Starting phenix.real_space_refine on Wed Jul 23 10:20:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xa4_38194/07_2025/8xa4_38194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xa4_38194/07_2025/8xa4_38194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xa4_38194/07_2025/8xa4_38194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xa4_38194/07_2025/8xa4_38194.map" model { file = "/net/cci-nas-00/data/ceres_data/8xa4_38194/07_2025/8xa4_38194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xa4_38194/07_2025/8xa4_38194.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 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 12 5.16 5 C 1906 2.51 5 N 509 2.21 5 O 616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3043 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 631 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 648 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 948 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Time building chain proxies: 2.49, per 1000 atoms: 0.82 Number of scatterers: 3043 At special positions: 0 Unit cell: (59.976, 79.135, 78.302, 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 12 16.00 O 616 8.00 N 509 7.00 C 1906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 388.5 milliseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 726 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 10 sheets defined 17.2% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 135 through 141 removed outlier: 3.702A pdb=" N VAL A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 removed outlier: 4.165A pdb=" N TYR A 147 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.751A pdb=" N GLN A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.450A pdb=" N SER C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.573A pdb=" N THR C 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 117 removed outlier: 7.108A pdb=" N ASP A 115 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR A 178 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 117 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 117 removed outlier: 6.933A pdb=" N ASP B 115 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR B 178 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 117 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.074A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N CYS C 97 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TRP C 115 " --> pdb=" O CYS C 97 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG C 99 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP C 113 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.074A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.802A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.802A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 267 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: 0.74 Time building geometry restraints manager: 0.93 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: 986 1.34 - 1.46: 785 1.46 - 1.58: 1328 1.58 - 1.70: 0 1.70 - 1.81: 12 Bond restraints: 3111 Sorted by residual: bond pdb=" N SER A 99 " pdb=" CA SER A 99 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.28e+00 bond pdb=" N SER B 99 " pdb=" CA SER B 99 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N GLU D 1 " pdb=" CA GLU D 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 GLN C 1 " pdb=" CA GLN C 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" CA ILE D 59 " pdb=" CB ILE D 59 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 1.08e+00 ... (remaining 3106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 3979 0.95 - 1.91: 192 1.91 - 2.86: 38 2.86 - 3.82: 18 3.82 - 4.77: 3 Bond angle restraints: 4230 Sorted by residual: angle pdb=" N SER D 94 " pdb=" CA SER D 94 " pdb=" C SER D 94 " ideal model delta sigma weight residual 113.56 110.30 3.26 1.39e+00 5.18e-01 5.51e+00 angle pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " pdb=" CG TYR B 105 " ideal model delta sigma weight residual 113.90 117.11 -3.21 1.80e+00 3.09e-01 3.18e+00 angle pdb=" N GLY C 51 " pdb=" CA GLY C 51 " pdb=" C GLY C 51 " ideal model delta sigma weight residual 110.75 113.29 -2.54 1.46e+00 4.69e-01 3.03e+00 angle pdb=" CA VAL B 139 " pdb=" CB VAL B 139 " pdb=" CG1 VAL B 139 " ideal model delta sigma weight residual 110.40 113.34 -2.94 1.70e+00 3.46e-01 2.99e+00 angle pdb=" C GLN C 79 " pdb=" N PHE C 80 " pdb=" CA PHE C 80 " ideal model delta sigma weight residual 122.94 120.39 2.55 1.50e+00 4.44e-01 2.89e+00 ... (remaining 4225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1598 17.98 - 35.96: 184 35.96 - 53.94: 41 53.94 - 71.91: 18 71.91 - 89.89: 7 Dihedral angle restraints: 1848 sinusoidal: 707 harmonic: 1141 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 180 " pdb=" CB CYS B 180 " ideal model delta sinusoidal sigma weight residual -86.00 -166.19 80.19 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 97 " pdb=" CB CYS C 97 " ideal model delta sinusoidal sigma weight residual 93.00 45.14 47.86 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 89 " pdb=" CB CYS D 89 " ideal model delta sinusoidal sigma weight residual 93.00 60.72 32.28 1 1.00e+01 1.00e-02 1.48e+01 ... (remaining 1845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 260 0.028 - 0.056: 150 0.056 - 0.083: 30 0.083 - 0.111: 20 0.111 - 0.139: 7 Chirality restraints: 467 Sorted by residual: chirality pdb=" CA ILE C 39 " pdb=" N ILE C 39 " pdb=" C ILE C 39 " pdb=" CB ILE C 39 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE D 76 " pdb=" N ILE D 76 " pdb=" C ILE D 76 " pdb=" CB ILE D 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 464 not shown) Planarity restraints: 542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 44 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO D 45 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 45 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 45 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 13 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO C 14 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 46 " 0.099 9.50e-02 1.11e+02 4.44e-02 1.22e+00 pdb=" NE ARG D 46 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG D 46 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 46 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 46 " 0.004 2.00e-02 2.50e+03 ... (remaining 539 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1300 2.91 - 3.41: 2786 3.41 - 3.90: 4663 3.90 - 4.40: 5415 4.40 - 4.90: 9330 Nonbonded interactions: 23494 Sorted by model distance: nonbonded pdb=" O THR A 141 " pdb=" OG1 THR A 141 " model vdw 2.411 3.040 nonbonded pdb=" OH TYR D 37 " pdb=" OE1 GLN D 90 " model vdw 2.485 3.040 nonbonded pdb=" OE1 GLU B 174 " pdb=" O ASP D 93 " model vdw 2.516 3.040 nonbonded pdb=" O VAL B 139 " pdb=" CG1 VAL B 139 " model vdw 2.528 3.460 nonbonded pdb=" O ARG C 101 " pdb=" O TYR C 109 " model vdw 2.531 3.040 ... (remaining 23489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 99 through 164 or (resid 165 through 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 180)) } 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: 1.100 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.003 0.034 3117 Z= 0.149 Angle : 0.529 4.774 4242 Z= 0.288 Chirality : 0.039 0.139 467 Planarity : 0.004 0.044 542 Dihedral : 17.082 89.892 1104 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.18 % Allowed : 25.74 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.43), residues: 387 helix: -0.18 (0.88), residues: 44 sheet: 1.28 (0.61), residues: 78 loop : 0.36 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.001 0.000 HIS D 91 PHE 0.016 0.002 PHE C 80 TYR 0.010 0.001 TYR C 96 ARG 0.003 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.16397 ( 97) hydrogen bonds : angle 7.18209 ( 267) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.57766 ( 12) covalent geometry : bond 0.00308 ( 3111) covalent geometry : angle 0.52877 ( 4230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.335 Fit side-chains REVERT: A 170 ASP cc_start: 0.8384 (t70) cc_final: 0.7915 (t0) REVERT: B 117 LYS cc_start: 0.8915 (mttp) cc_final: 0.8709 (mttm) REVERT: D 37 TYR cc_start: 0.8800 (m-80) cc_final: 0.8557 (m-80) outliers start: 4 outliers final: 0 residues processed: 128 average time/residue: 0.1654 time to fit residues: 24.8261 Evaluate side-chains 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.0270 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 157 ASN C 32 ASN C 33 ASN D 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.099818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.078162 restraints weight = 5654.844| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.40 r_work: 0.2905 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3117 Z= 0.128 Angle : 0.615 6.659 4242 Z= 0.316 Chirality : 0.041 0.135 467 Planarity : 0.004 0.028 542 Dihedral : 4.138 13.737 431 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.85 % Allowed : 24.26 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.43), residues: 387 helix: -0.08 (0.77), residues: 50 sheet: 1.39 (0.61), residues: 78 loop : 0.53 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 143 HIS 0.001 0.001 HIS B 113 PHE 0.013 0.002 PHE C 80 TYR 0.011 0.001 TYR B 105 ARG 0.005 0.001 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 97) hydrogen bonds : angle 5.23964 ( 267) SS BOND : bond 0.00220 ( 6) SS BOND : angle 0.69570 ( 12) covalent geometry : bond 0.00285 ( 3111) covalent geometry : angle 0.61523 ( 4230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8706 (t70) cc_final: 0.8409 (t0) REVERT: B 101 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8381 (t0) REVERT: C 72 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8528 (p) REVERT: C 91 ASP cc_start: 0.8996 (m-30) cc_final: 0.8485 (m-30) REVERT: D 71 ASP cc_start: 0.8279 (t0) cc_final: 0.8028 (m-30) outliers start: 13 outliers final: 7 residues processed: 113 average time/residue: 0.1608 time to fit residues: 21.4769 Evaluate side-chains 105 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 157 ASN C 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077303 restraints weight = 5689.348| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.46 r_work: 0.2884 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3117 Z= 0.116 Angle : 0.582 7.793 4242 Z= 0.301 Chirality : 0.040 0.138 467 Planarity : 0.004 0.024 542 Dihedral : 4.047 13.383 431 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.55 % Allowed : 22.78 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.43), residues: 387 helix: -0.11 (0.76), residues: 50 sheet: 1.54 (0.63), residues: 78 loop : 0.46 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.001 0.000 HIS C 107 PHE 0.015 0.001 PHE C 80 TYR 0.017 0.001 TYR B 105 ARG 0.005 0.001 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 97) hydrogen bonds : angle 5.09095 ( 267) SS BOND : bond 0.00161 ( 6) SS BOND : angle 0.63561 ( 12) covalent geometry : bond 0.00256 ( 3111) covalent geometry : angle 0.58164 ( 4230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.361 Fit side-chains REVERT: A 170 ASP cc_start: 0.8702 (t70) cc_final: 0.8388 (t0) REVERT: C 16 GLU cc_start: 0.8655 (mm-30) cc_final: 0.7818 (mm-30) REVERT: C 91 ASP cc_start: 0.8964 (m-30) cc_final: 0.8478 (m-30) REVERT: D 71 ASP cc_start: 0.8243 (t0) cc_final: 0.7982 (m-30) outliers start: 12 outliers final: 7 residues processed: 106 average time/residue: 0.1442 time to fit residues: 18.4560 Evaluate side-chains 102 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.0070 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.077287 restraints weight = 5751.081| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.44 r_work: 0.2874 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3117 Z= 0.108 Angle : 0.572 8.975 4242 Z= 0.292 Chirality : 0.040 0.173 467 Planarity : 0.004 0.026 542 Dihedral : 3.968 13.736 431 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.78 % Allowed : 24.85 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.43), residues: 387 helix: -0.21 (0.75), residues: 50 sheet: 1.50 (0.62), residues: 78 loop : 0.41 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.001 0.000 HIS C 107 PHE 0.015 0.001 PHE C 80 TYR 0.013 0.001 TYR B 105 ARG 0.006 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 97) hydrogen bonds : angle 5.04201 ( 267) SS BOND : bond 0.00138 ( 6) SS BOND : angle 0.56294 ( 12) covalent geometry : bond 0.00239 ( 3111) covalent geometry : angle 0.57167 ( 4230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8706 (t70) cc_final: 0.8399 (t0) REVERT: C 16 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8108 (mm-30) REVERT: C 55 TYR cc_start: 0.8820 (p90) cc_final: 0.8489 (p90) REVERT: C 72 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8606 (p) REVERT: C 91 ASP cc_start: 0.8945 (m-30) cc_final: 0.8477 (m-30) REVERT: D 71 ASP cc_start: 0.8260 (t0) cc_final: 0.7995 (m-30) outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 0.1465 time to fit residues: 18.3473 Evaluate side-chains 101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain D residue 10 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 101 ASN C 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.089691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.067415 restraints weight = 5847.217| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.41 r_work: 0.2699 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 3117 Z= 0.297 Angle : 0.678 7.082 4242 Z= 0.356 Chirality : 0.044 0.146 467 Planarity : 0.004 0.027 542 Dihedral : 4.500 14.906 431 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.62 % Allowed : 19.82 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.42), residues: 387 helix: -0.86 (0.65), residues: 56 sheet: 1.04 (0.61), residues: 76 loop : 0.34 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 115 HIS 0.002 0.001 HIS A 113 PHE 0.018 0.002 PHE C 80 TYR 0.025 0.002 TYR D 33 ARG 0.009 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 97) hydrogen bonds : angle 5.43433 ( 267) SS BOND : bond 0.00210 ( 6) SS BOND : angle 1.91519 ( 12) covalent geometry : bond 0.00696 ( 3111) covalent geometry : angle 0.67075 ( 4230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8733 (t70) cc_final: 0.8364 (t0) REVERT: B 173 GLN cc_start: 0.8231 (pm20) cc_final: 0.7620 (pm20) REVERT: C 16 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8306 (mm-30) REVERT: C 91 ASP cc_start: 0.8964 (m-30) cc_final: 0.8409 (m-30) REVERT: D 70 THR cc_start: 0.9040 (p) cc_final: 0.8668 (p) REVERT: D 71 ASP cc_start: 0.8166 (t0) cc_final: 0.7860 (m-30) outliers start: 19 outliers final: 12 residues processed: 116 average time/residue: 0.1581 time to fit residues: 21.7032 Evaluate side-chains 113 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.091480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.069826 restraints weight = 5938.547| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.41 r_work: 0.2750 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3117 Z= 0.143 Angle : 0.606 9.448 4242 Z= 0.313 Chirality : 0.040 0.137 467 Planarity : 0.004 0.025 542 Dihedral : 4.264 15.221 431 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.55 % Allowed : 22.78 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.43), residues: 387 helix: -0.74 (0.69), residues: 56 sheet: 1.10 (0.61), residues: 78 loop : 0.40 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.000 0.000 HIS C 107 PHE 0.015 0.002 PHE C 80 TYR 0.012 0.001 TYR D 33 ARG 0.006 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 97) hydrogen bonds : angle 5.36679 ( 267) SS BOND : bond 0.00185 ( 6) SS BOND : angle 1.01028 ( 12) covalent geometry : bond 0.00336 ( 3111) covalent geometry : angle 0.60472 ( 4230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.337 Fit side-chains REVERT: A 170 ASP cc_start: 0.8703 (t70) cc_final: 0.8341 (t0) REVERT: C 16 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8134 (mm-30) REVERT: C 48 GLU cc_start: 0.8732 (tt0) cc_final: 0.8520 (tt0) REVERT: C 72 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8721 (p) REVERT: C 91 ASP cc_start: 0.8939 (m-30) cc_final: 0.8431 (m-30) REVERT: D 37 TYR cc_start: 0.9234 (m-80) cc_final: 0.8905 (m-80) REVERT: D 70 THR cc_start: 0.9057 (p) cc_final: 0.8661 (p) REVERT: D 71 ASP cc_start: 0.8143 (t0) cc_final: 0.7841 (m-30) REVERT: D 93 ASP cc_start: 0.8362 (t0) cc_final: 0.8005 (t0) outliers start: 12 outliers final: 8 residues processed: 113 average time/residue: 0.1532 time to fit residues: 20.5984 Evaluate side-chains 110 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 0.0070 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.092593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.070789 restraints weight = 5738.282| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.37 r_work: 0.2796 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3117 Z= 0.126 Angle : 0.619 10.369 4242 Z= 0.319 Chirality : 0.040 0.134 467 Planarity : 0.004 0.026 542 Dihedral : 4.121 13.530 431 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.66 % Allowed : 24.85 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.43), residues: 387 helix: -0.40 (0.76), residues: 50 sheet: 1.11 (0.61), residues: 78 loop : 0.54 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.001 0.000 HIS C 107 PHE 0.015 0.002 PHE C 80 TYR 0.012 0.001 TYR D 33 ARG 0.008 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 97) hydrogen bonds : angle 5.27257 ( 267) SS BOND : bond 0.00261 ( 6) SS BOND : angle 0.74338 ( 12) covalent geometry : bond 0.00292 ( 3111) covalent geometry : angle 0.61850 ( 4230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.515 Fit side-chains REVERT: A 170 ASP cc_start: 0.8668 (t70) cc_final: 0.8350 (t0) REVERT: B 106 GLN cc_start: 0.8874 (pt0) cc_final: 0.8662 (pt0) REVERT: C 16 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8098 (mm-30) REVERT: C 72 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8739 (p) REVERT: C 91 ASP cc_start: 0.8892 (m-30) cc_final: 0.8474 (m-30) REVERT: D 37 TYR cc_start: 0.9219 (m-80) cc_final: 0.8803 (m-80) REVERT: D 70 THR cc_start: 0.9096 (p) cc_final: 0.8724 (p) REVERT: D 71 ASP cc_start: 0.8157 (t0) cc_final: 0.7898 (m-30) outliers start: 9 outliers final: 6 residues processed: 112 average time/residue: 0.1604 time to fit residues: 21.3464 Evaluate side-chains 108 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.0060 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.0000 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.3498 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.094402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.072502 restraints weight = 5787.872| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.41 r_work: 0.2802 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3117 Z= 0.115 Angle : 0.611 10.989 4242 Z= 0.315 Chirality : 0.039 0.134 467 Planarity : 0.004 0.035 542 Dihedral : 4.097 14.134 431 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.07 % Allowed : 25.74 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.44), residues: 387 helix: -0.46 (0.75), residues: 50 sheet: 1.07 (0.62), residues: 78 loop : 0.60 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.001 0.000 HIS C 107 PHE 0.016 0.001 PHE C 80 TYR 0.010 0.001 TYR D 37 ARG 0.008 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 97) hydrogen bonds : angle 5.18738 ( 267) SS BOND : bond 0.00356 ( 6) SS BOND : angle 0.78658 ( 12) covalent geometry : bond 0.00261 ( 3111) covalent geometry : angle 0.61090 ( 4230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.360 Fit side-chains REVERT: A 170 ASP cc_start: 0.8678 (t70) cc_final: 0.8370 (t0) REVERT: C 16 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8241 (mm-30) REVERT: C 91 ASP cc_start: 0.8858 (m-30) cc_final: 0.8552 (m-30) REVERT: D 37 TYR cc_start: 0.9194 (m-80) cc_final: 0.8848 (m-80) REVERT: D 62 ARG cc_start: 0.8711 (mtm-85) cc_final: 0.8191 (mtm-85) REVERT: D 70 THR cc_start: 0.9095 (p) cc_final: 0.8710 (p) REVERT: D 71 ASP cc_start: 0.8206 (t0) cc_final: 0.7909 (m-30) REVERT: D 93 ASP cc_start: 0.8351 (t0) cc_final: 0.8095 (t70) outliers start: 7 outliers final: 5 residues processed: 111 average time/residue: 0.1654 time to fit residues: 21.6416 Evaluate side-chains 111 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 10 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.093725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.071244 restraints weight = 5781.749| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.44 r_work: 0.2772 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3117 Z= 0.136 Angle : 0.627 11.823 4242 Z= 0.323 Chirality : 0.040 0.133 467 Planarity : 0.004 0.036 542 Dihedral : 4.099 13.850 431 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.66 % Allowed : 26.04 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.44), residues: 387 helix: -0.56 (0.76), residues: 50 sheet: 1.04 (0.62), residues: 78 loop : 0.60 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.001 0.000 HIS B 113 PHE 0.017 0.002 PHE C 80 TYR 0.013 0.001 TYR D 33 ARG 0.008 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 97) hydrogen bonds : angle 5.16284 ( 267) SS BOND : bond 0.00215 ( 6) SS BOND : angle 0.96539 ( 12) covalent geometry : bond 0.00316 ( 3111) covalent geometry : angle 0.62599 ( 4230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.378 Fit side-chains REVERT: A 170 ASP cc_start: 0.8700 (t70) cc_final: 0.8392 (t0) REVERT: C 79 GLN cc_start: 0.8295 (mt0) cc_final: 0.8092 (mm-40) REVERT: C 91 ASP cc_start: 0.8809 (m-30) cc_final: 0.8499 (m-30) REVERT: D 37 TYR cc_start: 0.9223 (m-80) cc_final: 0.8860 (m-80) REVERT: D 70 THR cc_start: 0.9099 (p) cc_final: 0.8729 (p) REVERT: D 71 ASP cc_start: 0.8167 (t0) cc_final: 0.7878 (m-30) REVERT: D 93 ASP cc_start: 0.8390 (t0) cc_final: 0.8136 (t70) outliers start: 9 outliers final: 7 residues processed: 111 average time/residue: 0.1724 time to fit residues: 22.5305 Evaluate side-chains 110 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 10 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.0040 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN C 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.070490 restraints weight = 5635.415| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.40 r_work: 0.2772 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3117 Z= 0.142 Angle : 0.640 11.892 4242 Z= 0.330 Chirality : 0.040 0.134 467 Planarity : 0.004 0.038 542 Dihedral : 4.132 14.008 431 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.07 % Allowed : 27.22 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.44), residues: 387 helix: -0.60 (0.74), residues: 50 sheet: 0.99 (0.62), residues: 78 loop : 0.60 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 36 HIS 0.001 0.000 HIS B 113 PHE 0.015 0.002 PHE C 80 TYR 0.014 0.001 TYR D 33 ARG 0.009 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 97) hydrogen bonds : angle 5.14205 ( 267) SS BOND : bond 0.00157 ( 6) SS BOND : angle 1.02221 ( 12) covalent geometry : bond 0.00336 ( 3111) covalent geometry : angle 0.63889 ( 4230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.348 Fit side-chains REVERT: A 170 ASP cc_start: 0.8708 (t70) cc_final: 0.8394 (t0) REVERT: B 117 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8026 (mtmm) REVERT: C 79 GLN cc_start: 0.8386 (mt0) cc_final: 0.8118 (mm-40) REVERT: C 91 ASP cc_start: 0.8785 (m-30) cc_final: 0.8495 (m-30) REVERT: D 37 TYR cc_start: 0.9211 (m-80) cc_final: 0.8782 (m-80) REVERT: D 70 THR cc_start: 0.9137 (p) cc_final: 0.8765 (p) REVERT: D 71 ASP cc_start: 0.8150 (t0) cc_final: 0.7881 (m-30) REVERT: D 93 ASP cc_start: 0.8387 (t0) cc_final: 0.8114 (t70) outliers start: 7 outliers final: 6 residues processed: 106 average time/residue: 0.1673 time to fit residues: 20.9658 Evaluate side-chains 107 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 10 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.070581 restraints weight = 5800.497| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.45 r_work: 0.2770 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3117 Z= 0.143 Angle : 0.675 16.985 4242 Z= 0.338 Chirality : 0.040 0.173 467 Planarity : 0.004 0.039 542 Dihedral : 4.157 15.737 431 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.25 % Allowed : 26.33 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.44), residues: 387 helix: -0.62 (0.74), residues: 50 sheet: 1.02 (0.62), residues: 78 loop : 0.56 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.001 0.000 HIS C 107 PHE 0.015 0.001 PHE C 80 TYR 0.016 0.001 TYR D 33 ARG 0.009 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 97) hydrogen bonds : angle 5.15771 ( 267) SS BOND : bond 0.00163 ( 6) SS BOND : angle 1.00129 ( 12) covalent geometry : bond 0.00334 ( 3111) covalent geometry : angle 0.67390 ( 4230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2010.83 seconds wall clock time: 35 minutes 11.56 seconds (2111.56 seconds total)