix.real_space_refine on Wed Sep 17 21:27:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k42_62040/09_2025/9k42_62040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k42_62040/09_2025/9k42_62040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k42_62040/09_2025/9k42_62040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k42_62040/09_2025/9k42_62040.map" model { file = "/net/cci-nas-00/data/ceres_data/9k42_62040/09_2025/9k42_62040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k42_62040/09_2025/9k42_62040.cif" } resolution = 3.14 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= 0.043 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 289 5.49 5 S 12 5.16 5 C 6552 2.51 5 N 2191 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11824 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2985 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 3.30, per 1000 atoms: 0.28 Number of scatterers: 11824 At special positions: 0 Unit cell: (88.976, 120.064, 114.704, 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 12 16.00 P 289 15.00 O 2780 8.00 N 2191 7.00 C 6552 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: 1.10 Conformation dependent library (CDL) restraints added in 459.6 milliseconds Enol-peptide restraints added in 1.4 microseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 75.1% alpha, 2.7% beta 126 base pairs and 278 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.596A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.859A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.571A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 46 through 75 removed outlier: 4.584A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 60 through 72 Processing helix chain 'D' and resid 78 through 108 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 126 through 146 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.560A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.882A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.501A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.059A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.384A pdb=" N ARG C 43 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.894A pdb=" N THR C 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.840A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.258A pdb=" N ARG G 43 " --> pdb=" O ILE H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 417 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 320 hydrogen bonds 640 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 278 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2717 1.34 - 1.45: 3756 1.45 - 1.57: 5557 1.57 - 1.69: 577 1.69 - 1.81: 22 Bond restraints: 12629 Sorted by residual: bond pdb=" CA VAL G 80 " pdb=" CB VAL G 80 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 9.63e-01 bond pdb=" C SER G 19 " pdb=" O SER G 19 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.15e-02 7.56e+03 9.59e-01 bond pdb=" O3' DG J 27 " pdb=" P DA J 28 " ideal model delta sigma weight residual 1.607 1.592 0.015 1.50e-02 4.44e+03 9.57e-01 bond pdb=" CA LYS C 75 " pdb=" CB LYS C 75 " ideal model delta sigma weight residual 1.531 1.545 -0.014 1.45e-02 4.76e+03 9.36e-01 bond pdb=" O3' DC I -56 " pdb=" P DG I -55 " ideal model delta sigma weight residual 1.607 1.593 0.014 1.50e-02 4.44e+03 8.63e-01 ... (remaining 12624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 17678 2.04 - 4.09: 554 4.09 - 6.13: 59 6.13 - 8.17: 9 8.17 - 10.22: 3 Bond angle restraints: 18303 Sorted by residual: angle pdb=" O3' DG I 54 " pdb=" C3' DG I 54 " pdb=" C2' DG I 54 " ideal model delta sigma weight residual 111.50 101.28 10.22 1.50e+00 4.44e-01 4.64e+01 angle pdb=" O3' DT J -17 " pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 111.50 102.85 8.65 1.50e+00 4.44e-01 3.33e+01 angle pdb=" O3' DG I 26 " pdb=" C3' DG I 26 " pdb=" C2' DG I 26 " ideal model delta sigma weight residual 111.50 103.91 7.59 1.50e+00 4.44e-01 2.56e+01 angle pdb=" O3' DT J 14 " pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 111.50 104.42 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" O3' DG I 25 " pdb=" C3' DG I 25 " pdb=" C2' DG I 25 " ideal model delta sigma weight residual 111.50 104.51 6.99 1.50e+00 4.44e-01 2.17e+01 ... (remaining 18298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 3992 18.09 - 36.18: 997 36.18 - 54.26: 1393 54.26 - 72.35: 430 72.35 - 90.44: 27 Dihedral angle restraints: 6839 sinusoidal: 4681 harmonic: 2158 Sorted by residual: dihedral pdb=" CA ASN B 64 " pdb=" CB ASN B 64 " pdb=" CG ASN B 64 " pdb=" OD1 ASN B 64 " ideal model delta sinusoidal sigma weight residual 120.00 -165.78 -74.22 2 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU D 99 " pdb=" CG GLU D 99 " pdb=" CD GLU D 99 " pdb=" OE1 GLU D 99 " ideal model delta sinusoidal sigma weight residual 0.00 -90.44 90.44 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " pdb=" CD GLU C 65 " pdb=" OE1 GLU C 65 " ideal model delta sinusoidal sigma weight residual 0.00 89.99 -89.99 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 6836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1591 0.057 - 0.114: 384 0.114 - 0.172: 89 0.172 - 0.229: 23 0.229 - 0.286: 2 Chirality restraints: 2089 Sorted by residual: chirality pdb=" C3' DG I 54 " pdb=" C4' DG I 54 " pdb=" O3' DG I 54 " pdb=" C2' DG I 54 " both_signs ideal model delta sigma weight residual False -2.66 -2.95 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' DG J 4 " pdb=" C4' DG J 4 " pdb=" O3' DG J 4 " pdb=" C2' DG J 4 " both_signs ideal model delta sigma weight residual False -2.66 -2.89 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C3' DG I -7 " pdb=" C4' DG I -7 " pdb=" O3' DG I -7 " pdb=" C2' DG I -7 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2086 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 43 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO E 43 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 125 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO D 126 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " 0.026 5.00e-02 4.00e+02 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 157 2.62 - 3.19: 8833 3.19 - 3.76: 21959 3.76 - 4.33: 31580 4.33 - 4.90: 43083 Nonbonded interactions: 105612 Sorted by model distance: nonbonded pdb=" C2' DG I 11 " pdb=" O5' DT I 12 " model vdw 2.050 3.440 nonbonded pdb=" OG1 THR D 59 " pdb=" OD1 ASN D 86 " model vdw 2.273 3.040 nonbonded pdb=" O THR D 142 " pdb=" OG SER D 146 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU H 94 " pdb=" NE2 GLN H 98 " model vdw 2.282 3.120 nonbonded pdb=" NH1 ARG F 92 " pdb=" OE1 GLU H 99 " model vdw 2.289 3.120 ... (remaining 105607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.270 Find NCS groups from input model: 0.110 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 0.027 12629 Z= 0.256 Angle : 0.840 10.218 18303 Z= 0.532 Chirality : 0.055 0.286 2089 Planarity : 0.005 0.054 1310 Dihedral : 31.947 90.437 5443 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.49 % Allowed : 13.27 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.30), residues: 730 helix: 2.17 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.15 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 30 TYR 0.018 0.002 TYR B 98 PHE 0.007 0.001 PHE E 67 HIS 0.004 0.001 HIS H 132 Details of bonding type rmsd covalent geometry : bond 0.00580 (12629) covalent geometry : angle 0.84001 (18303) hydrogen bonds : bond 0.15768 ( 737) hydrogen bonds : angle 9.50804 ( 1867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8169 (m-10) cc_final: 0.7154 (m-80) REVERT: F 88 TYR cc_start: 0.8177 (m-10) cc_final: 0.7359 (m-80) REVERT: H 74 ASP cc_start: 0.7813 (p0) cc_final: 0.7497 (p0) outliers start: 3 outliers final: 2 residues processed: 202 average time/residue: 0.1527 time to fit residues: 40.9989 Evaluate side-chains 155 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain F residue 23 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN C 74 ASN C 85 GLN E 39 HIS E 108 ASN G 25 GLN G 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.073834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.051565 restraints weight = 54260.762| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.68 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12629 Z= 0.227 Angle : 0.637 8.141 18303 Z= 0.379 Chirality : 0.038 0.137 2089 Planarity : 0.005 0.049 1310 Dihedral : 33.874 97.608 3984 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.24 % Allowed : 17.80 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.30), residues: 730 helix: 2.52 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.28 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 43 TYR 0.018 0.002 TYR B 98 PHE 0.013 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00502 (12629) covalent geometry : angle 0.63660 (18303) hydrogen bonds : bond 0.05189 ( 737) hydrogen bonds : angle 3.30008 ( 1867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8639 (tm-30) REVERT: C 74 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8538 (t0) REVERT: D 82 MET cc_start: 0.9259 (tpp) cc_final: 0.8989 (tpp) REVERT: D 91 ASP cc_start: 0.9014 (t0) cc_final: 0.8805 (t0) REVERT: D 116 GLU cc_start: 0.8710 (mp0) cc_final: 0.8285 (mp0) REVERT: E 42 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7739 (ttm-80) REVERT: E 58 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9293 (t) REVERT: E 73 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8574 (tt0) REVERT: H 74 ASP cc_start: 0.9049 (p0) cc_final: 0.8659 (p0) REVERT: H 91 ASP cc_start: 0.8981 (t0) cc_final: 0.8733 (t0) REVERT: H 94 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8519 (mm-30) REVERT: H 98 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8874 (mm110) REVERT: H 116 GLU cc_start: 0.8615 (mp0) cc_final: 0.8064 (mp0) REVERT: H 145 THR cc_start: 0.9631 (OUTLIER) cc_final: 0.9404 (p) outliers start: 20 outliers final: 14 residues processed: 184 average time/residue: 0.1353 time to fit residues: 34.1045 Evaluate side-chains 174 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 145 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 56 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.070605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.047581 restraints weight = 53546.878| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.70 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12629 Z= 0.236 Angle : 0.594 7.013 18303 Z= 0.357 Chirality : 0.036 0.148 2089 Planarity : 0.004 0.046 1310 Dihedral : 33.125 90.335 3980 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.53 % Allowed : 16.83 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.04 (0.31), residues: 730 helix: 2.65 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.01 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 30 TYR 0.014 0.002 TYR B 98 PHE 0.010 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00524 (12629) covalent geometry : angle 0.59439 (18303) hydrogen bonds : bond 0.04464 ( 737) hydrogen bonds : angle 3.23414 ( 1867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8562 (m-80) cc_final: 0.8335 (m-80) REVERT: A 54 TYR cc_start: 0.8736 (m-80) cc_final: 0.8387 (m-80) REVERT: A 58 THR cc_start: 0.9462 (OUTLIER) cc_final: 0.9192 (t) REVERT: A 73 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8612 (tt0) REVERT: B 22 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6642 (mt) REVERT: B 88 TYR cc_start: 0.9306 (m-10) cc_final: 0.9057 (m-80) REVERT: B 96 THR cc_start: 0.9388 (m) cc_final: 0.9020 (p) REVERT: C 92 GLU cc_start: 0.8902 (tp30) cc_final: 0.8237 (tp30) REVERT: C 95 SER cc_start: 0.9536 (t) cc_final: 0.9316 (p) REVERT: C 96 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8409 (mmmt) REVERT: C 109 MET cc_start: 0.6985 (mmm) cc_final: 0.6480 (mpp) REVERT: D 56 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8045 (t0) REVERT: D 91 ASP cc_start: 0.9037 (t0) cc_final: 0.8816 (t0) REVERT: D 94 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8181 (tp30) REVERT: D 98 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8748 (mm-40) REVERT: D 116 GLU cc_start: 0.8741 (mp0) cc_final: 0.8185 (mp0) REVERT: D 136 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8355 (mm-30) REVERT: E 42 ARG cc_start: 0.8167 (mtp180) cc_final: 0.7748 (ttm-80) REVERT: E 54 TYR cc_start: 0.8667 (m-80) cc_final: 0.8430 (m-80) REVERT: E 58 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9163 (t) REVERT: E 73 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8730 (tm-30) REVERT: F 27 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8894 (mp10) REVERT: G 57 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: G 91 ASP cc_start: 0.8794 (t0) cc_final: 0.8494 (t70) REVERT: G 93 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8621 (mm-30) REVERT: H 58 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7904 (mm-30) REVERT: H 74 ASP cc_start: 0.9179 (p0) cc_final: 0.8849 (p0) REVERT: H 82 MET cc_start: 0.9254 (tpp) cc_final: 0.8934 (tpp) REVERT: H 84 ILE cc_start: 0.9556 (mt) cc_final: 0.9354 (mt) REVERT: H 91 ASP cc_start: 0.8949 (t0) cc_final: 0.8673 (t0) REVERT: H 94 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8426 (tp30) REVERT: H 98 GLN cc_start: 0.9326 (mm-40) cc_final: 0.8876 (mm110) REVERT: H 116 GLU cc_start: 0.8685 (mp0) cc_final: 0.8176 (mp0) REVERT: H 145 THR cc_start: 0.9603 (OUTLIER) cc_final: 0.9315 (p) outliers start: 28 outliers final: 13 residues processed: 183 average time/residue: 0.1401 time to fit residues: 34.9043 Evaluate side-chains 175 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 145 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.070451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.048124 restraints weight = 53144.928| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.72 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12629 Z= 0.178 Angle : 0.553 8.696 18303 Z= 0.333 Chirality : 0.034 0.156 2089 Planarity : 0.004 0.045 1310 Dihedral : 32.693 95.351 3980 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.91 % Allowed : 19.26 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.32 (0.31), residues: 730 helix: 2.85 (0.22), residues: 550 sheet: None (None), residues: 0 loop : 0.09 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 89 TYR 0.012 0.002 TYR C 58 PHE 0.011 0.001 PHE A 67 HIS 0.005 0.001 HIS D 132 Details of bonding type rmsd covalent geometry : bond 0.00391 (12629) covalent geometry : angle 0.55343 (18303) hydrogen bonds : bond 0.03761 ( 737) hydrogen bonds : angle 3.01682 ( 1867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8628 (tt0) REVERT: B 22 LEU cc_start: 0.6815 (mt) cc_final: 0.6482 (mt) REVERT: B 96 THR cc_start: 0.9380 (m) cc_final: 0.9046 (p) REVERT: C 95 SER cc_start: 0.9586 (t) cc_final: 0.9364 (p) REVERT: D 56 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8231 (t0) REVERT: D 91 ASP cc_start: 0.9053 (t0) cc_final: 0.8803 (t0) REVERT: D 94 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8456 (tp30) REVERT: D 98 GLN cc_start: 0.9312 (mm-40) cc_final: 0.9060 (mm-40) REVERT: D 116 GLU cc_start: 0.8740 (mp0) cc_final: 0.8092 (mp0) REVERT: D 136 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8350 (mm-30) REVERT: E 42 ARG cc_start: 0.8219 (mtp180) cc_final: 0.8001 (mtp85) REVERT: E 73 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8613 (tt0) REVERT: F 22 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6822 (mt) REVERT: G 91 ASP cc_start: 0.8723 (t0) cc_final: 0.8482 (t70) REVERT: G 93 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8503 (mm-30) REVERT: H 58 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7941 (mm-30) REVERT: H 74 ASP cc_start: 0.9142 (p0) cc_final: 0.8821 (p0) REVERT: H 91 ASP cc_start: 0.8945 (t0) cc_final: 0.8699 (t0) REVERT: H 94 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8282 (tp30) REVERT: H 98 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8841 (mm-40) REVERT: H 106 TYR cc_start: 0.8330 (m-10) cc_final: 0.8098 (m-80) REVERT: H 116 GLU cc_start: 0.8686 (mp0) cc_final: 0.8176 (mp0) outliers start: 18 outliers final: 11 residues processed: 185 average time/residue: 0.1397 time to fit residues: 34.9967 Evaluate side-chains 170 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS D 56 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.069779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047903 restraints weight = 53376.832| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.61 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12629 Z= 0.167 Angle : 0.556 9.011 18303 Z= 0.332 Chirality : 0.033 0.166 2089 Planarity : 0.004 0.045 1310 Dihedral : 32.290 90.775 3979 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.75 % Allowed : 20.23 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.40 (0.31), residues: 730 helix: 2.90 (0.22), residues: 550 sheet: None (None), residues: 0 loop : 0.12 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 89 TYR 0.012 0.002 TYR H 63 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00366 (12629) covalent geometry : angle 0.55560 (18303) hydrogen bonds : bond 0.03628 ( 737) hydrogen bonds : angle 2.98948 ( 1867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8674 (m-80) cc_final: 0.8453 (m-80) REVERT: A 73 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8525 (tt0) REVERT: B 22 LEU cc_start: 0.6884 (mt) cc_final: 0.6610 (mt) REVERT: B 88 TYR cc_start: 0.9242 (m-80) cc_final: 0.8930 (m-80) REVERT: B 96 THR cc_start: 0.9384 (m) cc_final: 0.9157 (p) REVERT: C 93 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8043 (mt-10) REVERT: C 95 SER cc_start: 0.9469 (t) cc_final: 0.9257 (p) REVERT: D 91 ASP cc_start: 0.9045 (t0) cc_final: 0.8780 (t0) REVERT: D 94 GLU cc_start: 0.8818 (mm-30) cc_final: 0.7925 (tp30) REVERT: D 98 GLN cc_start: 0.9330 (mm-40) cc_final: 0.8718 (mm-40) REVERT: D 116 GLU cc_start: 0.8675 (mp0) cc_final: 0.8103 (mp0) REVERT: D 136 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8271 (mm-30) REVERT: E 42 ARG cc_start: 0.8268 (mtp180) cc_final: 0.8061 (mtp85) REVERT: E 54 TYR cc_start: 0.8605 (m-80) cc_final: 0.8395 (m-80) REVERT: E 73 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8467 (tt0) REVERT: F 22 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6906 (mt) REVERT: G 57 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8609 (tt0) REVERT: G 91 ASP cc_start: 0.8687 (t0) cc_final: 0.8332 (t0) REVERT: G 93 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8490 (mm-30) REVERT: H 58 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7947 (mm-30) REVERT: H 74 ASP cc_start: 0.9097 (p0) cc_final: 0.8744 (p0) REVERT: H 82 MET cc_start: 0.9159 (tpp) cc_final: 0.8922 (tpp) REVERT: H 91 ASP cc_start: 0.8970 (t0) cc_final: 0.8728 (t0) REVERT: H 94 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8256 (tp30) REVERT: H 98 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8814 (mm-40) REVERT: H 116 GLU cc_start: 0.8691 (mp0) cc_final: 0.8114 (mp0) outliers start: 17 outliers final: 9 residues processed: 182 average time/residue: 0.1410 time to fit residues: 34.7335 Evaluate side-chains 171 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** 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 = 0.3512 r_free = 0.3512 target = 0.067650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045143 restraints weight = 54849.331| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.73 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 12629 Z= 0.259 Angle : 0.607 9.982 18303 Z= 0.359 Chirality : 0.036 0.177 2089 Planarity : 0.004 0.045 1310 Dihedral : 32.457 94.897 3979 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.24 % Allowed : 22.01 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.31), residues: 730 helix: 2.73 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.06 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 89 TYR 0.035 0.002 TYR H 106 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00579 (12629) covalent geometry : angle 0.60707 (18303) hydrogen bonds : bond 0.04660 ( 737) hydrogen bonds : angle 3.23246 ( 1867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8564 (tt0) REVERT: A 97 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 96 THR cc_start: 0.9367 (m) cc_final: 0.8981 (p) REVERT: C 85 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8344 (tm-30) REVERT: D 91 ASP cc_start: 0.9060 (t0) cc_final: 0.8762 (t0) REVERT: D 94 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8265 (tp30) REVERT: D 98 GLN cc_start: 0.9325 (mm-40) cc_final: 0.9000 (mm-40) REVERT: D 116 GLU cc_start: 0.8866 (mp0) cc_final: 0.8124 (mp0) REVERT: D 136 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8293 (mm-30) REVERT: E 42 ARG cc_start: 0.8179 (mtp180) cc_final: 0.7973 (mtp85) REVERT: E 73 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8491 (tt0) REVERT: G 57 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: G 85 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: G 91 ASP cc_start: 0.8774 (t0) cc_final: 0.8395 (t0) REVERT: G 93 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8561 (mm-30) REVERT: H 56 ASN cc_start: 0.8607 (m-40) cc_final: 0.8043 (t0) REVERT: H 58 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7922 (mm-30) REVERT: H 74 ASP cc_start: 0.9131 (p0) cc_final: 0.8801 (p0) REVERT: H 91 ASP cc_start: 0.8990 (t0) cc_final: 0.8705 (t0) REVERT: H 94 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8518 (tp30) REVERT: H 98 GLN cc_start: 0.9268 (mm-40) cc_final: 0.9002 (mm110) REVERT: H 106 TYR cc_start: 0.8247 (m-10) cc_final: 0.7886 (m-80) REVERT: H 116 GLU cc_start: 0.8819 (mp0) cc_final: 0.8147 (mp0) outliers start: 20 outliers final: 10 residues processed: 176 average time/residue: 0.1453 time to fit residues: 34.7416 Evaluate side-chains 161 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** 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 = 0.3535 r_free = 0.3535 target = 0.067638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.045692 restraints weight = 54891.613| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.63 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12629 Z= 0.196 Angle : 0.586 10.649 18303 Z= 0.345 Chirality : 0.035 0.179 2089 Planarity : 0.004 0.046 1310 Dihedral : 32.194 94.220 3979 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.43 % Allowed : 23.14 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.20 (0.31), residues: 730 helix: 2.79 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.08 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 89 TYR 0.024 0.002 TYR H 106 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00438 (12629) covalent geometry : angle 0.58580 (18303) hydrogen bonds : bond 0.03904 ( 737) hydrogen bonds : angle 3.06050 ( 1867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8563 (tt0) REVERT: B 96 THR cc_start: 0.9377 (m) cc_final: 0.9021 (p) REVERT: C 36 LYS cc_start: 0.9561 (mmtm) cc_final: 0.9335 (mmtt) REVERT: C 85 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8420 (tm-30) REVERT: D 91 ASP cc_start: 0.9026 (t0) cc_final: 0.8752 (t0) REVERT: D 94 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8232 (tp30) REVERT: D 98 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8966 (mm-40) REVERT: D 116 GLU cc_start: 0.8763 (mp0) cc_final: 0.8065 (mp0) REVERT: D 136 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8313 (mm-30) REVERT: E 73 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8532 (tt0) REVERT: F 88 TYR cc_start: 0.9189 (m-80) cc_final: 0.8388 (m-80) REVERT: G 57 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: G 91 ASP cc_start: 0.8681 (t0) cc_final: 0.8338 (t0) REVERT: G 93 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8572 (mm-30) REVERT: H 56 ASN cc_start: 0.8687 (m-40) cc_final: 0.8131 (t0) REVERT: H 74 ASP cc_start: 0.9085 (p0) cc_final: 0.8742 (p0) REVERT: H 82 MET cc_start: 0.9116 (tpp) cc_final: 0.8890 (tpp) REVERT: H 91 ASP cc_start: 0.8948 (t0) cc_final: 0.8713 (t0) REVERT: H 94 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8514 (tp30) REVERT: H 98 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8959 (mm110) REVERT: H 106 TYR cc_start: 0.8197 (m-10) cc_final: 0.7774 (m-80) REVERT: H 116 GLU cc_start: 0.8728 (mp0) cc_final: 0.8083 (mp0) outliers start: 15 outliers final: 10 residues processed: 170 average time/residue: 0.1351 time to fit residues: 31.5278 Evaluate side-chains 164 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 0.0670 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.067390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.045541 restraints weight = 54504.214| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.63 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12629 Z= 0.200 Angle : 0.590 10.669 18303 Z= 0.348 Chirality : 0.035 0.173 2089 Planarity : 0.004 0.045 1310 Dihedral : 32.124 94.409 3979 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.43 % Allowed : 22.82 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.16 (0.31), residues: 730 helix: 2.71 (0.22), residues: 556 sheet: None (None), residues: 0 loop : 0.01 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 89 TYR 0.019 0.002 TYR H 106 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00450 (12629) covalent geometry : angle 0.58976 (18303) hydrogen bonds : bond 0.03991 ( 737) hydrogen bonds : angle 3.10150 ( 1867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8595 (tt0) REVERT: B 88 TYR cc_start: 0.9214 (m-80) cc_final: 0.8971 (m-80) REVERT: B 96 THR cc_start: 0.9383 (m) cc_final: 0.9023 (p) REVERT: C 36 LYS cc_start: 0.9459 (mmtm) cc_final: 0.9245 (mmtt) REVERT: C 85 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: D 91 ASP cc_start: 0.9036 (t0) cc_final: 0.8743 (t0) REVERT: D 94 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8244 (tp30) REVERT: D 98 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8955 (mm-40) REVERT: D 116 GLU cc_start: 0.8734 (mp0) cc_final: 0.8016 (mp0) REVERT: D 136 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8387 (mm-30) REVERT: E 40 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5588 (ttt-90) REVERT: E 54 TYR cc_start: 0.8599 (m-80) cc_final: 0.8292 (m-80) REVERT: E 73 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8538 (tt0) REVERT: F 88 TYR cc_start: 0.9232 (m-80) cc_final: 0.8995 (m-80) REVERT: G 57 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: G 85 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8575 (tm-30) REVERT: G 91 ASP cc_start: 0.8667 (t0) cc_final: 0.8296 (t0) REVERT: G 93 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8551 (mm-30) REVERT: H 56 ASN cc_start: 0.8698 (m-40) cc_final: 0.8222 (t0) REVERT: H 58 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8255 (mm-30) REVERT: H 74 ASP cc_start: 0.9075 (p0) cc_final: 0.8778 (p0) REVERT: H 82 MET cc_start: 0.9104 (tpp) cc_final: 0.8866 (tpp) REVERT: H 91 ASP cc_start: 0.8953 (t0) cc_final: 0.8706 (t0) REVERT: H 94 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8511 (tp30) REVERT: H 98 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8974 (mm110) REVERT: H 116 GLU cc_start: 0.8743 (mp0) cc_final: 0.8139 (mp0) outliers start: 15 outliers final: 10 residues processed: 170 average time/residue: 0.1413 time to fit residues: 32.6906 Evaluate side-chains 167 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN C 105 ASN D 98 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.068388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.046793 restraints weight = 53893.697| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.52 r_work: 0.2716 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12629 Z= 0.160 Angle : 0.584 11.316 18303 Z= 0.341 Chirality : 0.034 0.181 2089 Planarity : 0.004 0.046 1310 Dihedral : 31.977 93.173 3979 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.10 % Allowed : 23.95 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.33 (0.31), residues: 730 helix: 2.89 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.04 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 89 TYR 0.018 0.002 TYR H 106 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00355 (12629) covalent geometry : angle 0.58362 (18303) hydrogen bonds : bond 0.03485 ( 737) hydrogen bonds : angle 3.00917 ( 1867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 THR cc_start: 0.9428 (m) cc_final: 0.9157 (p) REVERT: C 36 LYS cc_start: 0.9430 (mmtm) cc_final: 0.9202 (mmtt) REVERT: C 85 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8700 (tm-30) REVERT: D 91 ASP cc_start: 0.9162 (t0) cc_final: 0.8923 (t0) REVERT: D 94 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8465 (tp30) REVERT: D 98 GLN cc_start: 0.9352 (mm110) cc_final: 0.9022 (mm-40) REVERT: D 116 GLU cc_start: 0.8952 (mp0) cc_final: 0.8368 (mp0) REVERT: D 136 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8719 (mm-30) REVERT: E 73 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8859 (tt0) REVERT: F 88 TYR cc_start: 0.9403 (m-80) cc_final: 0.9148 (m-80) REVERT: G 57 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8963 (tt0) REVERT: G 91 ASP cc_start: 0.8476 (t0) cc_final: 0.8257 (t0) REVERT: G 93 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8522 (mm-30) REVERT: H 56 ASN cc_start: 0.8743 (m-40) cc_final: 0.8230 (t0) REVERT: H 58 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8212 (mm-30) REVERT: H 74 ASP cc_start: 0.9122 (p0) cc_final: 0.8793 (p0) REVERT: H 82 MET cc_start: 0.9185 (tpp) cc_final: 0.8949 (tpp) REVERT: H 91 ASP cc_start: 0.9050 (t0) cc_final: 0.8848 (t0) REVERT: H 94 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8579 (tp30) REVERT: H 98 GLN cc_start: 0.9337 (mm-40) cc_final: 0.8989 (mm-40) REVERT: H 116 GLU cc_start: 0.9023 (mp0) cc_final: 0.8473 (mp0) REVERT: H 146 SER cc_start: 0.9190 (m) cc_final: 0.8853 (p) outliers start: 13 outliers final: 9 residues processed: 170 average time/residue: 0.1428 time to fit residues: 32.9584 Evaluate side-chains 168 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.067244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.045295 restraints weight = 53877.192| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.63 r_work: 0.2645 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12629 Z= 0.202 Angle : 0.601 11.257 18303 Z= 0.352 Chirality : 0.035 0.186 2089 Planarity : 0.004 0.045 1310 Dihedral : 32.018 93.747 3979 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.78 % Allowed : 24.60 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.22 (0.31), residues: 730 helix: 2.76 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.03 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 89 TYR 0.023 0.002 TYR H 106 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00452 (12629) covalent geometry : angle 0.60115 (18303) hydrogen bonds : bond 0.03994 ( 737) hydrogen bonds : angle 3.14866 ( 1867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9395 (m-80) cc_final: 0.8899 (m-80) REVERT: B 96 THR cc_start: 0.9441 (m) cc_final: 0.9128 (p) REVERT: C 36 LYS cc_start: 0.9452 (mmtm) cc_final: 0.9236 (mmtt) REVERT: C 85 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.8691 (tm-30) REVERT: D 91 ASP cc_start: 0.9169 (t0) cc_final: 0.8906 (t0) REVERT: D 94 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8442 (tp30) REVERT: D 98 GLN cc_start: 0.9362 (mm110) cc_final: 0.8924 (mm-40) REVERT: D 106 TYR cc_start: 0.8267 (m-80) cc_final: 0.7768 (m-80) REVERT: D 116 GLU cc_start: 0.9029 (mp0) cc_final: 0.8375 (mp0) REVERT: D 136 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8776 (mm-30) REVERT: E 40 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.5191 (ttt-90) REVERT: E 73 GLU cc_start: 0.9282 (tm-30) cc_final: 0.8907 (tt0) REVERT: G 57 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8959 (tt0) REVERT: G 91 ASP cc_start: 0.8511 (t0) cc_final: 0.8252 (t0) REVERT: G 93 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8483 (mm-30) REVERT: H 56 ASN cc_start: 0.8730 (m-40) cc_final: 0.8231 (t0) REVERT: H 58 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8287 (mm-30) REVERT: H 74 ASP cc_start: 0.9176 (p0) cc_final: 0.8827 (p0) REVERT: H 91 ASP cc_start: 0.9088 (t0) cc_final: 0.8843 (t0) REVERT: H 94 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8872 (tp30) REVERT: H 106 TYR cc_start: 0.8188 (m-10) cc_final: 0.7973 (m-80) REVERT: H 116 GLU cc_start: 0.9042 (mp0) cc_final: 0.8444 (mp0) outliers start: 11 outliers final: 8 residues processed: 162 average time/residue: 0.1408 time to fit residues: 30.8984 Evaluate side-chains 161 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.068497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047625 restraints weight = 53897.049| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.48 r_work: 0.2735 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12629 Z= 0.155 Angle : 0.597 11.489 18303 Z= 0.347 Chirality : 0.034 0.209 2089 Planarity : 0.004 0.045 1310 Dihedral : 31.830 92.355 3979 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 25.73 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.32 (0.31), residues: 730 helix: 2.81 (0.22), residues: 556 sheet: None (None), residues: 0 loop : 0.10 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 89 TYR 0.023 0.002 TYR H 106 PHE 0.011 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00341 (12629) covalent geometry : angle 0.59738 (18303) hydrogen bonds : bond 0.03423 ( 737) hydrogen bonds : angle 3.03690 ( 1867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2862.90 seconds wall clock time: 49 minutes 53.50 seconds (2993.50 seconds total)