Starting phenix.real_space_refine on Wed Sep 17 03:11:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyy_61004/09_2025/9iyy_61004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyy_61004/09_2025/9iyy_61004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iyy_61004/09_2025/9iyy_61004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyy_61004/09_2025/9iyy_61004.map" model { file = "/net/cci-nas-00/data/ceres_data/9iyy_61004/09_2025/9iyy_61004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyy_61004/09_2025/9iyy_61004.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.139 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 1592 2.51 5 N 430 2.21 5 O 482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2534 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 432 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 381 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 44} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.89, per 1000 atoms: 0.35 Number of scatterers: 2534 At special positions: 0 Unit cell: (54.417, 65.087, 80.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 482 8.00 N 430 7.00 C 1592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 138 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 149 " distance=2.02 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 138 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 75.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 604 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 13.2% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.539A pdb=" N MET B 125 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.670A pdb=" N THR H 91 " --> pdb=" O VAL H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.936A pdb=" N GLU L 82 " --> pdb=" O CYS L 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.501A pdb=" N CYS B 137 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.547A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLY H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS H 98 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.547A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.748A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP L 34 " --> pdb=" O ILE L 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.748A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 22 97 hydrogen bonds defined for protein. 222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.34 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 813 1.34 - 1.46: 582 1.46 - 1.58: 1161 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 2593 Sorted by residual: bond pdb=" CB CYS B 107 " pdb=" SG CYS B 107 " ideal model delta sigma weight residual 1.808 1.781 0.027 3.30e-02 9.18e+02 6.48e-01 bond pdb=" CB LEU H 48 " pdb=" CG LEU H 48 " ideal model delta sigma weight residual 1.530 1.515 0.015 2.00e-02 2.50e+03 5.88e-01 bond pdb=" CG LEU A 104 " pdb=" CD2 LEU A 104 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.86e-01 bond pdb=" CG LEU H 45 " pdb=" CD1 LEU H 45 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.62e-01 bond pdb=" CG LEU L 97 " pdb=" CD2 LEU L 97 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.34e-01 ... (remaining 2588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 3465 1.77 - 3.55: 52 3.55 - 5.32: 2 5.32 - 7.09: 2 7.09 - 8.87: 1 Bond angle restraints: 3522 Sorted by residual: angle pdb=" C ASP L 49 " pdb=" N ASP L 50 " pdb=" CA ASP L 50 " ideal model delta sigma weight residual 121.54 126.96 -5.42 1.91e+00 2.74e-01 8.06e+00 angle pdb=" CA LEU A 104 " pdb=" CB LEU A 104 " pdb=" CG LEU A 104 " ideal model delta sigma weight residual 116.30 125.17 -8.87 3.50e+00 8.16e-02 6.42e+00 angle pdb=" CA LEU A 98 " pdb=" CB LEU A 98 " pdb=" CG LEU A 98 " ideal model delta sigma weight residual 116.30 123.03 -6.73 3.50e+00 8.16e-02 3.69e+00 angle pdb=" NE ARG L 60 " pdb=" CZ ARG L 60 " pdb=" NH1 ARG L 60 " ideal model delta sigma weight residual 121.50 119.89 1.61 1.00e+00 1.00e+00 2.59e+00 angle pdb=" NE ARG H 67 " pdb=" CZ ARG H 67 " pdb=" NH1 ARG H 67 " ideal model delta sigma weight residual 121.50 119.97 1.53 1.00e+00 1.00e+00 2.34e+00 ... (remaining 3517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 1420 16.90 - 33.79: 91 33.79 - 50.68: 25 50.68 - 67.58: 4 67.58 - 84.47: 2 Dihedral angle restraints: 1542 sinusoidal: 591 harmonic: 951 Sorted by residual: dihedral pdb=" CA PHE H 95 " pdb=" C PHE H 95 " pdb=" N CYS H 96 " pdb=" CA CYS H 96 " ideal model delta harmonic sigma weight residual 180.00 164.05 15.95 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CB GLU H 6 " pdb=" CG GLU H 6 " pdb=" CD GLU H 6 " pdb=" OE1 GLU H 6 " ideal model delta sinusoidal sigma weight residual 0.00 -84.47 84.47 1 3.00e+01 1.11e-03 9.64e+00 dihedral pdb=" N CYS L 87 " pdb=" CA CYS L 87 " pdb=" CB CYS L 87 " pdb=" SG CYS L 87 " ideal model delta sinusoidal sigma weight residual -60.00 -119.59 59.59 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 202 0.026 - 0.052: 115 0.052 - 0.078: 40 0.078 - 0.104: 14 0.104 - 0.130: 18 Chirality restraints: 389 Sorted by residual: chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE B 110 " pdb=" N ILE B 110 " pdb=" C ILE B 110 " pdb=" CB ILE B 110 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 386 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 53 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO L 54 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 54 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 54 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 104 " 0.020 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO A 105 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 42 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO L 43 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO L 43 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 43 " 0.016 5.00e-02 4.00e+02 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 692 2.80 - 3.32: 2283 3.32 - 3.85: 4195 3.85 - 4.37: 5163 4.37 - 4.90: 9146 Nonbonded interactions: 21479 Sorted by model distance: nonbonded pdb=" NH2 ARG B 122 " pdb=" O GLY L 28 " model vdw 2.275 3.120 nonbonded pdb=" O SER H 52 " pdb=" NH1 ARG H 72 " model vdw 2.312 3.120 nonbonded pdb=" NH1 ARG H 106 " pdb=" OD1 ASP L 95 " model vdw 2.326 3.120 nonbonded pdb=" N VAL L 32 " pdb=" OD1 ASP L 50 " model vdw 2.349 3.120 nonbonded pdb=" OE1 GLN H 39 " pdb=" NE2 GLN L 37 " model vdw 2.386 3.120 ... (remaining 21474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.550 Find NCS groups from input model: 0.010 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.004 0.027 2602 Z= 0.176 Angle : 0.576 8.866 3540 Z= 0.303 Chirality : 0.043 0.130 389 Planarity : 0.004 0.038 450 Dihedral : 12.045 84.468 911 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.12 % Allowed : 7.55 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.47), residues: 326 helix: -0.52 (0.96), residues: 30 sheet: -1.22 (0.47), residues: 108 loop : 0.11 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 60 TYR 0.006 0.001 TYR L 2 PHE 0.008 0.002 PHE L 99 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 2593) covalent geometry : angle 0.57425 ( 3522) SS BOND : bond 0.00416 ( 9) SS BOND : angle 0.87074 ( 18) hydrogen bonds : bond 0.16908 ( 82) hydrogen bonds : angle 8.99881 ( 222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.083 Fit side-chains REVERT: A 133 MET cc_start: 0.7351 (mtp) cc_final: 0.7026 (mtp) REVERT: H 110 MET cc_start: 0.8525 (mpt) cc_final: 0.7982 (mpt) REVERT: L 26 ASN cc_start: 0.7290 (t0) cc_final: 0.7066 (t0) outliers start: 17 outliers final: 9 residues processed: 52 average time/residue: 0.0662 time to fit residues: 4.0520 Evaluate side-chains 43 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.0040 chunk 13 optimal weight: 0.0170 overall best weight: 0.3030 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.158768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143560 restraints weight = 2361.145| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 0.97 r_work: 0.3556 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2602 Z= 0.124 Angle : 0.560 9.192 3540 Z= 0.287 Chirality : 0.043 0.155 389 Planarity : 0.005 0.035 450 Dihedral : 7.128 58.967 372 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.96 % Allowed : 9.71 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.46), residues: 326 helix: -0.20 (0.94), residues: 31 sheet: -0.91 (0.51), residues: 99 loop : 0.02 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.008 0.001 TYR H 101 PHE 0.009 0.002 PHE A 161 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 2593) covalent geometry : angle 0.55896 ( 3522) SS BOND : bond 0.00366 ( 9) SS BOND : angle 0.75352 ( 18) hydrogen bonds : bond 0.03073 ( 82) hydrogen bonds : angle 6.16866 ( 222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.094 Fit side-chains REVERT: H 110 MET cc_start: 0.8462 (mpt) cc_final: 0.7999 (mpt) outliers start: 11 outliers final: 9 residues processed: 41 average time/residue: 0.0588 time to fit residues: 2.9445 Evaluate side-chains 41 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.157608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141232 restraints weight = 2387.432| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.05 r_work: 0.3548 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2602 Z= 0.142 Angle : 0.547 9.057 3540 Z= 0.277 Chirality : 0.043 0.135 389 Planarity : 0.004 0.034 450 Dihedral : 6.925 59.174 369 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.24 % Allowed : 10.07 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.47), residues: 326 helix: -0.20 (0.94), residues: 32 sheet: -0.62 (0.53), residues: 99 loop : 0.09 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 38 TYR 0.008 0.001 TYR H 101 PHE 0.009 0.002 PHE A 161 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2593) covalent geometry : angle 0.54473 ( 3522) SS BOND : bond 0.00409 ( 9) SS BOND : angle 0.85442 ( 18) hydrogen bonds : bond 0.02894 ( 82) hydrogen bonds : angle 5.88293 ( 222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.056 Fit side-chains REVERT: A 133 MET cc_start: 0.7620 (mtp) cc_final: 0.7411 (ptm) REVERT: H 110 MET cc_start: 0.8553 (mpt) cc_final: 0.8074 (mpt) REVERT: L 26 ASN cc_start: 0.7293 (t0) cc_final: 0.7045 (m-40) outliers start: 9 outliers final: 9 residues processed: 41 average time/residue: 0.0505 time to fit residues: 2.5149 Evaluate side-chains 42 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.156042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139719 restraints weight = 2379.335| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.05 r_work: 0.3525 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2602 Z= 0.165 Angle : 0.562 8.993 3540 Z= 0.284 Chirality : 0.043 0.131 389 Planarity : 0.004 0.033 450 Dihedral : 6.972 55.301 369 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.96 % Allowed : 10.79 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.47), residues: 326 helix: -0.14 (0.94), residues: 32 sheet: -0.58 (0.53), residues: 99 loop : 0.08 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.006 0.001 TYR H 101 PHE 0.009 0.002 PHE A 161 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 2593) covalent geometry : angle 0.55989 ( 3522) SS BOND : bond 0.00446 ( 9) SS BOND : angle 0.93484 ( 18) hydrogen bonds : bond 0.02828 ( 82) hydrogen bonds : angle 5.85824 ( 222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.105 Fit side-chains REVERT: H 53 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8026 (p0) REVERT: H 110 MET cc_start: 0.8576 (mpt) cc_final: 0.8035 (mpt) REVERT: L 26 ASN cc_start: 0.7314 (t0) cc_final: 0.7066 (m-40) outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.0574 time to fit residues: 2.9173 Evaluate side-chains 44 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 29 optimal weight: 0.3980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138791 restraints weight = 2332.930| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.01 r_work: 0.3515 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2602 Z= 0.182 Angle : 0.575 9.011 3540 Z= 0.289 Chirality : 0.043 0.130 389 Planarity : 0.004 0.034 450 Dihedral : 7.051 54.360 369 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.40 % Allowed : 10.79 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.47), residues: 326 helix: -0.21 (0.93), residues: 32 sheet: -0.52 (0.55), residues: 92 loop : 0.00 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 28 TYR 0.007 0.001 TYR H 101 PHE 0.009 0.002 PHE A 161 TRP 0.008 0.002 TRP H 47 HIS 0.003 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 2593) covalent geometry : angle 0.57160 ( 3522) SS BOND : bond 0.00486 ( 9) SS BOND : angle 1.01724 ( 18) hydrogen bonds : bond 0.02911 ( 82) hydrogen bonds : angle 5.98311 ( 222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.098 Fit side-chains REVERT: A 98 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8137 (tt) REVERT: H 110 MET cc_start: 0.8600 (mpt) cc_final: 0.8055 (mpt) REVERT: L 26 ASN cc_start: 0.7355 (t0) cc_final: 0.7120 (m-40) outliers start: 15 outliers final: 10 residues processed: 45 average time/residue: 0.0497 time to fit residues: 2.8018 Evaluate side-chains 46 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139233 restraints weight = 2373.049| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.04 r_work: 0.3241 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2602 Z= 0.167 Angle : 0.566 9.156 3540 Z= 0.283 Chirality : 0.043 0.131 389 Planarity : 0.004 0.034 450 Dihedral : 6.988 55.820 369 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.32 % Allowed : 11.87 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.47), residues: 326 helix: -0.17 (0.93), residues: 32 sheet: -0.49 (0.55), residues: 92 loop : -0.04 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.007 0.001 TYR H 101 PHE 0.010 0.002 PHE A 161 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 2593) covalent geometry : angle 0.56345 ( 3522) SS BOND : bond 0.00453 ( 9) SS BOND : angle 0.95572 ( 18) hydrogen bonds : bond 0.02761 ( 82) hydrogen bonds : angle 5.84568 ( 222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.094 Fit side-chains REVERT: A 98 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8118 (tt) REVERT: H 110 MET cc_start: 0.8554 (mpt) cc_final: 0.8084 (mpt) outliers start: 12 outliers final: 11 residues processed: 43 average time/residue: 0.0572 time to fit residues: 2.9775 Evaluate side-chains 44 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.154908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138799 restraints weight = 2354.995| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.02 r_work: 0.3517 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2602 Z= 0.199 Angle : 0.592 9.131 3540 Z= 0.296 Chirality : 0.044 0.132 389 Planarity : 0.004 0.034 450 Dihedral : 7.069 56.467 369 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.04 % Allowed : 11.51 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.47), residues: 326 helix: -0.10 (0.93), residues: 32 sheet: -0.58 (0.54), residues: 92 loop : -0.07 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 28 TYR 0.007 0.001 TYR H 101 PHE 0.010 0.002 PHE A 161 TRP 0.009 0.002 TRP H 47 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 2593) covalent geometry : angle 0.58831 ( 3522) SS BOND : bond 0.00506 ( 9) SS BOND : angle 1.06256 ( 18) hydrogen bonds : bond 0.02875 ( 82) hydrogen bonds : angle 5.99716 ( 222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.089 Fit side-chains REVERT: A 98 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8171 (tt) REVERT: H 110 MET cc_start: 0.8618 (mpt) cc_final: 0.8148 (mpt) REVERT: L 26 ASN cc_start: 0.7426 (t0) cc_final: 0.7159 (m-40) outliers start: 14 outliers final: 11 residues processed: 43 average time/residue: 0.0520 time to fit residues: 2.7302 Evaluate side-chains 45 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.139202 restraints weight = 2399.654| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.03 r_work: 0.3515 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2602 Z= 0.163 Angle : 0.571 9.222 3540 Z= 0.285 Chirality : 0.043 0.131 389 Planarity : 0.004 0.035 450 Dihedral : 6.992 57.144 369 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.68 % Allowed : 11.87 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.47), residues: 326 helix: 0.03 (0.95), residues: 32 sheet: -0.48 (0.55), residues: 92 loop : -0.07 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 28 TYR 0.007 0.001 TYR H 101 PHE 0.010 0.002 PHE A 161 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 2593) covalent geometry : angle 0.56854 ( 3522) SS BOND : bond 0.00448 ( 9) SS BOND : angle 0.97967 ( 18) hydrogen bonds : bond 0.02743 ( 82) hydrogen bonds : angle 5.82540 ( 222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.092 Fit side-chains REVERT: A 98 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8157 (tt) REVERT: H 110 MET cc_start: 0.8583 (mpt) cc_final: 0.8134 (mpt) REVERT: L 4 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8212 (mp) outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.0547 time to fit residues: 2.9501 Evaluate side-chains 48 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140461 restraints weight = 2417.690| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.04 r_work: 0.3530 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2602 Z= 0.146 Angle : 0.563 9.174 3540 Z= 0.279 Chirality : 0.042 0.131 389 Planarity : 0.004 0.035 450 Dihedral : 6.922 58.179 369 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.68 % Allowed : 12.23 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.47), residues: 326 helix: 0.12 (0.96), residues: 32 sheet: -0.39 (0.55), residues: 92 loop : -0.06 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 28 TYR 0.008 0.001 TYR H 101 PHE 0.010 0.002 PHE A 161 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 2593) covalent geometry : angle 0.56061 ( 3522) SS BOND : bond 0.00416 ( 9) SS BOND : angle 0.93454 ( 18) hydrogen bonds : bond 0.02679 ( 82) hydrogen bonds : angle 5.68046 ( 222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.098 Fit side-chains REVERT: A 98 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8127 (tt) REVERT: H 110 MET cc_start: 0.8569 (mpt) cc_final: 0.8124 (mpt) REVERT: L 4 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8174 (mp) outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.0494 time to fit residues: 2.6391 Evaluate side-chains 47 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.0030 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141615 restraints weight = 2428.342| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.03 r_work: 0.3544 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2602 Z= 0.130 Angle : 0.566 10.872 3540 Z= 0.277 Chirality : 0.042 0.132 389 Planarity : 0.004 0.035 450 Dihedral : 6.874 59.529 369 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.32 % Allowed : 13.31 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.47), residues: 326 helix: 0.27 (0.97), residues: 32 sheet: -0.30 (0.56), residues: 92 loop : -0.03 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.012 0.001 TYR A 100 PHE 0.010 0.002 PHE A 161 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2593) covalent geometry : angle 0.56395 ( 3522) SS BOND : bond 0.00378 ( 9) SS BOND : angle 0.86513 ( 18) hydrogen bonds : bond 0.02562 ( 82) hydrogen bonds : angle 5.51440 ( 222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.072 Fit side-chains REVERT: A 98 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8141 (tt) REVERT: H 83 MET cc_start: 0.8762 (mtp) cc_final: 0.8524 (mtm) REVERT: H 110 MET cc_start: 0.8530 (mpt) cc_final: 0.8118 (mpt) REVERT: L 4 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8164 (mp) outliers start: 12 outliers final: 10 residues processed: 42 average time/residue: 0.0522 time to fit residues: 2.6881 Evaluate side-chains 45 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 29 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.157080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141156 restraints weight = 2401.300| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.01 r_work: 0.3532 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.179 2602 Z= 0.408 Angle : 1.490 59.198 3540 Z= 0.935 Chirality : 0.060 0.832 389 Planarity : 0.005 0.054 450 Dihedral : 7.256 59.539 369 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.32 % Allowed : 13.31 % Favored : 82.37 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.47), residues: 326 helix: 0.28 (0.97), residues: 32 sheet: -0.29 (0.56), residues: 92 loop : -0.07 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 28 TYR 0.008 0.001 TYR H 101 PHE 0.010 0.002 PHE A 161 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00736 ( 2593) covalent geometry : angle 1.49271 ( 3522) SS BOND : bond 0.00397 ( 9) SS BOND : angle 0.85498 ( 18) hydrogen bonds : bond 0.02549 ( 82) hydrogen bonds : angle 5.51272 ( 222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 880.90 seconds wall clock time: 15 minutes 47.58 seconds (947.58 seconds total)