Starting phenix.real_space_refine on Tue Feb 11 03:25:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqs_28544/02_2025/8eqs_28544_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqs_28544/02_2025/8eqs_28544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eqs_28544/02_2025/8eqs_28544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqs_28544/02_2025/8eqs_28544.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqs_28544/02_2025/8eqs_28544_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqs_28544/02_2025/8eqs_28544_neut.cif" } resolution = 3.1 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 20 5.16 5 C 2406 2.51 5 N 570 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3654 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1573 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 3, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 229 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Restraints were copied for chains: D, B Time building chain proxies: 3.18, per 1000 atoms: 0.87 Number of scatterers: 3654 At special positions: 0 Unit cell: (73.428, 64.988, 89.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 2 15.00 O 656 8.00 N 570 7.00 C 2406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 421.4 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 53.9% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.553A pdb=" N VAL A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 100 removed outlier: 3.600A pdb=" N LEU A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 134 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.553A pdb=" N VAL B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 100 removed outlier: 3.600A pdb=" N LEU B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 78 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 134 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'C' and resid 26 through 48 Proline residue: C 34 - end of helix removed outlier: 4.378A pdb=" N GLN C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 48 Proline residue: D 34 - end of helix removed outlier: 4.378A pdb=" N GLN D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160 removed outlier: 5.812A pdb=" N HIS A 150 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 232 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160 removed outlier: 5.812A pdb=" N HIS B 150 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE B 232 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 678 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: 1.00 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 566 1.31 - 1.44: 1140 1.44 - 1.56: 2016 1.56 - 1.69: 4 1.69 - 1.81: 24 Bond restraints: 3750 Sorted by residual: bond pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C30 PEE A 401 " pdb=" O3 PEE A 401 " ideal model delta sigma weight residual 1.327 1.411 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C30 PEE B 401 " pdb=" O3 PEE B 401 " ideal model delta sigma weight residual 1.327 1.410 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C10 PEE A 401 " pdb=" C11 PEE A 401 " ideal model delta sigma weight residual 1.504 1.549 -0.045 2.00e-02 2.50e+03 5.17e+00 ... (remaining 3745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 5049 3.37 - 6.74: 29 6.74 - 10.11: 4 10.11 - 13.48: 2 13.48 - 16.85: 2 Bond angle restraints: 5086 Sorted by residual: angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.76 -16.85 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 109.76 -16.85 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O1P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sigma weight residual 119.43 109.24 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O1P PEE B 401 " pdb=" P PEE B 401 " pdb=" O2P PEE B 401 " ideal model delta sigma weight residual 119.43 109.24 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C11 PEE B 401 " pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 111.70 120.37 -8.67 3.00e+00 1.11e-01 8.35e+00 ... (remaining 5081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.50: 2070 31.50 - 63.00: 58 63.00 - 94.50: 12 94.50 - 126.00: 0 126.00 - 157.50: 6 Dihedral angle restraints: 2146 sinusoidal: 858 harmonic: 1288 Sorted by residual: dihedral pdb=" C3 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C2 PEE A 401 " pdb=" O3P PEE A 401 " ideal model delta sinusoidal sigma weight residual 62.73 -94.77 157.50 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C3 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C2 PEE B 401 " pdb=" O3P PEE B 401 " ideal model delta sinusoidal sigma weight residual 62.73 -94.74 157.47 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C2 PEE A 401 " pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " pdb=" O4 PEE A 401 " ideal model delta sinusoidal sigma weight residual 2.73 -153.71 156.44 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 2143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 485 0.063 - 0.125: 61 0.125 - 0.188: 8 0.188 - 0.251: 0 0.251 - 0.314: 2 Chirality restraints: 556 Sorted by residual: chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.64 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.64 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 553 not shown) Planarity restraints: 622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 80 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C ILE A 80 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE A 80 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS A 81 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 80 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.70e+00 pdb=" C ILE B 80 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE B 80 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS B 81 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 82 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C ASN A 82 " 0.022 2.00e-02 2.50e+03 pdb=" O ASN A 82 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 83 " -0.007 2.00e-02 2.50e+03 ... (remaining 619 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 532 2.76 - 3.29: 3664 3.29 - 3.83: 6165 3.83 - 4.36: 7026 4.36 - 4.90: 12093 Nonbonded interactions: 29480 Sorted by model distance: nonbonded pdb=" OG SER A 58 " pdb=" NE2 GLN B 116 " model vdw 2.219 3.120 nonbonded pdb=" NE2 GLN A 116 " pdb=" OG SER B 58 " model vdw 2.219 3.120 nonbonded pdb=" OH TYR A 154 " pdb=" OE2 GLU A 191 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR B 154 " pdb=" OE2 GLU B 191 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU C 38 " pdb=" ND2 ASN C 42 " model vdw 2.258 3.120 ... (remaining 29475 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.970 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.740 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 0.092 3750 Z= 0.322 Angle : 0.737 16.848 5086 Z= 0.344 Chirality : 0.045 0.314 556 Planarity : 0.003 0.024 622 Dihedral : 19.168 157.496 1322 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.01 (0.38), residues: 426 helix: 1.25 (0.35), residues: 198 sheet: -0.34 (0.60), residues: 82 loop : -1.49 (0.38), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 131 HIS 0.002 0.001 HIS B 150 PHE 0.012 0.001 PHE A 56 TYR 0.004 0.001 TYR A 91 ARG 0.001 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.430 Fit side-chains REVERT: A 45 TRP cc_start: 0.8227 (m100) cc_final: 0.7956 (m100) REVERT: A 67 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8474 (mmmm) REVERT: A 87 PHE cc_start: 0.8744 (t80) cc_final: 0.8543 (t80) REVERT: A 130 CYS cc_start: 0.8322 (p) cc_final: 0.7785 (p) REVERT: A 136 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7438 (mmtt) REVERT: A 152 HIS cc_start: 0.7813 (t-90) cc_final: 0.7579 (t70) REVERT: A 198 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8446 (mmmm) REVERT: B 41 LEU cc_start: 0.8950 (mm) cc_final: 0.8687 (mt) REVERT: B 45 TRP cc_start: 0.8227 (m100) cc_final: 0.7955 (m100) REVERT: B 67 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8478 (mmmm) REVERT: B 87 PHE cc_start: 0.8753 (t80) cc_final: 0.8545 (t80) REVERT: B 130 CYS cc_start: 0.8324 (p) cc_final: 0.7783 (p) REVERT: B 136 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7446 (mmtt) REVERT: B 152 HIS cc_start: 0.7806 (t-90) cc_final: 0.7576 (t70) REVERT: B 198 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8446 (mmmm) REVERT: C 25 PHE cc_start: 0.4370 (m-10) cc_final: 0.3971 (m-10) REVERT: C 42 ASN cc_start: 0.8145 (m-40) cc_final: 0.7757 (m-40) REVERT: D 25 PHE cc_start: 0.4364 (m-10) cc_final: 0.3958 (m-10) REVERT: D 42 ASN cc_start: 0.8143 (m-40) cc_final: 0.7756 (m-40) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1942 time to fit residues: 31.6057 Evaluate side-chains 121 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 82 ASN A 161 ASN A 185 GLN B 57 GLN B 82 ASN B 161 ASN B 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.088892 restraints weight = 5838.618| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.15 r_work: 0.2973 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3750 Z= 0.239 Angle : 0.509 4.306 5086 Z= 0.284 Chirality : 0.043 0.163 556 Planarity : 0.003 0.027 622 Dihedral : 16.976 149.782 516 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.06 % Allowed : 11.60 % Favored : 86.34 % 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: 1.30 (0.39), residues: 426 helix: 2.52 (0.33), residues: 212 sheet: -0.42 (0.57), residues: 88 loop : -1.08 (0.46), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.002 0.001 HIS B 204 PHE 0.010 0.001 PHE B 56 TYR 0.014 0.001 TYR A 74 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.389 Fit side-chains REVERT: A 67 LYS cc_start: 0.9056 (mmmm) cc_final: 0.8345 (mmmm) REVERT: A 130 CYS cc_start: 0.8712 (p) cc_final: 0.7915 (p) REVERT: A 185 GLN cc_start: 0.9018 (tm130) cc_final: 0.8683 (tm130) REVERT: A 193 ARG cc_start: 0.8911 (ptm160) cc_final: 0.8501 (ptm160) REVERT: A 198 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8595 (mmmm) REVERT: B 43 PHE cc_start: 0.7956 (m-10) cc_final: 0.7684 (m-80) REVERT: B 67 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8362 (mmmm) REVERT: B 130 CYS cc_start: 0.8714 (p) cc_final: 0.7918 (p) REVERT: B 193 ARG cc_start: 0.8926 (ptm160) cc_final: 0.8519 (ptm160) REVERT: B 198 LYS cc_start: 0.8876 (mmtm) cc_final: 0.8585 (mmmm) REVERT: C 42 ASN cc_start: 0.8521 (m-40) cc_final: 0.8091 (m-40) REVERT: D 42 ASN cc_start: 0.8520 (m-40) cc_final: 0.8094 (m-40) outliers start: 8 outliers final: 4 residues processed: 131 average time/residue: 0.1878 time to fit residues: 29.1990 Evaluate side-chains 119 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN B 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088835 restraints weight = 5797.358| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.08 r_work: 0.2962 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3750 Z= 0.193 Angle : 0.488 4.317 5086 Z= 0.270 Chirality : 0.041 0.140 556 Planarity : 0.003 0.028 622 Dihedral : 16.141 144.799 516 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.09 % Allowed : 13.40 % Favored : 83.51 % 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: 1.48 (0.40), residues: 426 helix: 2.83 (0.33), residues: 222 sheet: -0.56 (0.55), residues: 88 loop : -1.53 (0.46), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 149 HIS 0.003 0.001 HIS B 204 PHE 0.009 0.001 PHE B 207 TYR 0.008 0.001 TYR A 74 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.447 Fit side-chains REVERT: A 109 TYR cc_start: 0.9000 (m-80) cc_final: 0.8674 (m-80) REVERT: A 128 TRP cc_start: 0.8544 (t60) cc_final: 0.8024 (t60) REVERT: A 130 CYS cc_start: 0.8774 (p) cc_final: 0.7946 (p) REVERT: A 150 HIS cc_start: 0.7763 (m-70) cc_final: 0.7273 (m-70) REVERT: A 155 ASP cc_start: 0.8212 (m-30) cc_final: 0.7618 (t0) REVERT: A 185 GLN cc_start: 0.9065 (tm130) cc_final: 0.8781 (tm130) REVERT: A 193 ARG cc_start: 0.8956 (ptm160) cc_final: 0.8592 (ptm160) REVERT: A 198 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8585 (mmmm) REVERT: B 109 TYR cc_start: 0.8995 (m-80) cc_final: 0.8671 (m-80) REVERT: B 128 TRP cc_start: 0.8531 (t60) cc_final: 0.8008 (t60) REVERT: B 130 CYS cc_start: 0.8775 (p) cc_final: 0.7947 (p) REVERT: B 150 HIS cc_start: 0.7764 (m-70) cc_final: 0.7274 (m-70) REVERT: B 155 ASP cc_start: 0.8205 (m-30) cc_final: 0.7620 (t0) REVERT: B 185 GLN cc_start: 0.9068 (tm130) cc_final: 0.8787 (tm130) REVERT: B 193 ARG cc_start: 0.8957 (ptm160) cc_final: 0.8590 (ptm160) REVERT: B 198 LYS cc_start: 0.8911 (mmtm) cc_final: 0.8584 (mmmm) REVERT: C 29 ARG cc_start: 0.6965 (ttt-90) cc_final: 0.6522 (mtt-85) REVERT: C 42 ASN cc_start: 0.8514 (m-40) cc_final: 0.8092 (m-40) REVERT: D 29 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6533 (mtt-85) REVERT: D 42 ASN cc_start: 0.8515 (m-40) cc_final: 0.8094 (m-40) outliers start: 12 outliers final: 7 residues processed: 124 average time/residue: 0.1916 time to fit residues: 28.3103 Evaluate side-chains 118 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN B 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.116568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087341 restraints weight = 5913.140| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.10 r_work: 0.2919 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3750 Z= 0.215 Angle : 0.475 4.370 5086 Z= 0.263 Chirality : 0.041 0.139 556 Planarity : 0.003 0.027 622 Dihedral : 15.824 143.606 516 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.61 % Allowed : 13.92 % Favored : 82.47 % 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: 1.56 (0.41), residues: 426 helix: 2.93 (0.33), residues: 224 sheet: -0.89 (0.55), residues: 90 loop : -1.29 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.002 0.001 HIS B 204 PHE 0.015 0.001 PHE B 207 TYR 0.007 0.001 TYR B 109 ARG 0.001 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 CYS cc_start: 0.8877 (p) cc_final: 0.8123 (p) REVERT: A 193 ARG cc_start: 0.8977 (ptm160) cc_final: 0.8607 (ptm160) REVERT: A 198 LYS cc_start: 0.8922 (mmtm) cc_final: 0.8581 (mmmm) REVERT: B 130 CYS cc_start: 0.8878 (p) cc_final: 0.8125 (p) REVERT: B 193 ARG cc_start: 0.8985 (ptm160) cc_final: 0.8615 (ptm160) REVERT: B 198 LYS cc_start: 0.8935 (mmtm) cc_final: 0.8599 (mmmm) REVERT: C 42 ASN cc_start: 0.8489 (m-40) cc_final: 0.8052 (m-40) REVERT: D 42 ASN cc_start: 0.8495 (m-40) cc_final: 0.8060 (m-40) outliers start: 14 outliers final: 11 residues processed: 118 average time/residue: 0.1811 time to fit residues: 25.6214 Evaluate side-chains 115 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 213 GLN B 82 ASN B 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087052 restraints weight = 5943.318| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.07 r_work: 0.2910 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3750 Z= 0.219 Angle : 0.479 4.401 5086 Z= 0.266 Chirality : 0.041 0.139 556 Planarity : 0.003 0.027 622 Dihedral : 15.582 141.579 516 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.38 % Allowed : 12.11 % Favored : 83.51 % 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: 1.59 (0.41), residues: 426 helix: 2.92 (0.33), residues: 224 sheet: -0.64 (0.54), residues: 88 loop : -1.44 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.002 0.001 HIS B 204 PHE 0.015 0.002 PHE B 207 TYR 0.007 0.001 TYR A 109 ARG 0.002 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.9158 (mt0) cc_final: 0.8765 (mt0) REVERT: A 130 CYS cc_start: 0.8788 (p) cc_final: 0.8027 (p) REVERT: A 150 HIS cc_start: 0.7462 (m-70) cc_final: 0.6994 (m-70) REVERT: A 155 ASP cc_start: 0.8350 (m-30) cc_final: 0.7407 (t0) REVERT: A 193 ARG cc_start: 0.9010 (ptm160) cc_final: 0.8616 (ptm160) REVERT: A 198 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8598 (mmmm) REVERT: B 78 GLN cc_start: 0.9164 (mt0) cc_final: 0.8765 (mt0) REVERT: B 130 CYS cc_start: 0.8793 (p) cc_final: 0.8033 (p) REVERT: B 150 HIS cc_start: 0.7477 (m-70) cc_final: 0.7007 (m-70) REVERT: B 155 ASP cc_start: 0.8350 (m-30) cc_final: 0.7409 (t0) REVERT: B 193 ARG cc_start: 0.9012 (ptm160) cc_final: 0.8615 (ptm160) REVERT: B 198 LYS cc_start: 0.8946 (mmtm) cc_final: 0.8590 (mmmm) REVERT: C 42 ASN cc_start: 0.8493 (m-40) cc_final: 0.8064 (m-40) REVERT: D 42 ASN cc_start: 0.8496 (m-40) cc_final: 0.8070 (m-40) outliers start: 17 outliers final: 12 residues processed: 122 average time/residue: 0.1753 time to fit residues: 25.6108 Evaluate side-chains 120 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087359 restraints weight = 5959.320| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.04 r_work: 0.2915 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3750 Z= 0.197 Angle : 0.482 4.462 5086 Z= 0.266 Chirality : 0.041 0.141 556 Planarity : 0.003 0.027 622 Dihedral : 15.253 139.702 516 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.58 % Allowed : 13.92 % Favored : 83.51 % 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: 1.62 (0.40), residues: 426 helix: 2.95 (0.33), residues: 224 sheet: -0.70 (0.54), residues: 88 loop : -1.36 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.002 0.000 HIS B 204 PHE 0.016 0.001 PHE B 207 TYR 0.006 0.001 TYR A 74 ARG 0.001 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.9184 (mt0) cc_final: 0.8757 (mt0) REVERT: A 125 MET cc_start: 0.9103 (mmm) cc_final: 0.8729 (mmt) REVERT: A 130 CYS cc_start: 0.8754 (p) cc_final: 0.7979 (p) REVERT: A 150 HIS cc_start: 0.7447 (m-70) cc_final: 0.6935 (m-70) REVERT: A 155 ASP cc_start: 0.8373 (m-30) cc_final: 0.7363 (t0) REVERT: A 193 ARG cc_start: 0.8966 (ptm160) cc_final: 0.8532 (ptm160) REVERT: A 198 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8644 (mmmm) REVERT: B 78 GLN cc_start: 0.9192 (mt0) cc_final: 0.8766 (mt0) REVERT: B 125 MET cc_start: 0.9101 (mmm) cc_final: 0.8715 (mmt) REVERT: B 130 CYS cc_start: 0.8763 (p) cc_final: 0.7992 (p) REVERT: B 150 HIS cc_start: 0.7454 (m-70) cc_final: 0.6936 (m-70) REVERT: B 155 ASP cc_start: 0.8367 (m-30) cc_final: 0.7352 (t0) REVERT: B 193 ARG cc_start: 0.8973 (ptm160) cc_final: 0.8537 (ptm160) REVERT: B 198 LYS cc_start: 0.8944 (mmtm) cc_final: 0.8645 (mmmm) REVERT: C 42 ASN cc_start: 0.8492 (m-40) cc_final: 0.8072 (m-40) REVERT: D 42 ASN cc_start: 0.8496 (m-40) cc_final: 0.8079 (m-40) outliers start: 10 outliers final: 9 residues processed: 120 average time/residue: 0.1813 time to fit residues: 25.7936 Evaluate side-chains 122 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.115720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.086821 restraints weight = 5856.503| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.06 r_work: 0.2914 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3750 Z= 0.184 Angle : 0.481 4.482 5086 Z= 0.265 Chirality : 0.041 0.142 556 Planarity : 0.003 0.027 622 Dihedral : 14.780 139.457 516 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.09 % Allowed : 14.18 % Favored : 82.73 % 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: 1.66 (0.40), residues: 426 helix: 2.98 (0.33), residues: 224 sheet: -0.69 (0.54), residues: 88 loop : -1.33 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.002 0.000 HIS A 204 PHE 0.016 0.001 PHE A 207 TYR 0.006 0.001 TYR B 74 ARG 0.001 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.9174 (mt0) cc_final: 0.8749 (mt0) REVERT: A 125 MET cc_start: 0.9101 (mmm) cc_final: 0.8725 (mmt) REVERT: A 130 CYS cc_start: 0.8754 (p) cc_final: 0.7982 (p) REVERT: A 134 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8430 (mmtt) REVERT: A 150 HIS cc_start: 0.7452 (m-70) cc_final: 0.7154 (m-70) REVERT: A 193 ARG cc_start: 0.8974 (ptm160) cc_final: 0.8536 (ptm160) REVERT: A 198 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8605 (mmmm) REVERT: A 199 ASP cc_start: 0.8761 (p0) cc_final: 0.8547 (p0) REVERT: B 78 GLN cc_start: 0.9179 (mt0) cc_final: 0.8753 (mt0) REVERT: B 125 MET cc_start: 0.9103 (mmm) cc_final: 0.8713 (mmt) REVERT: B 130 CYS cc_start: 0.8765 (p) cc_final: 0.7995 (p) REVERT: B 134 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8431 (mmtt) REVERT: B 150 HIS cc_start: 0.7459 (m-70) cc_final: 0.7157 (m-70) REVERT: B 193 ARG cc_start: 0.8973 (ptm160) cc_final: 0.8530 (ptm160) REVERT: B 198 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8588 (mmmm) REVERT: B 199 ASP cc_start: 0.8767 (p0) cc_final: 0.8551 (p0) REVERT: C 42 ASN cc_start: 0.8480 (m-40) cc_final: 0.8068 (m-40) REVERT: D 42 ASN cc_start: 0.8485 (m-40) cc_final: 0.8075 (m-40) outliers start: 12 outliers final: 9 residues processed: 118 average time/residue: 0.1728 time to fit residues: 24.3180 Evaluate side-chains 122 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.116934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.088099 restraints weight = 5961.340| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.06 r_work: 0.2908 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3750 Z= 0.197 Angle : 0.490 4.444 5086 Z= 0.269 Chirality : 0.041 0.149 556 Planarity : 0.003 0.027 622 Dihedral : 14.234 139.436 516 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.87 % Allowed : 13.66 % Favored : 82.47 % 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: 1.72 (0.40), residues: 426 helix: 3.01 (0.33), residues: 224 sheet: -0.66 (0.55), residues: 88 loop : -1.27 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.002 0.000 HIS A 204 PHE 0.025 0.002 PHE B 207 TYR 0.006 0.001 TYR B 91 ARG 0.001 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.9192 (mt0) cc_final: 0.8777 (mt0) REVERT: A 125 MET cc_start: 0.9121 (mmm) cc_final: 0.8744 (mmt) REVERT: A 130 CYS cc_start: 0.8798 (p) cc_final: 0.8067 (p) REVERT: A 150 HIS cc_start: 0.7324 (m-70) cc_final: 0.6891 (m-70) REVERT: A 155 ASP cc_start: 0.8406 (m-30) cc_final: 0.7351 (t0) REVERT: A 193 ARG cc_start: 0.9015 (ptm160) cc_final: 0.8574 (ptm160) REVERT: A 198 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8626 (mmmm) REVERT: B 78 GLN cc_start: 0.9201 (mt0) cc_final: 0.8787 (mt0) REVERT: B 125 MET cc_start: 0.9120 (mmm) cc_final: 0.8729 (mmt) REVERT: B 130 CYS cc_start: 0.8805 (p) cc_final: 0.8076 (p) REVERT: B 150 HIS cc_start: 0.7338 (m-70) cc_final: 0.6897 (m-70) REVERT: B 155 ASP cc_start: 0.8404 (m-30) cc_final: 0.7344 (t0) REVERT: B 193 ARG cc_start: 0.9014 (ptm160) cc_final: 0.8569 (ptm160) REVERT: B 198 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8623 (mmmm) REVERT: C 42 ASN cc_start: 0.8463 (m-40) cc_final: 0.8041 (m-40) REVERT: D 42 ASN cc_start: 0.8467 (m-40) cc_final: 0.8050 (m-40) outliers start: 15 outliers final: 10 residues processed: 123 average time/residue: 0.1705 time to fit residues: 25.1627 Evaluate side-chains 123 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088450 restraints weight = 5934.740| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.05 r_work: 0.2919 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3750 Z= 0.190 Angle : 0.502 5.879 5086 Z= 0.273 Chirality : 0.041 0.149 556 Planarity : 0.003 0.027 622 Dihedral : 13.258 136.633 516 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.84 % Allowed : 14.69 % Favored : 82.47 % 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: 1.77 (0.40), residues: 426 helix: 3.01 (0.33), residues: 224 sheet: -0.56 (0.55), residues: 88 loop : -1.22 (0.48), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.002 0.000 HIS A 204 PHE 0.025 0.002 PHE A 207 TYR 0.006 0.001 TYR B 74 ARG 0.001 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.9195 (mt0) cc_final: 0.8771 (mt0) REVERT: A 125 MET cc_start: 0.9120 (mmm) cc_final: 0.8753 (mmt) REVERT: A 130 CYS cc_start: 0.8775 (p) cc_final: 0.8049 (p) REVERT: A 150 HIS cc_start: 0.7336 (m-70) cc_final: 0.6901 (m-70) REVERT: A 155 ASP cc_start: 0.8387 (m-30) cc_final: 0.7348 (t0) REVERT: A 193 ARG cc_start: 0.9028 (ptm160) cc_final: 0.8590 (ptm160) REVERT: A 198 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8585 (mmmm) REVERT: A 209 GLU cc_start: 0.8666 (tt0) cc_final: 0.8412 (tp30) REVERT: B 78 GLN cc_start: 0.9189 (mt0) cc_final: 0.8762 (mt0) REVERT: B 125 MET cc_start: 0.9130 (mmm) cc_final: 0.8749 (mmt) REVERT: B 130 CYS cc_start: 0.8791 (p) cc_final: 0.8072 (p) REVERT: B 150 HIS cc_start: 0.7347 (m-70) cc_final: 0.6906 (m-70) REVERT: B 155 ASP cc_start: 0.8376 (m-30) cc_final: 0.7336 (t0) REVERT: B 193 ARG cc_start: 0.9029 (ptm160) cc_final: 0.8586 (ptm160) REVERT: B 198 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8573 (mmmm) REVERT: B 209 GLU cc_start: 0.8682 (tt0) cc_final: 0.8403 (tp30) REVERT: C 42 ASN cc_start: 0.8488 (m-40) cc_final: 0.8079 (m-40) REVERT: D 42 ASN cc_start: 0.8491 (m-40) cc_final: 0.8083 (m-40) outliers start: 11 outliers final: 9 residues processed: 123 average time/residue: 0.1795 time to fit residues: 26.5558 Evaluate side-chains 125 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.114446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085496 restraints weight = 5917.460| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.04 r_work: 0.2897 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3750 Z= 0.249 Angle : 0.529 5.996 5086 Z= 0.285 Chirality : 0.042 0.150 556 Planarity : 0.003 0.027 622 Dihedral : 12.574 132.907 516 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.58 % Allowed : 15.46 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.84 (0.40), residues: 426 helix: 3.02 (0.33), residues: 224 sheet: -0.44 (0.55), residues: 88 loop : -1.16 (0.48), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.002 0.001 HIS B 204 PHE 0.027 0.002 PHE B 207 TYR 0.007 0.001 TYR B 91 ARG 0.002 0.000 ARG A 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.9207 (mt0) cc_final: 0.8807 (mt0) REVERT: A 125 MET cc_start: 0.9130 (mmm) cc_final: 0.8752 (mmt) REVERT: A 130 CYS cc_start: 0.8774 (p) cc_final: 0.8040 (p) REVERT: A 150 HIS cc_start: 0.7401 (m-70) cc_final: 0.6907 (m-70) REVERT: A 155 ASP cc_start: 0.8420 (m-30) cc_final: 0.7330 (t0) REVERT: A 193 ARG cc_start: 0.9025 (ptm160) cc_final: 0.8578 (ptm160) REVERT: A 198 LYS cc_start: 0.8878 (mmtm) cc_final: 0.8574 (mmmm) REVERT: A 209 GLU cc_start: 0.8662 (tt0) cc_final: 0.8360 (tp30) REVERT: B 78 GLN cc_start: 0.9195 (mt0) cc_final: 0.8794 (mt0) REVERT: B 125 MET cc_start: 0.9144 (mmm) cc_final: 0.8756 (mmt) REVERT: B 130 CYS cc_start: 0.8781 (p) cc_final: 0.8053 (p) REVERT: B 150 HIS cc_start: 0.7403 (m-70) cc_final: 0.6866 (m-70) REVERT: B 155 ASP cc_start: 0.8419 (m-30) cc_final: 0.7321 (t0) REVERT: B 193 ARG cc_start: 0.9032 (ptm160) cc_final: 0.8585 (ptm160) REVERT: B 198 LYS cc_start: 0.8895 (mmtm) cc_final: 0.8602 (mmmm) REVERT: B 209 GLU cc_start: 0.8660 (tt0) cc_final: 0.8362 (tp30) REVERT: C 42 ASN cc_start: 0.8471 (m-40) cc_final: 0.8062 (m-40) REVERT: D 42 ASN cc_start: 0.8475 (m-40) cc_final: 0.8072 (m-40) outliers start: 10 outliers final: 10 residues processed: 117 average time/residue: 0.1798 time to fit residues: 25.1736 Evaluate side-chains 119 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.0050 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5292 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.115978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.087831 restraints weight = 5881.013| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.99 r_work: 0.2935 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3750 Z= 0.183 Angle : 0.501 6.021 5086 Z= 0.273 Chirality : 0.041 0.153 556 Planarity : 0.003 0.027 622 Dihedral : 11.998 129.056 516 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.06 % Allowed : 16.49 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.88 (0.40), residues: 426 helix: 2.99 (0.32), residues: 224 sheet: -0.37 (0.55), residues: 88 loop : -1.06 (0.49), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.002 0.000 HIS A 204 PHE 0.026 0.002 PHE A 207 TYR 0.005 0.001 TYR A 74 ARG 0.002 0.000 ARG A 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.74 seconds wall clock time: 40 minutes 1.69 seconds (2401.69 seconds total)