Starting phenix.real_space_refine on Wed Jul 23 17:41:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqs_28544/07_2025/8eqs_28544_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqs_28544/07_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_28544/07_2025/8eqs_28544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqs_28544/07_2025/8eqs_28544.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqs_28544/07_2025/8eqs_28544_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqs_28544/07_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-5711/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: 3.16, per 1000 atoms: 0.86 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: 0.98 Conformation dependent library (CDL) restraints added in 423.2 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: 0.40 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: 1.07 Time building geometry restraints manager: 1.15 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: 0.830 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.050 Find NCS groups from input model: 0.070 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- 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= 0.251 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 Details of bonding type rmsd hydrogen bonds : bond 0.19056 ( 234) hydrogen bonds : angle 7.32231 ( 678) covalent geometry : bond 0.00517 ( 3750) covalent geometry : angle 0.73687 ( 5086) *********************** 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 : 0.445 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: 0.1832 time to fit residues: 29.9109 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 : 0.399 ------------------------------------------------------------------------------- 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: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.118935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.089142 restraints weight = 5828.394| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.14 r_work: 0.2974 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3750 Z= 0.160 Angle : 0.506 4.342 5086 Z= 0.282 Chirality : 0.043 0.146 556 Planarity : 0.003 0.027 622 Dihedral : 16.883 150.004 516 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.50 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: 1.31 (0.39), residues: 426 helix: 2.52 (0.33), residues: 212 sheet: -0.43 (0.57), residues: 88 loop : -1.06 (0.46), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.003 0.001 HIS B 204 PHE 0.011 0.001 PHE B 56 TYR 0.014 0.001 TYR A 74 ARG 0.003 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 234) hydrogen bonds : angle 4.50379 ( 678) covalent geometry : bond 0.00369 ( 3750) covalent geometry : angle 0.50648 ( 5086) *********************** 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 : 0.455 Fit side-chains REVERT: A 67 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8329 (mmmm) REVERT: A 130 CYS cc_start: 0.8714 (p) cc_final: 0.7913 (p) REVERT: A 185 GLN cc_start: 0.9013 (tm130) cc_final: 0.8681 (tm130) REVERT: A 193 ARG cc_start: 0.8908 (ptm160) cc_final: 0.8522 (ptm160) REVERT: A 198 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8597 (mmmm) REVERT: B 43 PHE cc_start: 0.7951 (m-10) cc_final: 0.7681 (m-80) REVERT: B 67 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8344 (mmmm) REVERT: B 130 CYS cc_start: 0.8716 (p) cc_final: 0.7918 (p) REVERT: B 185 GLN cc_start: 0.9019 (tm130) cc_final: 0.8689 (tm130) REVERT: B 193 ARG cc_start: 0.8913 (ptm160) cc_final: 0.8523 (ptm160) REVERT: B 198 LYS cc_start: 0.8876 (mmtm) cc_final: 0.8586 (mmmm) REVERT: C 42 ASN cc_start: 0.8526 (m-40) cc_final: 0.8095 (m-40) REVERT: D 42 ASN cc_start: 0.8525 (m-40) cc_final: 0.8098 (m-40) outliers start: 8 outliers final: 4 residues processed: 131 average time/residue: 0.1768 time to fit residues: 27.7362 Evaluate side-chains 121 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.116612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.087514 restraints weight = 5808.125| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.06 r_work: 0.2938 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3750 Z= 0.164 Angle : 0.500 4.354 5086 Z= 0.277 Chirality : 0.042 0.142 556 Planarity : 0.003 0.028 622 Dihedral : 16.272 145.638 516 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.09 % Allowed : 13.92 % Favored : 82.99 % 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: 1.54 (0.40), residues: 426 helix: 2.89 (0.33), residues: 222 sheet: -0.58 (0.55), residues: 88 loop : -1.48 (0.46), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.003 0.001 HIS B 204 PHE 0.010 0.001 PHE B 56 TYR 0.008 0.001 TYR A 109 ARG 0.005 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 234) hydrogen bonds : angle 4.32310 ( 678) covalent geometry : bond 0.00379 ( 3750) covalent geometry : angle 0.49977 ( 5086) *********************** 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 125 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.401 Fit side-chains REVERT: A 109 TYR cc_start: 0.9058 (m-80) cc_final: 0.8664 (m-80) REVERT: A 128 TRP cc_start: 0.8548 (t60) cc_final: 0.8026 (t60) REVERT: A 130 CYS cc_start: 0.8812 (p) cc_final: 0.8043 (p) REVERT: A 185 GLN cc_start: 0.9090 (tm130) cc_final: 0.8793 (tm130) REVERT: A 193 ARG cc_start: 0.8950 (ptm160) cc_final: 0.8619 (ptm160) REVERT: A 198 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8569 (mmmm) REVERT: B 109 TYR cc_start: 0.9044 (m-80) cc_final: 0.8656 (m-80) REVERT: B 128 TRP cc_start: 0.8539 (t60) cc_final: 0.8017 (t60) REVERT: B 130 CYS cc_start: 0.8810 (p) cc_final: 0.8040 (p) REVERT: B 185 GLN cc_start: 0.9100 (tm130) cc_final: 0.8805 (tm130) REVERT: B 193 ARG cc_start: 0.8956 (ptm160) cc_final: 0.8623 (ptm160) REVERT: B 198 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8567 (mmmm) REVERT: C 29 ARG cc_start: 0.6973 (ttt-90) cc_final: 0.6523 (mtt-85) REVERT: C 42 ASN cc_start: 0.8511 (m-40) cc_final: 0.8083 (m-40) REVERT: D 29 ARG cc_start: 0.6979 (ttt-90) cc_final: 0.6528 (mtt-85) REVERT: D 42 ASN cc_start: 0.8516 (m-40) cc_final: 0.8088 (m-40) outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 0.1823 time to fit residues: 26.6056 Evaluate side-chains 116 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 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 = 0.3573 r_free = 0.3573 target = 0.117536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088239 restraints weight = 5899.792| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.08 r_work: 0.2929 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3757 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= 0.150 Angle : 0.481 4.376 5086 Z= 0.268 Chirality : 0.041 0.137 556 Planarity : 0.003 0.026 622 Dihedral : 15.938 143.114 516 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.09 % Allowed : 14.95 % 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: 1.68 (0.41), residues: 426 helix: 2.96 (0.34), residues: 224 sheet: -0.56 (0.54), residues: 88 loop : -1.36 (0.48), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.002 0.000 HIS B 204 PHE 0.015 0.001 PHE A 207 TYR 0.007 0.001 TYR A 109 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 234) hydrogen bonds : angle 4.29649 ( 678) covalent geometry : bond 0.00344 ( 3750) covalent geometry : angle 0.48109 ( 5086) *********************** 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 122 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 CYS cc_start: 0.8776 (p) cc_final: 0.8027 (p) REVERT: A 150 HIS cc_start: 0.7445 (m-70) cc_final: 0.7218 (m-70) REVERT: A 155 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7323 (t0) REVERT: A 193 ARG cc_start: 0.8968 (ptm160) cc_final: 0.8637 (ptm160) REVERT: A 198 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8623 (mmmm) REVERT: B 130 CYS cc_start: 0.8780 (p) cc_final: 0.8034 (p) REVERT: B 150 HIS cc_start: 0.7421 (m-70) cc_final: 0.7188 (m-70) REVERT: B 155 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7320 (t0) REVERT: B 193 ARG cc_start: 0.8975 (ptm160) cc_final: 0.8642 (ptm160) REVERT: B 198 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8621 (mmmm) REVERT: C 42 ASN cc_start: 0.8488 (m-40) cc_final: 0.8052 (m-40) REVERT: D 42 ASN cc_start: 0.8489 (m-40) cc_final: 0.8053 (m-40) outliers start: 12 outliers final: 8 residues processed: 118 average time/residue: 0.1725 time to fit residues: 24.5027 Evaluate side-chains 118 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 190 SER 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 155 ASP 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: 0.7980 chunk 2 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.086372 restraints weight = 5946.527| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.10 r_work: 0.2919 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3750 Z= 0.157 Angle : 0.494 4.377 5086 Z= 0.271 Chirality : 0.041 0.139 556 Planarity : 0.003 0.026 622 Dihedral : 15.730 141.109 516 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.64 % Allowed : 13.40 % 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: 1.59 (0.40), residues: 426 helix: 2.90 (0.33), residues: 224 sheet: -0.62 (0.53), residues: 88 loop : -1.40 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.002 0.001 HIS B 204 PHE 0.014 0.002 PHE B 207 TYR 0.011 0.001 TYR A 74 ARG 0.002 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 234) hydrogen bonds : angle 4.31945 ( 678) covalent geometry : bond 0.00363 ( 3750) covalent geometry : angle 0.49365 ( 5086) *********************** 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 122 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9071 (mmm) cc_final: 0.8706 (mmt) REVERT: A 130 CYS cc_start: 0.8747 (p) cc_final: 0.8013 (p) REVERT: A 150 HIS cc_start: 0.7417 (m-70) cc_final: 0.7194 (m-70) REVERT: A 155 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7355 (t0) REVERT: A 165 ASP cc_start: 0.8910 (m-30) cc_final: 0.8699 (m-30) REVERT: A 193 ARG cc_start: 0.9004 (ptm160) cc_final: 0.8624 (ptm160) REVERT: A 198 LYS cc_start: 0.8954 (mmtm) cc_final: 0.8639 (mmmm) REVERT: B 125 MET cc_start: 0.9068 (mmm) cc_final: 0.8693 (mmt) REVERT: B 130 CYS cc_start: 0.8753 (p) cc_final: 0.8019 (p) REVERT: B 150 HIS cc_start: 0.7424 (m-70) cc_final: 0.7181 (m-70) REVERT: B 155 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7336 (t0) REVERT: B 165 ASP cc_start: 0.8907 (m-30) cc_final: 0.8697 (m-30) REVERT: B 193 ARG cc_start: 0.9012 (ptm160) cc_final: 0.8631 (ptm160) REVERT: B 198 LYS cc_start: 0.8946 (mmtm) cc_final: 0.8632 (mmmm) REVERT: C 42 ASN cc_start: 0.8491 (m-40) cc_final: 0.8072 (m-40) REVERT: D 42 ASN cc_start: 0.8497 (m-40) cc_final: 0.8081 (m-40) outliers start: 18 outliers final: 10 residues processed: 118 average time/residue: 0.1856 time to fit residues: 26.4551 Evaluate side-chains 116 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 155 ASP 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 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 155 ASP 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: 0.9980 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 0.0770 chunk 16 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN B 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087370 restraints weight = 5985.756| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.13 r_work: 0.2933 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4041 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= 0.128 Angle : 0.474 4.355 5086 Z= 0.264 Chirality : 0.041 0.141 556 Planarity : 0.003 0.026 622 Dihedral : 15.367 138.614 516 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.58 % Allowed : 13.40 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.76 (0.40), residues: 426 helix: 2.91 (0.33), residues: 224 sheet: -0.54 (0.53), residues: 96 loop : -1.04 (0.49), residues: 106 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 0.015 0.001 PHE B 207 TYR 0.010 0.001 TYR B 74 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.02884 ( 234) hydrogen bonds : angle 4.31586 ( 678) covalent geometry : bond 0.00292 ( 3750) covalent geometry : angle 0.47404 ( 5086) *********************** 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 123 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9080 (mmm) cc_final: 0.8692 (mmt) REVERT: A 130 CYS cc_start: 0.8780 (p) cc_final: 0.8047 (p) REVERT: A 155 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7344 (t0) REVERT: A 193 ARG cc_start: 0.8987 (ptm160) cc_final: 0.8577 (ptm160) REVERT: A 198 LYS cc_start: 0.8946 (mmtm) cc_final: 0.8653 (mmmm) REVERT: B 125 MET cc_start: 0.9080 (mmm) cc_final: 0.8676 (mmt) REVERT: B 130 CYS cc_start: 0.8790 (p) cc_final: 0.8060 (p) REVERT: B 155 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7380 (t0) REVERT: B 193 ARG cc_start: 0.8994 (ptm160) cc_final: 0.8582 (ptm160) REVERT: B 198 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8646 (mmmm) REVERT: C 42 ASN cc_start: 0.8469 (m-40) cc_final: 0.8041 (m-40) REVERT: D 42 ASN cc_start: 0.8474 (m-40) cc_final: 0.8050 (m-40) outliers start: 10 outliers final: 6 residues processed: 117 average time/residue: 0.1694 time to fit residues: 23.8079 Evaluate side-chains 118 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 155 ASP 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: 0.5980 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN B 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087069 restraints weight = 5850.449| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.03 r_work: 0.2925 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4104 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= 0.132 Angle : 0.497 5.254 5086 Z= 0.271 Chirality : 0.041 0.143 556 Planarity : 0.003 0.026 622 Dihedral : 15.026 138.196 516 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.38 % Allowed : 12.37 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.91 (0.33), residues: 224 sheet: -0.31 (0.55), residues: 88 loop : -1.37 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.002 0.001 HIS A 204 PHE 0.016 0.001 PHE B 207 TYR 0.010 0.001 TYR A 74 ARG 0.001 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 234) hydrogen bonds : angle 4.31097 ( 678) covalent geometry : bond 0.00301 ( 3750) covalent geometry : angle 0.49693 ( 5086) *********************** 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 132 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9074 (mmm) cc_final: 0.8678 (mmt) REVERT: A 130 CYS cc_start: 0.8795 (p) cc_final: 0.8063 (p) REVERT: A 155 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7829 (t0) REVERT: A 193 ARG cc_start: 0.8973 (ptm160) cc_final: 0.8444 (ptm-80) REVERT: A 198 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8599 (mmmm) REVERT: B 125 MET cc_start: 0.9074 (mmm) cc_final: 0.8670 (mmt) REVERT: B 130 CYS cc_start: 0.8798 (p) cc_final: 0.8063 (p) REVERT: B 155 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7851 (t0) REVERT: B 193 ARG cc_start: 0.8977 (ptm160) cc_final: 0.8506 (ptm-80) REVERT: B 198 LYS cc_start: 0.8909 (mmtm) cc_final: 0.8593 (mmmm) REVERT: B 199 ASP cc_start: 0.8777 (p0) cc_final: 0.8562 (p0) REVERT: C 42 ASN cc_start: 0.8462 (m-40) cc_final: 0.8046 (m-40) REVERT: D 42 ASN cc_start: 0.8469 (m-40) cc_final: 0.8056 (m-40) outliers start: 17 outliers final: 9 residues processed: 126 average time/residue: 0.1707 time to fit residues: 25.8953 Evaluate side-chains 126 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN B 78 GLN 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 = 0.116612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.088344 restraints weight = 5926.108| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.02 r_work: 0.2941 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4192 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= 0.122 Angle : 0.490 5.534 5086 Z= 0.270 Chirality : 0.041 0.147 556 Planarity : 0.003 0.026 622 Dihedral : 14.445 137.809 516 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.84 % Allowed : 13.66 % 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: 1.83 (0.40), residues: 426 helix: 2.94 (0.33), residues: 224 sheet: -0.11 (0.57), residues: 88 loop : -1.33 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 149 HIS 0.002 0.001 HIS B 204 PHE 0.025 0.001 PHE A 207 TYR 0.010 0.001 TYR B 74 ARG 0.001 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.02894 ( 234) hydrogen bonds : angle 4.20791 ( 678) covalent geometry : bond 0.00274 ( 3750) covalent geometry : angle 0.49004 ( 5086) *********************** 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 132 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.9073 (mmm) cc_final: 0.8700 (mmt) REVERT: A 130 CYS cc_start: 0.8788 (p) cc_final: 0.8060 (p) REVERT: A 155 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7869 (t0) REVERT: A 193 ARG cc_start: 0.9007 (ptm160) cc_final: 0.8570 (ptm160) REVERT: A 198 LYS cc_start: 0.8889 (mmtm) cc_final: 0.8600 (mmmm) REVERT: B 109 TYR cc_start: 0.8973 (m-80) cc_final: 0.8648 (m-80) REVERT: B 125 MET cc_start: 0.9078 (mmm) cc_final: 0.8693 (mmt) REVERT: B 130 CYS cc_start: 0.8789 (p) cc_final: 0.8062 (p) REVERT: B 155 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7875 (t0) REVERT: B 193 ARG cc_start: 0.9014 (ptm160) cc_final: 0.8541 (ptm-80) REVERT: B 198 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8609 (mmmm) REVERT: C 42 ASN cc_start: 0.8468 (m-40) cc_final: 0.8064 (m-40) REVERT: D 42 ASN cc_start: 0.8474 (m-40) cc_final: 0.8073 (m-40) outliers start: 11 outliers final: 9 residues processed: 126 average time/residue: 0.1816 time to fit residues: 27.2557 Evaluate side-chains 125 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN B 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.087819 restraints weight = 5907.976| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.08 r_work: 0.2940 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4210 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= 0.124 Angle : 0.504 5.749 5086 Z= 0.274 Chirality : 0.041 0.149 556 Planarity : 0.003 0.026 622 Dihedral : 13.591 136.548 516 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.09 % Allowed : 13.92 % Favored : 82.99 % 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: 3.01 (0.33), residues: 224 sheet: -0.31 (0.55), residues: 92 loop : -1.17 (0.48), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 149 HIS 0.002 0.000 HIS A 204 PHE 0.025 0.001 PHE B 207 TYR 0.011 0.001 TYR B 74 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.02890 ( 234) hydrogen bonds : angle 4.18692 ( 678) covalent geometry : bond 0.00282 ( 3750) covalent geometry : angle 0.50380 ( 5086) *********************** 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 133 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.9103 (mmm) cc_final: 0.8703 (mmt) REVERT: A 130 CYS cc_start: 0.8793 (p) cc_final: 0.8098 (p) REVERT: A 155 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7865 (t0) REVERT: A 193 ARG cc_start: 0.9039 (ptm160) cc_final: 0.8509 (ptm-80) REVERT: A 198 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8580 (mmmm) REVERT: A 209 GLU cc_start: 0.8646 (tt0) cc_final: 0.8354 (tp30) REVERT: B 109 TYR cc_start: 0.8962 (m-80) cc_final: 0.8668 (m-80) REVERT: B 125 MET cc_start: 0.9106 (mmm) cc_final: 0.8701 (mmt) REVERT: B 130 CYS cc_start: 0.8801 (p) cc_final: 0.8105 (p) REVERT: B 155 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7871 (t0) REVERT: B 193 ARG cc_start: 0.9037 (ptm160) cc_final: 0.8613 (ptm160) REVERT: B 198 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8584 (mmmm) REVERT: B 209 GLU cc_start: 0.8719 (tt0) cc_final: 0.8347 (tp30) REVERT: C 42 ASN cc_start: 0.8472 (m-40) cc_final: 0.8062 (m-40) REVERT: D 42 ASN cc_start: 0.8477 (m-40) cc_final: 0.8069 (m-40) outliers start: 12 outliers final: 10 residues processed: 127 average time/residue: 0.2199 time to fit residues: 33.8043 Evaluate side-chains 131 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.114667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086450 restraints weight = 5940.971| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.00 r_work: 0.2910 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3750 Z= 0.158 Angle : 0.534 6.008 5086 Z= 0.287 Chirality : 0.042 0.150 556 Planarity : 0.003 0.027 622 Dihedral : 12.821 132.262 516 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.09 % Allowed : 15.46 % 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: 1.92 (0.41), residues: 426 helix: 3.01 (0.33), residues: 224 sheet: -0.31 (0.55), residues: 92 loop : -1.06 (0.49), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.002 0.001 HIS A 204 PHE 0.026 0.002 PHE A 207 TYR 0.014 0.001 TYR A 74 ARG 0.002 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 234) hydrogen bonds : angle 4.28039 ( 678) covalent geometry : bond 0.00363 ( 3750) covalent geometry : angle 0.53388 ( 5086) ********************** 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 124 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9103 (mmm) cc_final: 0.8725 (mmt) REVERT: A 130 CYS cc_start: 0.8807 (p) cc_final: 0.8127 (p) REVERT: A 155 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7948 (t0) REVERT: A 193 ARG cc_start: 0.9039 (ptm160) cc_final: 0.8602 (ptm160) REVERT: A 198 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8589 (mmmm) REVERT: A 209 GLU cc_start: 0.8656 (tt0) cc_final: 0.8354 (tp30) REVERT: B 125 MET cc_start: 0.9097 (mmm) cc_final: 0.8708 (mmt) REVERT: B 130 CYS cc_start: 0.8815 (p) cc_final: 0.8138 (p) REVERT: B 155 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7933 (t0) REVERT: B 193 ARG cc_start: 0.9044 (ptm160) cc_final: 0.8601 (ptm160) REVERT: B 198 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8590 (mmmm) REVERT: C 42 ASN cc_start: 0.8487 (m-40) cc_final: 0.8066 (m-40) REVERT: D 42 ASN cc_start: 0.8490 (m-40) cc_final: 0.8071 (m-40) outliers start: 12 outliers final: 10 residues processed: 118 average time/residue: 0.2107 time to fit residues: 29.7613 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 : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.0050 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.4952 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.116355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087648 restraints weight = 5887.344| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.04 r_work: 0.2942 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3750 Z= 0.128 Angle : 0.532 6.016 5086 Z= 0.287 Chirality : 0.042 0.150 556 Planarity : 0.003 0.026 622 Dihedral : 12.118 128.209 516 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.09 % Allowed : 16.49 % Favored : 80.41 % 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: 1.91 (0.40), residues: 426 helix: 2.97 (0.33), residues: 224 sheet: -0.31 (0.55), residues: 92 loop : -1.01 (0.49), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.002 0.000 HIS A 204 PHE 0.027 0.002 PHE A 207 TYR 0.012 0.001 TYR B 74 ARG 0.002 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 234) hydrogen bonds : angle 4.22144 ( 678) covalent geometry : bond 0.00292 ( 3750) covalent geometry : angle 0.53200 ( 5086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.95 seconds wall clock time: 44 minutes 5.44 seconds (2645.44 seconds total)