Starting phenix.real_space_refine on Tue Mar 3 12:26:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lkf_23405/03_2026/7lkf_23405.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lkf_23405/03_2026/7lkf_23405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lkf_23405/03_2026/7lkf_23405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lkf_23405/03_2026/7lkf_23405.map" model { file = "/net/cci-nas-00/data/ceres_data/7lkf_23405/03_2026/7lkf_23405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lkf_23405/03_2026/7lkf_23405.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 2634 2.51 5 N 710 2.21 5 O 787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4139 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2298 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 22, 'TRANS': 258} Chain breaks: 3 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 854 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.95, per 1000 atoms: 0.23 Number of scatterers: 4139 At special positions: 0 Unit cell: (74.52, 91.8, 95.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 787 8.00 N 710 7.00 C 2634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 667 " Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 124.7 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 25.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.716A pdb=" N ARG A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.899A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.601A pdb=" N TYR A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 697 through 701 removed outlier: 3.513A pdb=" N ALA A 701 " --> pdb=" O PRO A 698 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.777A pdb=" N GLN H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.831A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.301A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.301A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.473A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.748A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1333 1.34 - 1.46: 774 1.46 - 1.57: 2127 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 4243 Sorted by residual: bond pdb=" N GLY A 636 " pdb=" CA GLY A 636 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.49e+00 bond pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.13e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 ... (remaining 4238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 5513 1.39 - 2.77: 200 2.77 - 4.16: 45 4.16 - 5.55: 10 5.55 - 6.94: 1 Bond angle restraints: 5769 Sorted by residual: angle pdb=" CA PRO A 155 " pdb=" N PRO A 155 " pdb=" CD PRO A 155 " ideal model delta sigma weight residual 112.00 107.82 4.18 1.40e+00 5.10e-01 8.91e+00 angle pdb=" CA TYR H 99 " pdb=" CB TYR H 99 " pdb=" CG TYR H 99 " ideal model delta sigma weight residual 113.90 118.96 -5.06 1.80e+00 3.09e-01 7.91e+00 angle pdb=" N ASP H 103 " pdb=" CA ASP H 103 " pdb=" C ASP H 103 " ideal model delta sigma weight residual 113.18 109.67 3.51 1.33e+00 5.65e-01 6.95e+00 angle pdb=" N ASP A 190 " pdb=" CA ASP A 190 " pdb=" C ASP A 190 " ideal model delta sigma weight residual 107.37 112.16 -4.79 2.07e+00 2.33e-01 5.35e+00 angle pdb=" N THR L 51 " pdb=" CA THR L 51 " pdb=" C THR L 51 " ideal model delta sigma weight residual 110.80 115.21 -4.41 2.13e+00 2.20e-01 4.30e+00 ... (remaining 5764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 2362 17.68 - 35.36: 158 35.36 - 53.04: 20 53.04 - 70.72: 9 70.72 - 88.40: 7 Dihedral angle restraints: 2556 sinusoidal: 1060 harmonic: 1496 Sorted by residual: dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 169 " pdb=" CB CYS A 169 " ideal model delta sinusoidal sigma weight residual -86.00 -162.43 76.43 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CA THR L 93 " pdb=" C THR L 93 " pdb=" N LEU L 94 " pdb=" CA LEU L 94 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA PRO A 155 " pdb=" C PRO A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 2553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 550 0.062 - 0.124: 80 0.124 - 0.186: 8 0.186 - 0.248: 0 0.248 - 0.310: 1 Chirality restraints: 639 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 667 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA LEU L 94 " pdb=" N LEU L 94 " pdb=" C LEU L 94 " pdb=" CB LEU L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 636 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 154 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO A 155 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 117 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 118 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 99 " -0.002 2.00e-02 2.50e+03 1.08e-02 2.33e+00 pdb=" CG TYR H 99 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR H 99 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR H 99 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR H 99 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 99 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR H 99 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 99 " -0.001 2.00e-02 2.50e+03 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 56 2.66 - 3.22: 3758 3.22 - 3.78: 5969 3.78 - 4.34: 8951 4.34 - 4.90: 14737 Nonbonded interactions: 33471 Sorted by model distance: nonbonded pdb=" O3 NAG B 1 " pdb=" O7 NAG B 2 " model vdw 2.101 3.040 nonbonded pdb=" O GLY A 87 " pdb=" OH TYR A 674 " model vdw 2.199 3.040 nonbonded pdb=" O ARG A 161 " pdb=" OD1 ASN A 162 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASP L 17 " pdb=" N ARG L 18 " model vdw 2.358 3.120 nonbonded pdb=" O ASN L 31 " pdb=" OG1 THR L 51 " model vdw 2.393 3.040 ... (remaining 33466 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 4248 Z= 0.213 Angle : 0.675 6.936 5781 Z= 0.376 Chirality : 0.047 0.310 639 Planarity : 0.005 0.105 736 Dihedral : 12.764 88.404 1583 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 are not related in a simple way. whole: -0.59 (0.37), residues: 499 helix: 0.37 (0.64), residues: 73 sheet: -0.29 (0.39), residues: 173 loop : -0.59 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 230 TYR 0.022 0.002 TYR H 99 PHE 0.021 0.002 PHE A 97 TRP 0.009 0.001 TRP H 110 HIS 0.004 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 4243) covalent geometry : angle 0.66646 ( 5769) SS BOND : bond 0.00765 ( 3) SS BOND : angle 1.53022 ( 6) hydrogen bonds : bond 0.07942 ( 154) hydrogen bonds : angle 5.57887 ( 384) link_BETA1-4 : bond 0.00955 ( 1) link_BETA1-4 : angle 4.07060 ( 3) link_NAG-ASN : bond 0.00642 ( 1) link_NAG-ASN : angle 1.31730 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.187 Fit side-chains REVERT: A 128 GLU cc_start: 0.7584 (tp30) cc_final: 0.7380 (tp30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.7701 time to fit residues: 65.4168 Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.0770 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 697 HIS H 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.098741 restraints weight = 5244.144| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.34 r_work: 0.2938 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4248 Z= 0.127 Angle : 0.599 6.868 5781 Z= 0.302 Chirality : 0.045 0.158 639 Planarity : 0.004 0.051 736 Dihedral : 5.092 24.844 605 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.10 % Allowed : 10.33 % Favored : 88.57 % 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 are not related in a simple way. whole: -0.27 (0.38), residues: 499 helix: 0.48 (0.65), residues: 73 sheet: -0.17 (0.39), residues: 172 loop : -0.26 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 81 TYR 0.034 0.002 TYR H 99 PHE 0.016 0.001 PHE A 97 TRP 0.008 0.001 TRP L 96 HIS 0.002 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4243) covalent geometry : angle 0.59486 ( 5769) SS BOND : bond 0.00524 ( 3) SS BOND : angle 1.24564 ( 6) hydrogen bonds : bond 0.03137 ( 154) hydrogen bonds : angle 5.06516 ( 384) link_BETA1-4 : bond 0.01148 ( 1) link_BETA1-4 : angle 2.55043 ( 3) link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 0.85090 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.105 Fit side-chains REVERT: A 128 GLU cc_start: 0.7889 (tp30) cc_final: 0.7509 (tp30) REVERT: H 65 GLN cc_start: 0.8499 (mm-40) cc_final: 0.7902 (mm-40) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.7947 time to fit residues: 52.0801 Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.0670 chunk 34 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.128958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.099643 restraints weight = 5155.751| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.48 r_work: 0.2916 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4248 Z= 0.134 Angle : 0.578 6.059 5781 Z= 0.291 Chirality : 0.045 0.164 639 Planarity : 0.004 0.038 736 Dihedral : 4.860 23.365 605 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.54 % Allowed : 13.41 % Favored : 85.05 % 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 are not related in a simple way. whole: -0.17 (0.39), residues: 499 helix: 0.52 (0.65), residues: 73 sheet: -0.19 (0.39), residues: 172 loop : -0.10 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 59 TYR 0.027 0.002 TYR H 99 PHE 0.020 0.001 PHE A 97 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4243) covalent geometry : angle 0.57440 ( 5769) SS BOND : bond 0.00558 ( 3) SS BOND : angle 1.21458 ( 6) hydrogen bonds : bond 0.03080 ( 154) hydrogen bonds : angle 4.91925 ( 384) link_BETA1-4 : bond 0.00809 ( 1) link_BETA1-4 : angle 2.23864 ( 3) link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 0.98204 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.097 Fit side-chains REVERT: A 145 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8090 (mt-10) REVERT: L 45 LYS cc_start: 0.8932 (tttt) cc_final: 0.8716 (tttp) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.7525 time to fit residues: 46.2826 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.0870 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.096931 restraints weight = 5209.604| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.44 r_work: 0.2857 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4248 Z= 0.191 Angle : 0.633 9.622 5781 Z= 0.316 Chirality : 0.047 0.172 639 Planarity : 0.004 0.035 736 Dihedral : 5.004 24.438 605 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.42 % Allowed : 14.51 % Favored : 83.08 % 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 are not related in a simple way. whole: -0.16 (0.39), residues: 499 helix: 0.40 (0.64), residues: 73 sheet: -0.07 (0.39), residues: 166 loop : -0.15 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 81 TYR 0.029 0.002 TYR H 99 PHE 0.025 0.002 PHE A 97 TRP 0.011 0.002 TRP H 47 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 4243) covalent geometry : angle 0.63008 ( 5769) SS BOND : bond 0.00717 ( 3) SS BOND : angle 1.33315 ( 6) hydrogen bonds : bond 0.03406 ( 154) hydrogen bonds : angle 5.01259 ( 384) link_BETA1-4 : bond 0.00764 ( 1) link_BETA1-4 : angle 2.19859 ( 3) link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 0.96073 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.248 Fit side-chains REVERT: L 45 LYS cc_start: 0.8962 (tttt) cc_final: 0.8744 (tttp) outliers start: 11 outliers final: 5 residues processed: 58 average time/residue: 0.7635 time to fit residues: 45.5275 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 19 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.098294 restraints weight = 5152.702| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.53 r_work: 0.2895 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4248 Z= 0.105 Angle : 0.541 7.789 5781 Z= 0.272 Chirality : 0.043 0.167 639 Planarity : 0.004 0.031 736 Dihedral : 4.604 21.045 605 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.42 % Allowed : 14.95 % Favored : 82.64 % 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 are not related in a simple way. whole: 0.03 (0.39), residues: 499 helix: 0.60 (0.66), residues: 73 sheet: 0.02 (0.39), residues: 166 loop : -0.02 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.028 0.001 TYR H 99 PHE 0.011 0.001 PHE A 97 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4243) covalent geometry : angle 0.53827 ( 5769) SS BOND : bond 0.00666 ( 3) SS BOND : angle 1.03062 ( 6) hydrogen bonds : bond 0.02810 ( 154) hydrogen bonds : angle 4.80828 ( 384) link_BETA1-4 : bond 0.00801 ( 1) link_BETA1-4 : angle 2.11131 ( 3) link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 1.08122 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.132 Fit side-chains REVERT: H 46 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: L 45 LYS cc_start: 0.8911 (tttt) cc_final: 0.8701 (tttp) outliers start: 11 outliers final: 6 residues processed: 60 average time/residue: 0.6237 time to fit residues: 38.5622 Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.096740 restraints weight = 5263.103| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.48 r_work: 0.2844 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4248 Z= 0.207 Angle : 0.664 15.381 5781 Z= 0.326 Chirality : 0.047 0.167 639 Planarity : 0.005 0.033 736 Dihedral : 4.978 24.113 605 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.86 % Allowed : 15.60 % Favored : 81.54 % 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 are not related in a simple way. whole: -0.17 (0.39), residues: 499 helix: 0.31 (0.63), residues: 74 sheet: -0.02 (0.40), residues: 166 loop : -0.18 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 161 TYR 0.033 0.002 TYR H 99 PHE 0.022 0.002 PHE A 97 TRP 0.011 0.002 TRP L 96 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 4243) covalent geometry : angle 0.66120 ( 5769) SS BOND : bond 0.00787 ( 3) SS BOND : angle 1.39414 ( 6) hydrogen bonds : bond 0.03492 ( 154) hydrogen bonds : angle 5.03097 ( 384) link_BETA1-4 : bond 0.00793 ( 1) link_BETA1-4 : angle 2.16341 ( 3) link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 0.93774 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.159 Fit side-chains REVERT: L 45 LYS cc_start: 0.8960 (tttt) cc_final: 0.8742 (tttt) outliers start: 13 outliers final: 7 residues processed: 61 average time/residue: 0.6505 time to fit residues: 40.8091 Evaluate side-chains 58 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 7 optimal weight: 0.0030 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.097163 restraints weight = 5338.721| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.57 r_work: 0.2884 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4248 Z= 0.109 Angle : 0.586 15.860 5781 Z= 0.284 Chirality : 0.043 0.168 639 Planarity : 0.004 0.044 736 Dihedral : 4.653 22.252 605 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.76 % Allowed : 16.48 % Favored : 81.76 % 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 are not related in a simple way. whole: 0.03 (0.39), residues: 499 helix: 0.58 (0.66), residues: 73 sheet: 0.04 (0.40), residues: 166 loop : -0.02 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 59 TYR 0.032 0.001 TYR H 99 PHE 0.011 0.001 PHE A 97 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 4243) covalent geometry : angle 0.58258 ( 5769) SS BOND : bond 0.00499 ( 3) SS BOND : angle 1.12111 ( 6) hydrogen bonds : bond 0.02840 ( 154) hydrogen bonds : angle 4.81286 ( 384) link_BETA1-4 : bond 0.00802 ( 1) link_BETA1-4 : angle 2.05429 ( 3) link_NAG-ASN : bond 0.00086 ( 1) link_NAG-ASN : angle 1.10290 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.096 Fit side-chains REVERT: L 45 LYS cc_start: 0.8915 (tttt) cc_final: 0.8653 (tttm) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.6938 time to fit residues: 43.5063 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.126428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.097825 restraints weight = 5207.666| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.37 r_work: 0.2845 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4248 Z= 0.154 Angle : 0.631 15.265 5781 Z= 0.308 Chirality : 0.045 0.166 639 Planarity : 0.004 0.030 736 Dihedral : 4.727 23.110 605 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.98 % Allowed : 17.14 % Favored : 80.88 % 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 are not related in a simple way. whole: -0.03 (0.39), residues: 499 helix: 0.48 (0.64), residues: 74 sheet: 0.06 (0.40), residues: 166 loop : -0.09 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 81 TYR 0.036 0.002 TYR H 99 PHE 0.015 0.001 PHE A 97 TRP 0.010 0.001 TRP L 96 HIS 0.002 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 4243) covalent geometry : angle 0.62769 ( 5769) SS BOND : bond 0.00616 ( 3) SS BOND : angle 1.32687 ( 6) hydrogen bonds : bond 0.03102 ( 154) hydrogen bonds : angle 4.82534 ( 384) link_BETA1-4 : bond 0.00754 ( 1) link_BETA1-4 : angle 2.08449 ( 3) link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 1.03176 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.156 Fit side-chains REVERT: L 45 LYS cc_start: 0.9034 (tttt) cc_final: 0.8810 (tttm) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.6762 time to fit residues: 36.8547 Evaluate side-chains 51 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.126152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.096739 restraints weight = 5275.531| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.47 r_work: 0.2814 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4248 Z= 0.119 Angle : 0.601 16.260 5781 Z= 0.290 Chirality : 0.044 0.170 639 Planarity : 0.004 0.030 736 Dihedral : 4.559 21.614 605 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.32 % Allowed : 17.80 % Favored : 80.88 % 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 are not related in a simple way. whole: 0.05 (0.39), residues: 499 helix: 0.57 (0.65), residues: 74 sheet: 0.10 (0.40), residues: 166 loop : -0.04 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.036 0.001 TYR H 99 PHE 0.011 0.001 PHE A 97 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4243) covalent geometry : angle 0.59835 ( 5769) SS BOND : bond 0.00501 ( 3) SS BOND : angle 1.19124 ( 6) hydrogen bonds : bond 0.02853 ( 154) hydrogen bonds : angle 4.74992 ( 384) link_BETA1-4 : bond 0.00793 ( 1) link_BETA1-4 : angle 2.05178 ( 3) link_NAG-ASN : bond 0.00102 ( 1) link_NAG-ASN : angle 1.10379 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.157 Fit side-chains REVERT: A 81 ARG cc_start: 0.7861 (mpt-90) cc_final: 0.7259 (mpt180) REVERT: H 65 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7843 (mm-40) REVERT: L 45 LYS cc_start: 0.8869 (tttt) cc_final: 0.8641 (tttt) outliers start: 6 outliers final: 6 residues processed: 55 average time/residue: 0.6894 time to fit residues: 39.0243 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.127894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099557 restraints weight = 5178.761| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.42 r_work: 0.2813 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4248 Z= 0.138 Angle : 0.622 15.192 5781 Z= 0.305 Chirality : 0.045 0.176 639 Planarity : 0.004 0.031 736 Dihedral : 4.602 22.227 605 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.54 % Allowed : 17.58 % Favored : 80.88 % 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 are not related in a simple way. whole: 0.03 (0.39), residues: 499 helix: 0.54 (0.64), residues: 74 sheet: 0.10 (0.40), residues: 166 loop : -0.07 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.037 0.002 TYR H 99 PHE 0.013 0.001 PHE A 97 TRP 0.010 0.001 TRP L 96 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4243) covalent geometry : angle 0.61951 ( 5769) SS BOND : bond 0.00558 ( 3) SS BOND : angle 1.22935 ( 6) hydrogen bonds : bond 0.02958 ( 154) hydrogen bonds : angle 4.77860 ( 384) link_BETA1-4 : bond 0.00739 ( 1) link_BETA1-4 : angle 2.03813 ( 3) link_NAG-ASN : bond 0.00052 ( 1) link_NAG-ASN : angle 1.07572 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.108 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.6741 time to fit residues: 37.5263 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN H 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.091829 restraints weight = 5238.626| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.52 r_work: 0.2808 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4248 Z= 0.152 Angle : 0.629 14.697 5781 Z= 0.308 Chirality : 0.045 0.171 639 Planarity : 0.004 0.030 736 Dihedral : 4.667 22.669 605 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.20 % Allowed : 17.80 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.39), residues: 499 helix: 0.52 (0.64), residues: 74 sheet: 0.08 (0.40), residues: 166 loop : -0.10 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.042 0.002 TYR H 99 PHE 0.014 0.001 PHE A 97 TRP 0.010 0.001 TRP L 96 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 4243) covalent geometry : angle 0.62619 ( 5769) SS BOND : bond 0.00602 ( 3) SS BOND : angle 1.38536 ( 6) hydrogen bonds : bond 0.03064 ( 154) hydrogen bonds : angle 4.81347 ( 384) link_BETA1-4 : bond 0.00762 ( 1) link_BETA1-4 : angle 2.05060 ( 3) link_NAG-ASN : bond 0.00031 ( 1) link_NAG-ASN : angle 1.06911 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.25 seconds wall clock time: 26 minutes 13.29 seconds (1573.29 seconds total)