Starting phenix.real_space_refine on Wed Jul 1 23:35:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lkf_23405/07_2026/7lkf_23405.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lkf_23405/07_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_23405/07_2026/7lkf_23405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lkf_23405/07_2026/7lkf_23405.map" model { file = "/net/cci-nas-00/data/ceres_data/7lkf_23405/07_2026/7lkf_23405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lkf_23405/07_2026/7lkf_23405.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lkf_23405/07_2026/7lkf_23405.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lkf_23405/07_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-6108/lib/python3.11/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 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: 0.33 Conformation dependent library (CDL) restraints added in 134.6 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: 0.08 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: 0.42 Time building geometry restraints manager: 0.43 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: 2322 17.68 - 35.36: 156 35.36 - 53.04: 20 53.04 - 70.72: 9 70.72 - 88.40: 7 Dihedral angle restraints: 2514 sinusoidal: 1018 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 2511 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: 1.310 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.890 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:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 12.868 88.404 1541 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/Z covalent geometry : bond 0.00461 / 0.21 ( 4243) covalent geometry : angle 0.66646 / 0.37 ( 5769) SS BOND : bond 0.00765 / 0.39 ( 3) SS BOND : angle 1.53022 / 0.62 ( 6) hydrogen bonds : bond 0.07942 / 4.98 ( 154) hydrogen bonds : angle 5.57887 / 3.97 ( 384) link_BETA1-4 : bond 0.00955 / 0.60 ( 1) link_BETA1-4 : angle 4.07060 / 1.64 ( 3) link_NAG-ASN : bond 0.00642 / 0.40 ( 1) link_NAG-ASN : angle 1.31730 / 0.66 ( 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 : 0.153 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: 0.6267 time to fit residues: 53.3294 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 : 0.156 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3439 r_free = 0.3439 target = 0.128145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.099664 restraints weight = 5229.883| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.45 r_work: 0.2923 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4248 Z= 0.132 Angle : 0.600 6.723 5781 Z= 0.303 Chirality : 0.045 0.163 639 Planarity : 0.004 0.054 736 Dihedral : 4.949 24.515 563 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.32 % Allowed : 10.33 % Favored : 88.35 % 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: -0.28 (0.38), residues: 499 helix: 0.47 (0.65), residues: 73 sheet: -0.18 (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 0.017 0.001 PHE A 97 TRP 0.008 0.001 TRP L 96 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 4243) covalent geometry : angle 0.59733 / 0.30 ( 5769) SS BOND : bond 0.00508 / 0.25 ( 3) SS BOND : angle 1.23852 / 0.50 ( 6) hydrogen bonds : bond 0.03133 / 2.02 ( 154) hydrogen bonds : angle 5.06846 / 3.50 ( 384) link_BETA1-4 : bond 0.00917 / 0.57 ( 1) link_BETA1-4 : angle 1.96824 / 0.80 ( 3) link_NAG-ASN : bond 0.00126 / 0.08 ( 1) link_NAG-ASN : angle 0.80075 / 0.30 ( 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 67 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.089 Fit side-chains REVERT: A 128 GLU cc_start: 0.7744 (tp30) cc_final: 0.7378 (tp30) outliers start: 6 outliers final: 2 residues processed: 65 average time/residue: 0.5870 time to fit residues: 39.0922 Evaluate side-chains 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP 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: 0.0170 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.099226 restraints weight = 5144.530| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.52 r_work: 0.2808 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4248 Z= 0.138 Angle : 0.587 7.945 5781 Z= 0.294 Chirality : 0.045 0.167 639 Planarity : 0.004 0.040 736 Dihedral : 4.750 22.933 563 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.32 % Allowed : 14.29 % Favored : 84.40 % 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: 0.51 (0.65), residues: 73 sheet: -0.19 (0.39), residues: 172 loop : -0.09 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.027 0.002 TYR H 99 PHE 0.021 0.001 PHE A 97 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 4243) covalent geometry : angle 0.58485 / 0.29 ( 5769) SS BOND : bond 0.00584 / 0.30 ( 3) SS BOND : angle 1.20978 / 0.48 ( 6) hydrogen bonds : bond 0.03099 / 2.00 ( 154) hydrogen bonds : angle 4.93459 / 3.39 ( 384) link_BETA1-4 : bond 0.00668 / 0.42 ( 1) link_BETA1-4 : angle 1.63985 / 0.69 ( 3) link_NAG-ASN : bond 0.00042 / 0.03 ( 1) link_NAG-ASN : angle 0.82206 / 0.34 ( 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 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.114 Fit side-chains REVERT: A 145 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8117 (mt-10) REVERT: L 45 LYS cc_start: 0.8917 (tttt) cc_final: 0.8699 (tttp) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.5498 time to fit residues: 32.8098 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 : 0.147 ------------------------------------------------------------------------------- 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: 0.0060 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.101369 restraints weight = 5083.969| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.33 r_work: 0.2818 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4248 Z= 0.172 Angle : 0.610 6.898 5781 Z= 0.306 Chirality : 0.046 0.167 639 Planarity : 0.004 0.034 736 Dihedral : 4.810 23.690 563 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.76 % Allowed : 15.16 % 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: -0.13 (0.39), residues: 499 helix: 0.44 (0.65), residues: 73 sheet: -0.05 (0.39), residues: 166 loop : -0.14 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.028 0.002 TYR H 99 PHE 0.022 0.002 PHE A 97 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 4243) covalent geometry : angle 0.60732 / 0.31 ( 5769) SS BOND : bond 0.00663 / 0.33 ( 3) SS BOND : angle 1.28213 / 0.51 ( 6) hydrogen bonds : bond 0.03278 / 2.13 ( 154) hydrogen bonds : angle 4.98219 / 3.43 ( 384) link_BETA1-4 : bond 0.00715 / 0.45 ( 1) link_BETA1-4 : angle 1.68664 / 0.72 ( 3) link_NAG-ASN : bond 0.00139 / 0.09 ( 1) link_NAG-ASN : angle 0.75917 / 0.30 ( 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 61 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.090 Fit side-chains REVERT: H 65 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7878 (mm-40) outliers start: 8 outliers final: 4 residues processed: 60 average time/residue: 0.5886 time to fit residues: 36.2436 Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.098833 restraints weight = 5161.854| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.52 r_work: 0.2891 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4248 Z= 0.112 Angle : 0.542 5.800 5781 Z= 0.273 Chirality : 0.043 0.154 639 Planarity : 0.004 0.030 736 Dihedral : 4.556 21.853 563 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.20 % Allowed : 14.95 % Favored : 82.86 % 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: 0.02 (0.39), residues: 499 helix: 0.59 (0.66), residues: 73 sheet: 0.03 (0.39), residues: 166 loop : -0.03 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.029 0.001 TYR H 99 PHE 0.013 0.001 PHE A 97 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 4243) covalent geometry : angle 0.54002 / 0.27 ( 5769) SS BOND : bond 0.00535 / 0.27 ( 3) SS BOND : angle 1.03698 / 0.43 ( 6) hydrogen bonds : bond 0.02866 / 1.84 ( 154) hydrogen bonds : angle 4.85341 / 3.33 ( 384) link_BETA1-4 : bond 0.00719 / 0.45 ( 1) link_BETA1-4 : angle 1.65076 / 0.69 ( 3) link_NAG-ASN : bond 0.00009 / 0.01 ( 1) link_NAG-ASN : angle 0.80667 / 0.37 ( 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 62 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.091 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.5355 time to fit residues: 32.5189 Evaluate side-chains 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.087 ------------------------------------------------------------------------------- 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 63 LYS 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: 2.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3434 r_free = 0.3434 target = 0.127594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.097656 restraints weight = 5230.502| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.54 r_work: 0.2906 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1669 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= 0.143 Angle : 0.609 15.785 5781 Z= 0.297 Chirality : 0.044 0.167 639 Planarity : 0.004 0.030 736 Dihedral : 4.585 22.221 563 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.64 % Allowed : 15.16 % Favored : 82.20 % 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: 0.47 (0.65), residues: 74 sheet: 0.06 (0.39), residues: 166 loop : -0.12 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 81 TYR 0.032 0.002 TYR H 99 PHE 0.015 0.001 PHE A 97 TRP 0.009 0.001 TRP L 96 HIS 0.002 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 4243) covalent geometry : angle 0.60726 / 0.30 ( 5769) SS BOND : bond 0.00590 / 0.30 ( 3) SS BOND : angle 1.20328 / 0.49 ( 6) hydrogen bonds : bond 0.03037 / 1.96 ( 154) hydrogen bonds : angle 4.87156 / 3.35 ( 384) link_BETA1-4 : bond 0.00698 / 0.44 ( 1) link_BETA1-4 : angle 1.66359 / 0.71 ( 3) link_NAG-ASN : bond 0.00060 / 0.04 ( 1) link_NAG-ASN : angle 0.77168 / 0.33 ( 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 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.118 Fit side-chains REVERT: H 65 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7982 (mm-40) outliers start: 12 outliers final: 6 residues processed: 58 average time/residue: 0.5666 time to fit residues: 33.8909 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 : 0.128 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 42 optimal weight: 0.0970 chunk 49 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.095672 restraints weight = 5363.771| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.53 r_work: 0.2875 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4248 Z= 0.108 Angle : 0.566 13.554 5781 Z= 0.277 Chirality : 0.043 0.146 639 Planarity : 0.004 0.029 736 Dihedral : 4.402 21.529 563 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.42 % Allowed : 15.16 % Favored : 82.42 % 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: 0.60 (0.65), residues: 74 sheet: 0.10 (0.39), residues: 166 loop : -0.05 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.031 0.001 TYR H 99 PHE 0.010 0.001 PHE A 97 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 4243) covalent geometry : angle 0.56355 / 0.28 ( 5769) SS BOND : bond 0.00501 / 0.26 ( 3) SS BOND : angle 1.05296 / 0.45 ( 6) hydrogen bonds : bond 0.02784 / 1.79 ( 154) hydrogen bonds : angle 4.77540 / 3.27 ( 384) link_BETA1-4 : bond 0.00716 / 0.45 ( 1) link_BETA1-4 : angle 1.62971 / 0.68 ( 3) link_NAG-ASN : bond 0.00026 / 0.02 ( 1) link_NAG-ASN : angle 0.80926 / 0.36 ( 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 63 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.157 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.5414 time to fit residues: 34.1091 Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.127945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.099297 restraints weight = 5222.517| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.45 r_work: 0.2822 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4248 Z= 0.141 Angle : 0.597 12.821 5781 Z= 0.294 Chirality : 0.044 0.151 639 Planarity : 0.004 0.031 736 Dihedral : 4.488 22.698 563 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.42 % Allowed : 16.26 % Favored : 81.32 % 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: 0.02 (0.39), residues: 499 helix: 0.52 (0.64), residues: 74 sheet: 0.09 (0.39), residues: 166 loop : -0.07 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.033 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 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 4243) covalent geometry : angle 0.59532 / 0.29 ( 5769) SS BOND : bond 0.00583 / 0.29 ( 3) SS BOND : angle 1.22757 / 0.51 ( 6) hydrogen bonds : bond 0.03013 / 1.96 ( 154) hydrogen bonds : angle 4.82879 / 3.32 ( 384) link_BETA1-4 : bond 0.00684 / 0.43 ( 1) link_BETA1-4 : angle 1.64908 / 0.70 ( 3) link_NAG-ASN : bond 0.00056 / 0.03 ( 1) link_NAG-ASN : angle 0.75299 / 0.31 ( 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 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.097 Fit side-chains REVERT: A 229 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7649 (mptt) outliers start: 11 outliers final: 8 residues processed: 58 average time/residue: 0.5520 time to fit residues: 32.9745 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 : 0.089 ------------------------------------------------------------------------------- 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 211 ASP Chi-restraints excluded: chain A residue 229 LYS 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 63 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 0.0030 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.1426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.099597 restraints weight = 5305.386| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.48 r_work: 0.2935 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4248 Z= 0.091 Angle : 0.550 12.267 5781 Z= 0.269 Chirality : 0.042 0.144 639 Planarity : 0.004 0.030 736 Dihedral : 4.114 19.452 563 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.76 % Allowed : 17.80 % Favored : 80.44 % 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: 0.20 (0.39), residues: 499 helix: 0.73 (0.65), residues: 74 sheet: 0.20 (0.39), residues: 165 loop : 0.04 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.027 0.001 TYR H 99 PHE 0.007 0.001 PHE L 98 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 ( 4243) covalent geometry : angle 0.54759 / 0.27 ( 5769) SS BOND : bond 0.00609 / 0.36 ( 3) SS BOND : angle 1.05594 / 0.46 ( 6) hydrogen bonds : bond 0.02484 / 1.58 ( 154) hydrogen bonds : angle 4.60573 / 3.15 ( 384) link_BETA1-4 : bond 0.00725 / 0.45 ( 1) link_BETA1-4 : angle 1.60223 / 0.66 ( 3) link_NAG-ASN : bond 0.00149 / 0.09 ( 1) link_NAG-ASN : angle 0.90364 / 0.42 ( 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 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.149 Fit side-chains REVERT: L 3 GLN cc_start: 0.8219 (tp40) cc_final: 0.7995 (tp40) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.5669 time to fit residues: 34.5958 Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 673 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN L 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.090969 restraints weight = 5258.873| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.50 r_work: 0.2777 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4248 Z= 0.216 Angle : 0.660 12.279 5781 Z= 0.328 Chirality : 0.047 0.158 639 Planarity : 0.004 0.030 736 Dihedral : 4.677 24.090 563 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.54 % Allowed : 18.02 % Favored : 80.44 % 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: 0.47 (0.64), residues: 74 sheet: 0.07 (0.40), residues: 166 loop : -0.07 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 696 TYR 0.038 0.002 TYR H 99 PHE 0.019 0.002 PHE A 97 TRP 0.012 0.002 TRP L 96 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 ( 4243) covalent geometry : angle 0.65789 / 0.33 ( 5769) SS BOND : bond 0.00777 / 0.40 ( 3) SS BOND : angle 1.30516 / 0.50 ( 6) hydrogen bonds : bond 0.03438 / 2.25 ( 154) hydrogen bonds : angle 4.86240 / 3.35 ( 384) link_BETA1-4 : bond 0.00672 / 0.42 ( 1) link_BETA1-4 : angle 1.67581 / 0.73 ( 3) link_NAG-ASN : bond 0.00168 / 0.10 ( 1) link_NAG-ASN : angle 0.66280 / 0.24 ( 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 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.145 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 0.5628 time to fit residues: 31.2904 Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 63 LYS 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: 2.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 3 optimal weight: 0.3980 chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.093770 restraints weight = 5234.901| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.50 r_work: 0.2810 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1864 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= 0.125 Angle : 0.591 12.183 5781 Z= 0.291 Chirality : 0.043 0.149 639 Planarity : 0.004 0.030 736 Dihedral : 4.474 21.291 563 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.54 % Allowed : 18.68 % Favored : 79.78 % 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: 0.04 (0.39), residues: 499 helix: 0.59 (0.65), residues: 74 sheet: 0.06 (0.40), residues: 166 loop : -0.03 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 696 TYR 0.033 0.001 TYR H 99 PHE 0.012 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/Z covalent geometry : bond 0.00297 / 0.12 ( 4243) covalent geometry : angle 0.58827 / 0.29 ( 5769) SS BOND : bond 0.00537 / 0.27 ( 3) SS BOND : angle 1.48027 / 0.63 ( 6) hydrogen bonds : bond 0.02897 / 1.88 ( 154) hydrogen bonds : angle 4.73312 / 3.24 ( 384) link_BETA1-4 : bond 0.00689 / 0.43 ( 1) link_BETA1-4 : angle 1.62729 / 0.68 ( 3) link_NAG-ASN : bond 0.00026 / 0.02 ( 1) link_NAG-ASN : angle 0.80687 / 0.35 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1258.48 seconds wall clock time: 22 minutes 8.76 seconds (1328.76 seconds total)